BRPI0621690A2 - fatty acid binding protein 4 ("fabp4") gene polymorphisms and their associations with carcass traits - Google Patents

Abstract

POLYMORPHISMS IN FATTY ACID BINDING PROTEIN 4 GENE ("FABP4") AND ITS ASSOCIATIONS WITH CARCASS CAPACTERISTICS. The physiological regulation of energy intake, growth and partitioning in animals is under the control of multiple genes, which can be important candidates to solve the genetic variation of economically relevant characteristics in the production of beef. The present invention refers to the identification of unique nucleotide polymorphisms (SNPs), within the bovine genes that encode fatty acid binding proteins and their associations with economically relevant characteristics in the production of beef. The invention further encompasses methods and systems, including network-based processes, for managing SNP data and other data related to specific animals and livestock, veterinary care, quality control and diagnostic data, and the management of domestic animals, which, based on the genotype, have predictable meat quality characteristics, livestock conditions, animal welfare, food safety information, audit of existing processes and data from locations in the field.

Description

Patent Descriptive Report for: Acid-binding protein 4 gene polymorphisms

("fabp4") and its associations with carcass characteristics ".

INCORPORATION BY REFERENCE

All documents cited or referenced in the documents cited in the application, and all documents cited or referenced here ("documents cited here"), and all documents cited or referenced in the documents cited here, together with any instructions, descriptions, specifications of The manufacturer's product and product sheets, for any products mentioned herein or in any document incorporated herein by reference, are hereby incorporated by reference herein, and may be employed in the practice of the invention.

FIELD OF INVENTION

The present invention relates to the identification of single nucleotide polymorphisms (SNPs) within bovine genes encoding fatty acid binding protein 4 ("FABP4") and their associations with economically relevant characteristics in beef production. The invention further relates to methods and systems, including network-based processes, for managing SNP data and other animal and livestock-specific data, veterinary care, quality control data and animal diagnostics and management. which, based on the genotype, have predictable meat quality characteristics, livestock conditions, animal welfare, food safety information, audit of existing processes and data from field sites.

BACKGROUND OF THE INVENTION

Significant improvements in animal performance, carcass and meat quality and quality have been made over the years through the application of standard breeding and selection techniques. However, such classic breeding techniques require several years of genetic evaluation of performance records on individual animals and their relatives and are therefore very expensive. Other efforts have been made to improve productivity and quality through the application of such management practices, such as the use of feed additives, animal hormone implants, and chemotherapy. However, there is significant political and regulatory resistance to the introduction and use of such methodologies. Such methodologies are also nonhereditary and need to be applied differently in each production system. There is a demand for methods that allow relatively easy and efficient selection and breeding of farm animals with an advantage for a hereditary characteristic of circulating leptin levels, feed intake, growth rate, body weight, carcass merit and carcass composition. The economic significance of the use of genetic markers, which are associated with specific economically important traits (especially low heredity traits) in farmed animals by marker-assisted selection cannot therefore be overestimated.

The physiological regulation of energy intake, growth and distribution in animals is under the control of multiple genes, which may be important candidates for unraveling genetic variation in economically relevant traits (ERT) in beef production. Polymorphisms in these candidate genes, which show association with specific ERTs, are nucleotides of quantitative traits useful for marker-assisted selection. In the present study, associations were found between single nucleotide polymorphisms (SNPs) in the fatty acid binding protein 4 gene ("FABP4") with marbling and subcutaneous fat depth. Fatty acid binding proteins are a family of highly conserved small cytoplasmic proteins that bind to long chain fatty acids and other hydrophobic ligands (Kaikaus et al., 1990. Experientia, 46: 617-630). Main functions include assimilation, transport and metabolism of fatty acids. To date, nine distinct members have been identified in this gene family (Damcott et al., 2004. Metabolism, 53: 303-309), including adipocyte fatty acid binding protein or fatty acid binding protein 4 ("FABP4"). ). FABP4 plays an important role in the regulation of lipid and glucose homeostasis through its interaction with peroxisome proliferator activated receptors (PPARs) located in the cell nucleus. Specifically, the FABP4 / fatty acid complex activates the PPAR-γ isoform, which in turn regulates FABP4 transcription (Damcott et al., 2004. Metabolism, 53: 303-309). In addition, FABP4 appears to be involved in lipid hydrolysis and intracellular fatty acid trafficking through direct interaction and binding to hormone-sensitive lipase (Shen et al. 1999. Proc Natl Acad Sci USA, 96: 5528-5532). which is a primary enzyme involved in lipid catabolism (Tansey et al. 2003. J Biol Chem. 278: 8401-8406). Recently, FABP4 and FABP5 have been proposed as potential candidate genes for obesity as they are located within a region of quantitative trait loci (QTL) for serum leptin levels in mice (Ogino et al. 2003. Mamm Genome, 14: 839-844).

Leptin, a 16 KDa protein secreted from white adipocytes, is involved in regulating food intake, energy expenditure and whole-body energy balance (Jiang and Gibson 1999. Mamm Genome, 10: 191-193). All these factors indicate that FABP4 may play an important role in lipid metabolism and homeostasis in adipocytes.

It remains advantageous to provide additional SNPs that can more accurately predict an animal's meat quality phenotype as well as a business method that provides increased production efficiencies in cattle ranching as well as providing access to various animal records and allows comparisons with expected or desired objectives with respect to the quality and quantity of animals produced.

Citation or identification of any document in this application is not an admission that such document is available as prior art to the present invention.

SUMMARY OF THE INVENTION

The present invention relates to the identification of single nucleotide polymorphisms (SNPs) within bovine genes encoding fatty acid binding protein 4 ("FABP4") and their associations with economically relevant characteristics in beef production.

The invention encompasses a method for subgrouping animals according to genotype, animals in each subgroup having a similar polymorphism in a FABP4 gene, which may comprise determining the genotype of each animal to be subgrouped by determining the presence of a single nucleotide polymorphism in the FABP4 gene, and segregation of individual animals into subgroups, with each animal in a subgroup having a similar polymorphism in the FABP4 gene.

The invention also encompasses a method for subgrouping animals according to genotype, animals in each subgroup having a similar genotype in the FABP4 gene, which may comprise determining the genotype of each animal to be subgrouped by determining the presence of polymorphism ( s) of a single nucleotide of interest in the FABP4 gene, and the segregation of individual animals into subgroups depending on whether or not the animals have the single nucleotide polymorphism (s) of interest in the FABP4 gene.

The single nucleotide polymorphism (s) of interest may be selected from the group consisting of a G-C substitution at nucleotide position 7516 of the FABP4 gene and a G-C substitution at position 7713 of the FABP4 gene.

The invention further relates to a method for subgrouping animals according to genotype, wherein animals of each subgroup have a similar genotype in the FABP4 gene, which may comprise determining the genotype of each animal to be subgrouped by determining the presence of any of the above SNPs, and the segregation of individual animals into subgroups depending on whether or not the animals have any of the above SNPs in the FABP4 gene.

The invention also relates to a method for identifying an animal having a desirable phenotype as compared to the general animal population of that species which may comprise determining the presence of single nucleotide polymorphism in the animal's FABP4 gene, the presence of the SNP is indicative of a desirable phenotype.

In an advantageous embodiment, the animal may be a bovine. In another advantageous embodiment, the FABP4 gene may be a bovine FABP4 gene.

The invention also encompasses computer-aided methods and systems for improving production efficiency for animal husbandry having marketable soft meat using multiple data, and in particular the genotype of animals when it relates to FABP4 SNPs. The methods of the invention include obtaining a genetic sample from each animal in a herd of farmed animals, determining the genotype of each animal with respect to specific quality characteristics as defined by a panel of at least two polymorphisms of a single nucleotide (SNPs), the grouping of animals with similar genotypes and, optionally, additional subgrouping of animals based on similar phenotypes. The methods of the invention may also encompass obtaining and maintaining data relating to animals or herds, their livestock conditions, health and veterinary care and condition, genetic history or kinship, and providing such data to others. by means of systems that are network based, contained in a database or fixed to the animal itself, such as by an implanted microchip. Therefore, an advantageous aspect of the present invention is directed to a computer system and computer aided methods for tracking breeding quality traits having specific genetic predispositions.

The present invention advantageously encompasses computer aided methods and systems for the acquisition of genetic data, particularly genetic data as defined by the absence or presence of an SNP within a FAB P 4 gene related to meat quality characteristics. from breeding and associating that data with other data about the animal or its herd, and maintaining that data in ways that are accessible. Another aspect of the invention encompasses a computer aided method for predicting that livestock animals have a biological difference in meat quality, and which may include the steps of using a computer system, for example, a programmed computer comprising a processor, a data storage system, an input device and an output device, the steps of: (a) inputting into the programmed computer via the input device data including the genotype of an animal when it relates to any of the FABP4 SNPs described herein, (B) the predicted meat quality correlation by the FABP4 genotype using the processor and data storage system, and (c) output to the FABP4 meat correlated to the FABP4 genotype, whereby livestock are predicted to have a particular meat quality. Still another aspect of the invention relates to a method of doing business for livestock management, comprising providing a user with a computer system for livestock management, comprising physical characteristics and genotypes corresponding to one or more. or a computer readable medium for livestock management comprising physical characteristics and genotypes corresponding to one or more animals, or physical characteristics and genotypes corresponding to one or more animals, one physical characteristic being ingestion, growth or merit of carcass in beef cattle and the genotype is a FABP4 genotype.

It is noted that in this specification and particularly in the claims and / or paragraphs, terms such as "comprises", "understood", "comprising" and the like may have the meaning given in the US Patent Law; for example, they may mean "includes", "included", "including", and the like; and terms such as "consisting essentially of" and "consisting essentially of" have the meaning given to them in the US Patent Law, for example, they accept elements not explicitly mentioned, but exclude elements that are found in the prior art. or that affect a basic or novel feature of the invention.

These and other embodiments are disclosed or obvious from and encompassed by the following Detailed Description.

BRIEF DESCRIPTION OF DRAWINGS

The following detailed description, given by way of example, but not intended to limit the invention solely to the specific embodiments described, may be better understood in conjunction with the accompanying drawings, in which:

Figure 1 depicts sequence alignment between cDNA and genomic DNA to determine the genomic organization of the bovine FABP4 gene.

Figure 2 depicts two G / C substitutions detected at positions 7516 and 7713 in the bovine FABP4 gene.

Figure 3 depicts PCR-RFLP genotype determination of C / G substitution at position 7516 of the bovine FABP4 gene. Lane 1: 100 bp stairs. Lanes 2-7: A 452 bp amplicon was digested with the restriction enzyme MspAlI. Lanes 2-4, CG animals show 3 bands after complete digestion, 452, 352 and 100 bp; Lane 5, CG animals that lack a MspAlI site and the 452 bp amplicon is not digested; Lanes 6 and 7, GC animals that have an MspAlI site and reveal, after complete digestion, two bands: 352 bp and 100 bp.

Figure 4 depicts GenBank Accession Number AAFC01136716, Bos taurus Cont 136721, full genome shotgun sequence.

Figure 5 illustrates a flowchart of data input and output from analysis and correlation of data relevant to the rearing, veterinary history and performance requirements of a group of animals, such as from a herd of animals. cows, and the interactive flow of data from the computer aided device to a student body learning to use the method of the invention.

Figure 6 illustrates the potential relationships between data elements to be fed to the system. One-way arrows indicate, for example, that a stable typically belongs to a single farm, while a farm may own several stables. Similarly, a prescription may include veterinary products.

Figure 7A illustrates the flow of events in the use of the laptop-based system for data entry on rearing and maintaining a herd of cows.

Figure 7B illustrates the flow of events through data entry-related subroutines linked to farm management.

Figure 7C illustrates the flow of events through data entry-related subroutines linked to company-specific data.

Figure 8 illustrates a flowchart of data input and output from analysis and correlation of data pertaining to the breeding, veterinary history and performance requirements of a group of animals.

DETAILED DESCRIPTION

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA technology and immunology which are within the skill of the art. Such techniques are fully explained in the literature. See, for example, Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, third edition, Cold Spring Harbor Press; DNA Cloning, Vol. I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Animal Cell Culture (R. K. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL press, 1986); Perbal, B., A Practical Guide to Molecular Cloning (1984); the Methods In Enzymology series (S. Colowick and N. Kaplan eds., Academic Press, Inc.); and "Handbook of Experimental Immunology", Vols. I-IV (D.M. Weir and C.C. Blaekwell eds., 1986, Blaekwell Science Publishing).

Before describing the present invention in detail, it should be understood that this invention is not limited to particular DNA, polypeptide sequences or process parameters, as such, they may, of course, vary. It should also be understood that the terminology used herein is for the purpose of describing only particular embodiments of the invention, and is not intended to be limiting.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. While numerous methods and materials similar or equivalent to those described herein may be used in the practice of the present invention, preferred materials and methods are described herein.

In describing the present invention, the following terms will be employed and intended to be defined as indicated below.

The term "cow" or "cattle" is used generically to refer to an animal of bovine origin of any age. Interchangeable terms include "bovine", "calf", "calf", "bull", "veal" and the like. It also includes an individual animal at all stages of development, including the embryonic and fetal stages.

The animals referred to herein may also include individuals or groups of individuals that are reared for purposes other than food production, such as, but not limited to, transgenic animals for the production of biopharmaceuticals, including antibodies and other proteins. and protein products.

By the term "complementarity" or "complementary" is meant, for the purposes of the specification or claims, a sufficient number in the complementary base pair oligonucleotide in its sequence to specifically interact (hybridize) with a sequence of nucleic acids targeting the gene polymorphism to be amplified or detected. As known to those skilled in the art, a very high degree of complementarity is required for specificity and sensitivity involving hybridization, although it need not be 100%.

Therefore, for example, an oligonucleotide that is identical in nucleotide sequence to an oligonucleotide disclosed herein, except for a base change or substitution, may function equivalently to the disclosed oligonucleotides. A "complementary DNA" or "cDNA" gene includes recombinant genes synthesized by messenger RNA reverse transcription ("mRNA").

A "cyclic polymerase mediated reaction" refers to a biochemical reaction in which a mold molecule or a population of mold molecules is periodically and repeatedly copied to create a complementary mold molecule or complementary mold molecules, for example. through which the number of mold molecules increases over time.

By the term "detectable moiety" is meant, for purposes of the specification or claims, a label molecule (isotopic or non-isotopic) which is incorporated indirectly or directly into an oligonucleotide, the label molecule being facilitates detection of the oligonucleotide to which it is incorporated, for example when the oligonucleotide is hybridized to amplified polymorphic gene sequences. Therefore, "detectable moiety" is used synonymously with "label molecule". Oligonucleotide synthesis may be performed by any of several methods known to those skilled in the art. Label molecules, known to those skilled in the art to be useful for detection, include chemiluminescent, fluorescent or luminescent molecules. Several fluorescent molecules are known in the art which are suitable for use to label a nucleic acid for the method of the present invention. The protocol for such incorporation may vary depending on the fluorescent molecule used. Such protocols are known in the art for the respective fluorescent molecule.

"DNA amplification" as used herein refers to any process that increases the copy number of a specific DNA sequence by enzymatically amplifying the nucleic acid sequence. A variety of processes are known. One of the most commonly used is Mullis polymerase chain reaction (PCR) process as described in U.S. Patent Nos. 4,683,195 and 4,683,202. Methods, devices and reagents as described in U.S. Patent Nos. 6,951,726; 6,927,024; 6,924,127; 6,893,863; 6,887,664; 6,881,559; 6,855,522; 6,855,521; 6,849,430; 6,849,404; 6,846,631; 6,844,158; 6,844,155; 6,818,437; 6,818,402; 6,794,177; 6,794,133; 6,790,952; 6,783,940; 6,773,901; 6,770,440; 6,767,724; 6,750,022; 6,744,789; 6,733,999; 6,733,972; 6,703,236; 6,699,713; 6,696,277

6,664,080 6,645,758 6,617,107 6,517,233 6,566,052 6,537,752 6,503,750 6,465,903 6,465,637 6,426,215 6,395,518 6,368,834 6,346,384 6,309,840 6,287,781 6,268,153 6,258. 567 6,235,468 6,218,153 6,180,349 6,068,974 6,033,854 6,664,064 6,645,720 6,613,560 6,569,678 6,558,929 6,524,830 6,503,705 6,482,588 6,465,171 6,423,499 6,391,559 6,365 .375 6,319,673 6,309,837 6,284,455 6,268,143 6,258,537 6,232,079 6,207,425 6,664,044; RE 38,352 6,642,000; 6,638,716 6,610,487 6,569,627 6,558,909 6,518,020 6,493,640

6,475,729

6,448,014

6,410,223

6,383,755

6,358,680

6,316,195

6,303,343

6,596,492

6,566,103

6,551,783

6,514,750

6,492,114

6,468,743

6,432,646

6,403,341

6,379,932

6,355,422

6,316,192

6,300,073

6,277,605; 6,270,977

D445,907; 6,261,431

6,650,719 6,632,653 6,586,250 6,566,067 6,544,782 6,514,706 6,485,907 6,465,638 6,428,987 6,399,320 6,372,484 6,348,336 6,312,930 6,300,072 6,258,570

6,258,529; 6,251,607; 6,248,567 6,225,093; 6,221,595; D441,091 6,183,999; 6,183,963; 6,180.37 2

6.17 4,667; 6,153,412; 6.14 6,834; 6.14 3.4 96

6,140,613; 6,140,110; 6,103,468; 6,087,097

6,063,563

6,031,960

6,048,688

6,017,699

6,046,039

6,015,664

6,072,369

6,037,129

6,015,534 6,004,747; 6,001,612; 6,001,572; 5.98 5,619; 5.97 6.842

5,972,602

5,936,968

5,876,978

5,863,731

5,856,086

5,827,695

5,817,797

5,800,997

10 5,766,889

5,716,784

5,702,884

5,665,572

5,652,102

15 5,639,606

5,618,702

5,589,333

5,556,774

5,514,568

20 5,491,225

5,475,610

5,420,009

5,364,758

5,241,363

5,968,730

5,909,468

5,876,977

5,861,251

5,853,991

5,827,661

5,814,489

5,780,271

5,759,822

5,712,125

5,693,467

5,665,539

5,650,268

5,631,128

5,614,388

5,585,238

5,556,773

5,512,463

5,487,993

5,447,839

5,411,876

5,340,728

5,232,829

5,958,686

5,905,732

5,874,221

5,861,245

5,849,497

5,827,657

5,814,453

5,780,222

5,750,347

5,712,090

5,691,146

5,656,493

5,643,765

5,629,178

5,610,017

5,576,197

5,538,871

5,512,462

5,487,985

5,437,975

5,393,657

5,283,171

5,231,015

5,955,274

5,888. 740

5,869,318

5,858,725

5,837,468

5,824,516

5,811,296

5,776,686

5,747,251

5,710,381

5,681,741

5,656,461

5,639,871

5,627,054

5,602,756

5,565,340

5,527,898

5,501,947

5,484,699

5,436,144

5,389,512

5,279,952

5,229,297

5,952,200

5,883,924

5,863,772

5,858,718

5,830,663

5,824,479

5,804,383

5,774,497

5,741,656

5,705,627

5,674,717

5,654,144

5,639,611

5,618,703

5,599,674

5,565,339

5,527,510

5,494,795

5,476,774

5,426,026

5,364,790

5,254,469

5,224,778 5,219,727; 5,213,961; 5,198,337; 5,187,060; 5,142,033; 5.0 91.310; 5,082,780; 5,066,584; 5,023,171 and 5,008,182 may also be employed in the practice of the present invention. PCR involves the use of a thermostable DNA polymerase, sequences known as primers, and heating cycles, which separate replicating deoxyribonucleic acid (DNA) strands and exponentially amplify a gene of interest. Any kind of PCR such as quantitative PCR, RT-PCR, hot start PCR, LAPCR, multiplex PCR, touchdown PCR, etc. can be used. Advantageously, real time PCR is used. In general, the amplification process involves a cyclic enzyme chain reaction for the preparation of exponential amounts of a specific nucleic acid sequence. It requires a small amount of a sequence to initiate the chain reaction and oligonucleotide primers that will hybridize to the sequence. In PCR, primers are annealed to denatured nucleic acid followed by extension with an inducing agent (enzyme) and nucleotides. This results in newly synthesized extension products. Since these newly synthesized sequences become templates for the primers, repeated denaturation, primer annealing, and extension cycles result in exponential accumulation of the specific sequence being amplified. The chain reaction product product will be a discrete terminal duplex of nucleic acids corresponding to the ends of the specific primers employed.

By the terms "enzymatically amplifying" or "amplifying" is meant, for purposes of the specification and claims, DNA amplification, that is, a process by which nucleic acid sequences are amplified in number. There are numerous ways to enzymatically amplify nucleic acid sequences. Currently, the most commonly used method is polymerase chain reaction (PCR). Other amplification methods include LCR (ligase chain reaction), which utilizes DNA ligase, and a probe consisting of two halves of a DNA segment that is complementary to the DNA sequence to be amplified, QB replicase enzyme and a sequence template. ribonucleic acid (RNA) attached to a complementary probe to the DNA to be copied, which is used to make a DNA template for the exponential production of complementary RNA; tape shift amplification (SDA); QP replicase amplification (QPRA); self-sustained replication (3SR); and NASBA (nucleic acid sequence based amplification), which can be performed on RNA or DNA as the nucleic acid sequence to be amplified.

A "fragment" of a molecule, such as a protein or nucleic acid, is intended to refer to any portion of the amino acid sequence or nucleotide genetics.

As used herein, the term "genome" refers to all genetic material on the chromosomes of a particular organism. Their size is generally given as their total number of base pairs. Within the genome, the term "gene" refers to an ordered sequence of nucleotides located at a particular position on a particular chromosome, which encodes a specific functional product (for example, a protein or RNA molecule). In general, the genetic characteristics of an animal, as defined by the nucleotide sequence of its genome, are known as its "genotype", while the physical characteristics of an animal are described as its "phenotype".

By "heterozygote" or "heterozygous polymorphism" is meant that two alleles of a diploid cell or organism at a given locus are different, that is, that they have a different nucleotide exchanged for the same nucleotide in the same place in their sequences.

By "homozygote" or "homozygous polymorphism" is meant that two alleles of a diploid cell or organism at a given locus are identical, that is, that they have the same nucleotide by nucleotide exchange at the same place in their sequences.

By "hybridization" or "hybridizing" as used herein is meant the formation of AT and CG base pairs between the nucleotide sequence of a fragment of a segment of a polynucleotide and a complementary nucleotide sequence of an oligonucleotide. . By complementary it is meant that at the locus of each A, C, G or T (or U in a ribonucleotide) in the fragment sequence, the sequenced oligonucleotide has a T, G, C or A, respectively. The hybridized / oligonucleotide fragment is called a duplex.

A "hybridization complex", as in a sandwich assay, means a complex of nucleic acid molecules including at least one target nucleic acid and a sensor probe. It may also include an anchor probe.

As used herein, the term "locus" or "Ioci" refers to the site of a gene on a chromosome. Gene pairs, known as "alleles", control the inherited trait produced by a gene locus. It refers to each animal's particular allele combination as its "genotype". When both alleles are identical, they are said to be homozygous for the trait controlled by that pair of genes; when the alleles are different, the individual is said to be heterozygous for the trait.

A "melt temperature" is understood to be the temperature at which hybridized duplexes de-hybridize and return to their single-ribbon state. Also, hybridization will not occur in the first place between two oligonucleotides, or here an oligonucleotide and a fragment, at temperatures above the resulting duplex fusion temperature. At present, it is advantageous for the melting point temperature difference of oligonucleotide-fragment duplexes of this invention to be from about 1 ° C to about 10 ° C, so as to be readily detectable.

As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), DNA analogs or RNA generated using nucleotide analogs, and their derivatives. derivatives, fragments and homologs. The nucleic acid molecule may be single stranded or double stranded, but advantageously is double stranded DNA. "DNA" refers to the polymeric form of deoxyribonucleotides (adenine, guanine, thymine or cytosine) either in its single stranded form or a double stranded helix. This term refers only to the primary and secondary structures of the molecule, and does not limit it to any particular tertiary forms. Therefore, this term includes double-stranded DNA found among others in linear DNA molecules (e.g., restriction fragments), viruses, plasmids and chromosomes. In discussing the structure of particular double stranded DNA molecules sequences may be described herein in accordance with the normal convention of giving only the sequence in the 5 'to 3' direction along the untranscribed DNA strand (ie, the strand having a sequence homologous to mRNA). An "isolated" nucleic acid molecule is one that is separate from other nucleic acid molecules that are present in the natural source of nucleic acid.

A "nucleoside" refers to a base attached to a sugar. The base may be adenine (A), guanine (G) (or its substitute, inosine (I)), cytosine (C) or thymine (T) (or its substitute, uracil (U)). The sugar may be ribose (the sugar of a natural nucleotide in RNA) or 2-deoxyribose (the sugar of a natural nucleotide in DNA). A "nucleotide" refers to a nucleoside attached to a single phosphate group.

As used herein, the term "oligonucleotide" refers to a series of linked nucleotide residues, this oligonucleotide has a sufficient number of nucleotide bases to be used in a PCR reaction. A short oligonucleotide sequence may be based on, or project from, a genomic or cDNA sequence, and is used to amplify, confirm, or reveal the presence of a similar or complementary identical DNA or RNA in a cell or particular fabric.

Oligonucleotides may be chemically synthesized and may be used as primers or probes. Oligonucleotide means any nucleotide of more than 3 bases in length, used to facilitate the detection or identification of a target nucleic acid, including probes and primers.

A "polymerase" is an enzyme that catalyzes the sequential addition of monomer units to a polymer chain, or that binds two or more monomer units to initiate a polymer chain. The "polymerase" will work by adding monomer units whose identity is determined by and which is complementary to a template molecule of a specific sequence. For example, DNA polymerases such as DNA pol 1 and Taq polymerase add deoxyribonucleotides to the 3 'end of a polynucleotide chain in a template dependent manner whereby a nucleic acid is synthesized that is complementary to the template molecule. The polymerases may be added either to extend a primer once or repeatedly or to amplify a polynucleotide by repetitive priming of two complementary strands using two primers. A "thermostable polymerase" refers to a DNA or RNA polymerase enzyme that can withstand extremely high temperatures, such as those of approximately 100 ° C. Frequently, thermostable polymerases are derived from organisms that live in extreme temperatures, such as Thermus aquaticus. Examples of thermostable polymerases include Taq, Tth, pfu, Vent, deep vent, UlTma and their variations and derivatives.

A "polynucleotide" refers to a straight chain of nucleotides connected by a phosphodiester bond between the 3'-hydroxyl groups of one nucleoside and the 5'-hydroxyl group of a second nucleoside, which in turn is linked via its 3'-hydroxyl group to the 5'-hydroxyl group of a third nucleotide and so on, to form a polymer comprising nucleosides linked by a phosphodiester backbone. A "modified polynucleotide" refers to a polynucleotide, in which one or more natural nucleotides have been partially, substantially or completely replaced by modified nucleotides.

An "primer" is an oligonucleotide, the sequence of at least a portion of which is complementary to a segment of a template DNA that must be amplified or replicated. Typically, primers are used in carrying out the polymerase chain reaction (PCR). An primer hybridizes to (or "anneals" to) the template DNA and is used by the polymerase enzyme as the starting point for the replication / amplification process. Primers herein are selected to be "substantially" complementary to different strands of a particular target DNA sequence. This means that the primers must be complementary enough to hybridize with their respective ribbons. Therefore, the primer sequence need not reflect the exact mold sequence. For example, a non-complementary nucleotide fragment may be attached to the 5 'end of the primer, with the remainder of the primer sequence being complementary to the ribbon. Alternatively, non-complementary bases or longer sequences may be interspersed in the primer as long as the primer sequence has sufficient complementarity with the ribbon sequence to hybridize with it and thereby form the template for the synthesis of the extension product. .

"Probes" refer to oligonucleotides, variable length nucleic acid sequences, used in the detection of identical, similar or complementary nucleic acid sequences by hybridization. An oligonucleotide sequence used as a detection probe may be labeled with a detectable moiety.

The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, DNA isolated from any sequence, RNA isolated from any sequence, nucleic acid probes and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs, uracil, other sugars and linking groups, such as fluorourose and thiolate, and nucleotide branches. The nucleotide sequence may be further modified after polymerization, such as by conjugation, with a labeling component. Other types of modifications included in this definition are capping, replacement of one or more of the naturally occurring nucleotides with an analog, and introducing means for attaching polynucleotide to proteins, metal ions, labeling components, other polynucleotides, or solid support. .

An "isolated" polynucleotide or polypeptide is one that is substantially pure from the materials with which it is associated in its native environment. By substantially free is meant at least 50%, at least 55%, at least 60%, at least 65%, advantageously at least 70%, at least 75%, more advantageously at least 80%, at least 85%, even more advantageously at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, very advantageously at least 98% at least 99%, at least 99,5%, at least 99,9% free of these materials.

An "isolated" nucleic acid molecule is a discrete and discrete nucleic acid molecule from the organism as a whole with which the molecule is found in nature; or a nucleic acid molecule devoid, in whole or in part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences (as defined below) in association with it.

The term "protein-encoding polynucleotide" as used herein refers to an isolated DNA fragment or DNA molecule encoding a protein, or the complementary strand thereto; but, RNA is not excluded, as it is understood in the art that thymidine (T) in a DNA sequence is considered equal to uracil (U) in an RNA sequence. Therefore, RNA sequences for use in the invention, for example for use in RNA vectors, may be derived from DNA sequences, by thymidine (T) in the sequence being considered equal to uracil (U) in RNA sequences.

A "DNA coding sequence" or a "nucleotide sequence encoding" a particular protein is a DNA sequence that is transcribed and translated into a polypeptide in vitro or in vivo when placed under the control of appropriate regulatory elements. The boundaries of the coding sequence are determined by a 5 '(amino) terminal start codon and a 3' (carbon dioxide) translation stop codon. A coding sequence may include, but is not limited to, prokaryotic sequences, cDNA from eukaryotic mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA, and even synthetic DNA sequences. A transcription termination sequence will usually be located 3 'to the coding sequence.

"Homology" refers to the percent identity between two polynucleotide portions or two polypeptide portions. Two DNAs or two polypeptide sequences are "substantially homologous" to each other when the sequences display at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87% 88%, 89%, preferably at least about 90%, 91%, 92%, 93%, 94% and most preferably at least about 95%, 96%, 97%, 98%, 99% 99.5%, 99.9% sequence identity over a defined length of molecules. As used herein, substantially homologous also refers to sequences showing full identity (100% sequence identity) with respect to the specified DNA or polypeptide sequence.

Homology may be determined by hybridization of polynucleotides under conditions that form stable duplexes between homologous regions, followed by single strand specific nuclease (s) digestion, and size determination of the digested fragments. DNA sequences, which are substantially homologous, can be identified in a Southern hybridization experiment under, for example, severe conditions as defined for that particular system. The definition of appropriate hybridization conditions is within the skill of the skilled artisan. See, for example, Sambrook et al. above; DNA Cloning, supra; Nucleic Acid Hybridization, supra.

Two nucleic acid fragments are considered to be "selectively hybridizable" to a polynucleotide if they are capable of specifically hybridizing to a nucleic acid or variant thereof or specifically initiating a polymerase chain reaction: ( (i) under typical hybridization and wash conditions, as described, for example, in Sambrook et al., supra, and Nucleic Acid Hybridization, supra, (ii) using low stringency wash conditions, which allow at most about 25 ° C. - 30% base pair incompatibilities, for example: 2 χ SSc, 0.1% SDS, room temperature twice, 30 minutes each; then 2 χ SSC, 0.1% SDS, 37 ° C once, 30 minutes; then 2 χ SSC at room temperature twice, 10 minutes each, or (iii) selecting primers for use in typical polymerase chain reactions (PCR) under standard conditions (described, for example, in Saiki et al. (1988) Science 239 : 487-491).

The term "capable of hybridizing under severe conditions" as used herein refers to annealing a first nucleic acid with a second nucleic acid under severe conditions as defined below. Severe hybridization conditions typically allow for hybridization of nucleic acid molecules having at least 70% nucleic acid sequence identity to the nucleic acid molecule being used as a probe in the hybridization reaction. For example, the first nucleic acid may be a test sample or probe, and the second nucleic acid may be the sense or nonsense strand of a nucleic acid or a fragment thereof. Hybridization of the first and second nucleic acids may be conducted under severe conditions, for example, high temperature and / or low salt content, which tend to disadvantage hybridization of dissimilar nucleotide sequences. Alternatively, hybridization of the first and second nucleic acids may be conducted under conditions of reduced severity, for example, low temperature and / or high salt content, which tend to favor hybridization of dissimilar nucleotide sequences. Low stringency hybridization conditions may be followed by high stringency conditions or medium intermediate stringency conditions to increase binding selectivity of the first and second nucleic acids. Hybridization conditions may additionally include reagents such as, but not limited to dimethyl sulfoxide (DMSO) or formamide, to further disadvantage hybridization of dissimilar nucleotide sequences. A suitable hybridization protocol may involve, for example, 6 χ SSC hybridization (where χ SSC comprises 0.015 M sodium citrate and 0.15 Μ sodium chloride) at 65 ° C in an aqueous solution, followed by 1 χ SSC wash at 65 ° C. Formulas for calculating appropriate hybridization and wash conditions to achieve hybridization allowing 30% or less incompatibility between two nucleic acid molecules are disclosed, for example, in Meinkoth et al. (1984) Anal. Biochem. 138: 267-284; the content of which is incorporated herein by reference in its entirety. Protocols for hybridization techniques are well known to those skilled in the art and standard molecular biology manuals can be consulted to select an appropriate hybridization protocol without undue experimentation. Come, for example, Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, third edition, Cold Spring Harbor Press, the contents of which are incorporated herein by reference in their entirety.

Typically, severe conditions will be those in which the salt concentration is less than about 1.5 sódio sodium ion, typically a concentration of Na ions (or other salts) of about 0.01 to 1.0 M from from about pH 7.0 to about pH 8.3 and at a temperature of at least about 30 ° C for short probes (eg 10 to 50 nucleotides) and at least 60 ° C for long probes (eg , larger than 50 nucleotides). Severe conditions can also be achieved with the addition of destabilizing agents such as formamide. Examples of low severity conditions include hybridization with 30 to 35% formamide buffer solution, 1 M NaCl, 1% SDS (sodium dodecyl sulfate) at 37 ° C, and a 1 - 2 wash χ SSC at 50 to 55 ° C.

Examples of moderate severity conditions include hybridization to 40 to 45% formamide, 1 M NaCl, 1% SDS at 37 ° C, and a wash in 0.5 - 1 SSC at 55 to 60 ° C. Examples of high stringency conditions include hybridization to 50% formamide, 1 M NaCl, 1% SDS at 37 ° C, and a 0.1 SSC wash at 60 to 65 ° C.

Materials and methods of the invention may be used more generally to evaluate a DNA sample from an animal, genetically typify an individual animal and detect genetic differences in animals. In particular, a genomic DNA sample from an animal may be evaluated by reference to one or more controls to determine if an SNP, or group of SNPs, is present in a gene. Any method for genotype determination may be used for genotype determination in the present invention. Such methods include, but are not limited to, amplifier sequencing, DNA sequencing, fluorescence spectroscopy, fluorescence resonance energy transfer (or "FRET") based hybridization analysis, high capacity selection, mass spectroscopy. , micro-satellite analysis, nucleic acid hybridization, polymerase chain reaction (PCR), RFLP analysis and size chromatography (e.g., capillary or gel chromatography), all of which are well known in the art. In particular, methods for determining nucleotide polymorphisms, particularly single nucleotide polymorphisms, are described in U.S. Patent Nos. 6,514,700; 6,503,710; 6,468,742; 6,448,407; 6,410,231; 6,383,756; 6,358,679; 6,322,980; 6,316,230 and 6,287,766 and reviewed by Chen and Sullivan, Pharmacogenomics J 2003; 3 (2): 77-96, the disclosures of which are incorporated by reference in their entirety. Genotypic data useful in the methods of the invention and methods for identifying animal trait selection are based on the presence of SNPs.

A "restriction fragment" refers to a fragment of a polynucleotide generated by a restriction endonuclease (an enzyme that cleaves phosphodiester bonds within a polynucleotide chain), which cleaves DNA in response to a recognition site in DNA. The recognition site (restriction site) consists of a specific nucleotide sequence typically about 4-8 nucleotides in length.

A "single nucleotide polymorphism" or "SNP" refers to a variation in the nucleotide sequence of a polynucleotide that differs from another polynucleotide by difference of a single nucleotide. For example, without limitation, exchanging an A for a C, G, or T in the entire polynucleotide sequence constitutes an SNP. It is possible to have more than one SNP in a particular polynucleotide.

For example, in one position on a polynucleotide, a C may be replaced by a T, in another position, a G may be replaced by an A, and so on. When referring to SNPs, the polynucleotide is very often DNA.

As used herein, a "template" refers to a target polynucleotide strand, for example, without limitation, an unmodified naturally occurring DNA strand, which a polymerase uses as a means of recognizing which nucleotide to incorporate below to a growing ribbon to polymerize the naturally occurring ribbon complement. Such a DNA strand may be single stranded or may be part of a double stranded DNA template. In applications of the present invention requiring repeated polymerization cycles, for example, polymerase chain reaction (PCR), the template ribbon itself may be modified by incorporation of modified nucleotides, however, it still serves as a template for the polymerase to synthesize. additional polynucleotides.

A "thermocyclic reaction" is a multistep reaction in which at least two steps are performed by changing the reaction temperature.

A "variance" is a difference in nucleotide sequence among related polynucleotides. The difference may be the deletion of one or more nucleotides from the sequence of a polynucleotide compared to the sequence of a related polynucleotide, the addition of one or more nucleotides or the substitution of one nucleotide for another. The terms "mutation", "polymorphism" and "variance" are used interchangeably here. As used herein, the term "variance" in the singular must be constructed to include multiple variances; that is, two or more nucleotide additions, deletions and / or substitutions on the same polynucleotide. A "mutation point" refers to a single substitution of one nucleotide for another. As used herein, the terms "traits", "quality traits" or "phenotypes" refer to advantageous animal properties resulting from genetics. Quality traits include, but are not limited to, the animal's genetic ability to efficiently metabolize energy, produce meat or milk, establish intramuscular fat. Physical characteristics include, but are not limited to, marbled, soft or lean meats. The terms may be used interchangeably.

A "computer system" refers to the hardware media, software media, and data storage media used to compile the data of the present invention. The minimum hardware medium of computer-based systems of the invention may comprise a central processing unit (CPU), input means, output means and data storage means. Desirably, a monitor is provided to view the data structure. The data storage means may be RAM or other means for accessing computer readable media of the invention. Examples of such systems are microcomputer workstations available from Silicon Graphics Incorporated and Sun Microsystems running Unix, Linux, Windows NT, XP, or IBM OS / 2-based operating systems.

"Computer readable media" means any media that can be read and accessed directly from a computer, and includes, but is not limited to: magnetic storage media such as floppy disks, hard storage media, and magnetic tape ; optical storage media, such as optical discs or CD-ROMs; electrical storage media such as RAM and ROM; and hybrids of these categories, such as magnetic / optical media. By providing such computer readable media, data compiled on a particular animal can be routinely accessed by a user, for example a feedlot operator.

The term "data analysis module" is defined herein to include any person or machine, individually or working together, that analyzes the sample and determines the genetic information contained therein. The term may include a person or machine within a laboratory set.

As used herein, the term "data collection module" refers to any person, object or system that takes a tissue sample from an animal or embryo. For example, and without limitation, the term may define, individually or collectively, the person or machine in physical contact with the animal when the sample is taken, the containers holding the tissue samples, the packaging used for specimen transport and the like. . Advantageously, the data collector is an animal farmer, breeder or veterinarian.

The term "network interface" is defined herein to include any person or computer system capable of accessing data, depositing data, combining data, analyzing data, searching data, transmitting data or storing data. The term is broadly defined as being a person analyzing the data, the electronic hardware and software systems used in the analysis, the databases storing the data analysis, and any storage media capable of storing the data. Non-limiting examples of network interfaces include people, automated laboratory equipment, computers and computer networks, data storage devices such as, but not limited to, disks, hard drives or memory chips.

The term "breeding history" as used herein refers to a record of the life of an animal or group of animals, including, but not limited to, the location, breeding, shelter period, as well as the genetic history of animals. including kinship and descent from it (s), genotype, phenotype, transgenic history, if relevant, and the like.

The term "livestock conditions" as used herein refers to parameters that relate to animal keeping, including, but not limited to, corral and shelter temperature, weekly mortality of a herd, water consumption, livestock consumption. reaction, rate and quality of ventilation, debris condition and the like.

The term "veterinary history" as used herein refers to vaccination data for an animal or group of animals, including, but not limited to, vaccine type (s), vaccine batch number (s). , dose administered, target antigen, method of administration of the vaccine to the recipient animal (s), number of animals vaccinated, age of the animals and the vaccinator. Data related to the vaccine-induced serological or immunological response may also be included. "Veterinary history" as used herein is also intended to include the medication history of the target animal (s), including, but not limited to, animal-administered drugs and / or antibiotics, including the type of medication administered, amount and dose rates, by whom and when administered, by which route, for example, orally, subcutaneously and the like, and the response to medication, including its desired and undesirable effects.

The term "diagnostic data" as used herein refers to animal health-related data other than those detailing the animal's vaccination or veterinary history. For example, diagnostic data may be a record of the infections suffered by the animal (s) and their response to medications provided to treat such infections. Serological data, including antibody or protein composition of serum or other biofluids may also be useful diagnostic data to be fed into the methods of the invention. Surgical data regarding the animal (s) may be included, such as the type of surgical manipulation, result of surgery and complications arising from the surgical procedure. "Diagnostic data" may also include measurements of parameters such as weight, morbidity and other characteristics observed by a veterinary service, such as skin condition, paws, etc.

The term "welfare data" as used herein refers to the accumulation of collective data pertaining to an animal or group of animals, including, but not limited to, a breeding history, a veterinary history, a welfare profile. data, diagnostic data, quality control data or any combination thereof. The term "welfare profile" as used herein refers to parameters such as weight, meat density, agglomeration levels in breeding or rearing confinements, physiological behavior of the animal, growth rate and quality and the like. .

The term "quality control" as used herein refers to the desired characteristics of the animal (s). For domestic non-poultry animals such as cattle and sheep, for example, such parameters include muscle quantity and density, fat content, meat tenderness, milk yield and quality, rearing capacity, and the like.

The term "performance parameters" as used herein refers to factors such as meat yield, rearing yield, dairy form, meat quality and yield, productive life and the like, which may be the desired objectives from breeding and rearing of the animal (s). Performance parameters can be either generated from the animals themselves, or those parameters desired by a customer or market.

The term "nutritional data" as used herein refers to the composition, amount and frequency of feed delivery, including water, provided to the animal (s).

The term "food safety" as used herein refers to the quality of meat from a livestock animal, including, but limited to, time, place and mode of preparation, food storage, transport route, inspection records, texture, color, taste, odor, bacterial content, parasitic content and the like.

It will be apparent to one skilled in the art that animal health and maintenance data may be grouped in varying ways depending on the source or intent of the data collector and any grouping here is therefore not intended to be limiting.

Unless otherwise defined, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art of molecular biology. While materials and methods similar or equivalent to those described herein may be used in the practice or analysis of the present invention, suitable materials and methods are described herein.

In one embodiment, in which the gene of interest is bovine FABP, the bovine FABP nucleotide sequence may be selected from, but is not limited to, sequence corresponding to GenBank Accession Number AAFCO1136716 (Figure 4, SEQ ID NO: 1) or a fragment thereof or a region of the bovine genome comprising this sequence.

The present invention therefore provides isolated nucleic acids that can specifically hybridize to the nucleotide sequence corresponding to GenBank Accession Number AAFC01136716 (Figure 4, SEQ ID NO: 1) or its complement, and comprising the polymorphic site. the nucleotide position being a G-C substitution at nucleotide position 7516 of the FABP4 gene and a G-C substitution at position 7713 of the FABP4 gene.

Advantageous SNP in the present invention is associated with certain economically valuable and hereditary characteristics related to meat quality in cattle. Therefore, it is an object of the present invention to determine the genotype of a given animal of interest as defined by the FABP locus SNP according to the present invention. It is also contemplated that the genotype of the animal (s) may be defined by additional SNPs within the FABP gene or within other genes identified with desirable characteristics or other characteristics, and in particular by a panel or panels of SNPs.

There are many methods known in the art for determining the DNA sequence in a sample, and for identifying whether a given DNA sample contains a particular SNP. Any such technique known in the art may be used in carrying out the methods of the present invention.

The methods of the present invention allow animals with certain economically valuable hereditary traits to be identified based on the presence of SNPs in their genomes and particularly with an SNP located within a FABP gene. The methods further allow, by computer aided methods of the invention, to correlate the characteristics associated with SNP with other data pertaining to the welfare and productive capacity of the animal or group of animals.

To determine the genotype of a given animal according to the methods of the present invention, a genomic DNA sample must be obtained from the animal. Typically, that genomic DNA sample will be obtained from a tissue or cell sample taken from that animal. A tissue or cell sample may be taken from an animal at any time during the life of an animal, but before the carcass identity is lost. The tissue sample may comprise hair including root, skin, bone, buccal smears, blood, saliva, milk, semen, embryos, muscle or any internal organs. In the methods of the present invention, the source of the tissue sample, and thus also the source of the nucleic acid sample, is not critical. For example, the test nucleic acid may be obtained from cells within an animal's body fluid or from cells constituting an animal's body tissue. The particular body fluid from which cells are obtained is also not critical to the present invention. For example, body fluid may be selected from the group consisting of blood, ascites, pleural fluid and spinal fluid. Moreover, the particular body tissue from which cells are obtained is also not critical to the present invention. For example, body tissue may be selected from the group consisting of skin, endometrial, uterine and cervical tissue. Both normal and tumor tissues can be used.

Typically, the tissue sample is marked with an identification number or other evidence relating the sample to the individual animal from which the sample was taken. Advantageously, sample identity remains constant throughout the methods and systems of the invention, thereby ensuring the integrity and continuity of the sample during extraction and analysis. Alternatively, the evidence may be modified in a regular manner to ensure that the data, and any other associated data, can be related back to the animal from which the data was obtained.

The amount / size of sample required is known to the person skilled in the art and, for example, may be determined by the subsequent steps used in the method and system of the invention and the specific analysis methods used. Ideally, the size / volume of the recovered tissue sample should be as consistent as possible within the sample type and animal species. For example, for cattle, non-limiting examples of sample sizes / methods include non-fatty meat: 0.0002 g - 10.0 g; skin: 0.0004 g - 10.0 g; hair roots: at least one and, advantageously, more than five; mouth swabs: 15 to 20 seconds of modest pressure friction in the area between the upper lip and gum, using, for example, a cytology brush; bone: 0.0002 g - 10.0 g; blood: 30 to 50 mL.

In general, the tissue sample is placed in a container that is labeled using a numbering system carrying a code corresponding to the animal, for example the tag on the animal's ear. Consequently, the genotype of a particular animal is easily traceable at all times. The sampling device and / or container may be supplied to the farmer, a slaughterhouse or retailer. The sampling device advantageously takes a consistent and reproducible sample from the individual animals while simultaneously avoiding any cross-contamination of tissue. Consequently, the size and volume of sample tissues derived from individual animals would be consistent.

DNA can be isolated from tissue / cells by techniques known to those skilled in the art (see, for example, U.S. Patent Nos. 6,548,256 and 5,989,431; Hirota et al. (1989) Jinrui Idengaku Zasshi. 34: 217-23 and John et al (1991) Nucleic Acids Res. 19: 408, the disclosures of which are incorporated by reference in their entirety). For example, high molecular weight DNA may be purified from cells or tissue using proteinase K extraction and ethanol precipitation. DNA, however, can be extracted from an animal specimen using any other suitable methods known in the art.

In one embodiment, the presence or absence of SNP from any of the genes of the present invention may be determined by sequencing the region of the genomic DNA sample that encompasses the polymorphic locus. Many genomic DNA sequencing methods are known in the art, and any such methods may be used; see, for example, Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, third edition, Cold Spring Harbor Press. For example, as described below, a DNA fragment encompassing the location of the SNP of interest may be amplified using the polymerase chain reaction. The amplified region of the DNA form can then be sequenced using any method known in the art, for example using an automated nucleic acid sequencer. Detection of a given SNP can then be performed using probe hybridization and / or using PCR based amplification methods. Such methods are described in more detail below.

The methods of the present invention may use oligonucleotides useful as primers to amplify FABP4 gene-specific nucleic acid sequences from the region encompassing a FABP4 SNP. Such fragments should be of sufficient length to permit specific annealing or hybridization to the nucleic acid sample. Typically, the sequences will be from about 8 to about 44 nucleotides in length. Longer sequences, for example from about 14 to about 50, may be advantageous for certain embodiments. The initiators project is well known to a person skilled in the art.

Nucleic acid molecules of the invention include nucleic acid molecules having at least 70% identity or homology or similarity to a FABP4 gene or probes or primers derived therefrom, such as at least 75% identity or homology or similarity, preferably at least 80% identity or homology or similarity, more preferably at least 85% identity or homology or similarity, such as at least 90% identity or homology or similarity, more preferably at least 95% identity or homology or similarity, such as at least 97% identity or homology or similarity. The identity or homology or similarity of the nucleotide sequence can be determined using Myers and Miller's "Align" program ("Optimal Alignments in Linear Space", CABIOS 4, 11-17, 1988) and available from NCBI.

Alternatively or additionally, the terms "similarity", "identity" or "homology", for example with respect to a nucleotide sequence, are intended to indicate a quantitative measure of homology between two sequences. Percent sequence similarity can be calculated as (Nref - Ndif) x 100ZNzef, where Naif is the total number of non-identical residues in the two sequences, when aligned, and Nref being the number of residues in one of the sequences. Therefore, the AGTCAGTC DNA sequence will have a sequence similarity of 75% to the AATCAATC sequence (Nref = 8; Ndif = 2). Alternatively or additionally, "similarity" with respect to sequences refers to the number of positions with identical nucleotides divided by the number of nucleotides in the shortest of the two sequences, and the alignment of the two sequences can be determined according to Wilbur's algorithm. Lipman (Wilbur and Lipman, 1983 PNAS USA 80: 726), for example, using a window size of 20 nucleotides, a word length of 4 nucleotides and a range penalty of 4, and computer aided analysis and interpretation of the data. Sequences, including alignment, can be conveniently performed using commercially available programs (for example, Intelligenetics (TM) Suite, Intelligenetics Inc. CA). When RNA sequences are said to be similar, or have a degree of sequence identity to DNA sequences, thymidine (T) in the DNA sequence is considered equal to uracil (U) in the RNA sequence. A probe or primer can be any segment of at least 8, preferably at least 10, more preferably at least 12, 13, 14 or 15, such as at least 20, for example at least 23 or 25, for example. at least 27 or 30 nucleotides in a FABP4 gene that are unique to a FABP gene. As for PCR or hybridization primers or probes and optimal lengths for them, reference is also made to Kajimura et al., GATA 7 (4): 71-79 (1990).

RNA sequences within the scope of the invention are derived from the DNA sequences, by thymidine (T) in the DNA sequence being considered equal to uracil (U) in the RNA sequences.

Oligonucleotides may be produced by a conventional production process for general oligonucleotides. They may be produced, for example, by a chemical synthesis process or by a microbial process that makes use of a plasmid vector, a phage vector or the like. In addition, it is suitable to use a nucleic acid synthesizer.

To label an oligonucleotide with the fluorescent dye, one of the conventionally known labeling methods can be used (Tyagi & Kramer (1996) Nature Biotechnology 14: 303-308; Schofield et al. (1997) Appl. And Environ. Microbiol. 63: 1143-1147; Proudnikov & Mirzabekov (1996) Nucl. Aeids Res. 24: 4532-4535). Alternatively, the oligonucleotide may be labeled with a radioactive label, for example 3H, 125I, 35S, 14C, 32P, etc. Well-known labeling methods are described, for example, in Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, third edition, Cold Spring Harbor Press. The label is coupled directly or indirectly to an oligonucleotide component according to methods well known in the art. Reverse phase chromatography or the like used to provide a nucleic acid probe for use in the present invention can purify the synthesized oligonucleotide labeled with a marker. An advantageous probe form is that labeled with a fluorescent dye at the 3 'or 5' end and containing G or C as the base at the labeled end. If the 5 'end is labeled and the 3' end is not labeled, the OH group at the C atom at the 3 'position of the 3' end ribose or deoxyribose may be modified with a phosphate group or the like, although no limitation is imposed. in this regard.

During hybridization of the nucleic acid target with the probes, severe conditions may advantageously be used in conjunction with other severity affecting conditions to assist in hybridization. Differential disruption detection is particularly advantageous to reduce or eliminate hybridization slip between probes and target, and to promote more effective hybridization. In yet another aspect, conditions of severity may be varied during the determination of hybridization complex stability to more accurately or rapidly determine if an SNP is present in the target sequence.

One method for determining the genotype at the polymorphic gene locus involves obtaining a nucleic acid sample, hybridizing the nucleic acid sample with a probe, and disrupting hybridization to determine the level of disruption energy required, with the probe has a different burst energy for one allele compared to the other allele. In one example, there may be a lower disruption energy, for example melt temperature, for an allele harboring a cytosine residue at a polymorphic locus, and a higher required energy for an allele with a different residue at that polymorphic locus. . This can be achieved when the probe is 100% homology to an allele (a perfectly compatible probe) but has a single incompatibility with the alternative allele. Since the perfectly matched probe is more tightly bound to the target DNA than the non-matched probe, it requires more energy to make the hybridized probe dissociate.

In an additional step of the above method, a second probe ("anchor") may be used. In general, the anchor probe is not specific to each of the alleles, but hybridizes regardless of which nucleotide is present at the polymorphic locus. The anchor probe does not affect the disruption energy required to disassociate the hybridization complex, but instead contains a complementary label for use with the first probe ("sensor").

Hybridization stability can be influenced by a number of factors, including thermoregulation, chemical regulation, as well as electronic severity control, either alone or in combination with the other factors listed. Although the use of stringency conditions in one or both of the target hybridization or oligonucleotide sensor stringency steps, a rapid completion of the process can be achieved. This is desirable to achieve properly indexed hybridization of the target DNA, to achieve the maximum number of molecules at a test site with an accurate hybridization complex. By way of example, with the use of severity, the initial hybridization step may be completed in ten minutes or less, more advantageously five minutes or less, and most advantageously two minutes or less. All in all, the analytical process can be completed in less than half an hour.

In one mode, the hybridization complex is labeled and the step of determining the amount of hybridization includes detecting the amounts of labeled hybridization complex at the test sites. The device and detection method may include, but are not limited to, optical imaging, electronic imaging, imaging with a CCD camera, integrated optical imaging, and mass spectrometry. In addition, the amount of labeled or unlabelled probe bound to the target can be quantified. Such quantification may include statistical analysis. The labeled portion of the complex may be the target, the stabilizer, the probe or the hybridization complex as a whole. Labeling may be by fluorescent labeling selected from the group of, but not limited to, Cy3, Cy5, Bodipy Texas Red, Bodipy Far Red, Lucifer Yellow, BOdipy 630/650-X, Bodipy R6G-X and 5-CR 6G. Colorimetric labeling, bioluminescent labeling and / or chemiluminescent labeling may additionally carry out labeling. Labeling may further include the transfer of energy between molecules in the hybridization complex by perturbation analysis, quenching, electron transport between donor and receptor molecules, the latter of which may be facilitated by double-stranded compatibility hybridization complexes. Optionally, if the hybridization complex is not labeled, detection may be performed by measuring differential conductance between double stranded DNA and single stranded DNA. In addition, direct detection can be achieved by porous silicon-based optical interferometry or by mass spectrometry. When using mass spectrometry, no fluorescent label or any other label is required. Preferably, detection is achieved by extremely high levels of mass resolution achieved by direct measurement, for example by flight time (TOF) or by electron spray ionization (ESI). When mass spectrometry is contemplated, probes having a nucleic acid sequence of 50 bases or less are advantageous.

The label may be amplified, and may include, for example, branched or dendritic DNA. If the target DNA is purified, it may be unamplified or amplified. In addition, if the purified target is amplified and amplification is an exponential method, it may be, for example, amplified DNA or PCR or strand amplification amplified DNA (SDA). Linear methods of DNA amplification such as rolling circles or transcriptional runoff can also be used.

When it is desired to amplify a DNA fragment comprising an SNP according to the present invention, the forward and reverse primers may have contiguous segments of about 8, 9, 10, 11, 12, 13, 14, 15, 16. , 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or other length up to and including about 50 nucleotides in length. The sequences with which the forward and reverse ring primers are advantageously located on either side of the particular nucleotide position that is substituted in the SNP to be amplified.

A detectable label may be incorporated into a nucleic acid during at least one cycle of an amplification reaction. Spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical media may detect such labels. Labels useful in the present invention include fluorescent dyes (e.g., fluorescein isothiocyanate, Texas Red, rhodamine, and the like), radioactive labels (e.g., 3H, 125I, 35S, 14C, 32P, etc.), enzymes (e.g. , horseradish peroxidase, alkaline phosphatase, etc.), colorimetric labels such as colloidal gold or colored glass or plastic beads (eg polystyrene, polypropylene, latex, etc.). The label is coupled directly or indirectly to an assay component according to methods well known in the art. As indicated above, a wide variety of labels are used, with the choice of label depending on the sensitivity required, ease of conjugation with the compound, stability requirements, available instrumentation and disposal provisions. Non-radioactive labels are often linked by indirect means. Polymerases may also incorporate fluorescent nucleotides during nucleic acid synthesis.

Reagents allowing the sequencing of reaction products can be used here. For example, chain terminator nucleotides will often be incorporated into a reaction product during one or more cycles of a reaction. Commercial kits containing the most commonly used reagents for these DNA sequencing methods are available and widely used. PCR exonuclease digestion methods for DNA sequencing can also be used. Many genomic DNA sequencing methods are known in the art, and any such method can be used; see, for example, Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, third edition, Cold Spring Harbor Press. For example, as described below, a DNA fragment extending from the location of the SNP of interest may be amplified using the polymerase chain reaction or some other cyclic polymerase mediated amplification reaction. The amplified region of DNA can then be sequenced using any method known in the art. Advantageously, nucleic acid sequencing is done by automated methods (reviewed by Meldrum, (2000) Genome Res. 10: 1288-303, the disclosure of which is incorporated herein by reference in its entirety), for example using a Beckman CEQ 8000 Genetic instrument

Analysis System (Beckman Coulter Instruments, Inc.). Methods for nucleic acid sequencing include, but are not limited to, automated fluorescent DNA sequencing (see, for example, Watts & MacBeath, (2001) Methods MoI Biol. 167: 153-70 and MacBeath et al. (2001 ) Methods Mol Biol. 167: 119-52), capillary electrophoresis (see, for example, Bosserhoff et al. (2000) Comb Chem High Throughput Screen. 3: 455-66), DNA sequencing chips (see, for example , Jain, (2000) Pharmacogenomics. 1: 289-307), mass spectrometry (see, for example, Yates, (2000) Trends Genet. 16: 5-8), pyro-sequencing (see, for example, Ronaghi, (2001) Genome Res. 11: 3-11), and ultrafine layer gel electrophoresis (see, for example, Guttman & Ronai, (2000) Electrophoresis. 21: 3952-64), the disclosures of which are incorporated herein by reference in its entirety. Sequencing can also be done by a trading company. Examples of such companies include, but are not limited to, University of Georgia Molecular Genetics Instrumentation Facility (Athens, Georgia) or Seq Wright DNA Technologies Services (Houston, Texas).

An SNP-specific probe can also be used to detect SNP in amplified target gene specific nucleic acid sequences, such as amplified PCR products generated using the primers described above. In certain embodiments, such SNP-specific probes consist of oligonucleotide fragments. Advantageously, the fragments are of sufficient length to provide specific hybridization to the nucleic acid sample. Using a hybridization probe of 10 to 50 nucleotides in length allows the formation of a duplex molecule that is both stable and selective. Molecules having complementary sequences over lengths greater than 12 bases in length are generally advantageous in enhancing hybrid stability and selectivity, thereby improving the quality and degree of particular hybrid molecules obtained. . In general, it will be preferred to design nucleic acid molecules having extensions of 16 to 24 nucleotides, or even longer if desired. A tag nucleotide region may be included, as at the 5 'end of the primer, that can provide a site with which an oligonucleotide sequencing primer can hybridize to facilitate sequencing of multiple PCR samples.

The probe sequence must encompass the particular nucleotide position that can be substituted on the SNP to be detected. Advantageously, two or more different "allele-specific probes" may be used for analysis of an SNP, a first allele-specific probe for detecting an allele, and a second allele-specific probe for detecting the SNP. alternative allele.

It will be understood that this invention is not limited to the particular primers and probes disclosed herein and that it is intended to encompass at least nucleic acid sequences that are hybridizable to the nucleotide sequence disclosed herein, a complement or fragment thereof, or which are functional sequence analogs. of these sequences. It is also contemplated that a particular trait of an animal may be determined by use of a panel of SNPs associated with that trait. Several economically relevant features may be characterized by the presence or absence of one or more SNPs and a plurality of SNPs in different genes. One or more panels of SNPs may be used in the methods of the invention to define the phenotypic profile of the animal in question.

Homologs (ie nucleic acids derived from another species) or other related sequences (eg, paralogs) may be obtained under standard or severe hybridization conditions, with all or part of the particular sequence as a probe, using well known methods. in the technique for nucleic acid hybridization and cloning.

Genetic markers, probes, methods, and kits of the invention are also useful in a breeding program to select those animals having desirable phenotypes for a number of economically important traits, such as improved meat quality and yield, in particular, meat tenderness. beef. Continuous selection and rearing of animals, such as farmed animals, which are at least heterozygous and, advantageously, homozygous, to desired alleles of the FABP gene polymorphic sites, associated with economically relevant characteristics of growth, food intake, carcass efficiency and merit would lead to a race, lineage or population having higher numbers of offspring with economically relevant characteristics of growth, food intake, carcass efficiency and merit. Therefore, FABP SNPs of the present invention may be used as a selection tool.

Desirable phenotypes include, but are not limited to, food intake, growth rate, body weight, merit and carcass composition, and bed yield. Specific carcass characteristics with desirable phenotypes include, but are not limited to, additional carcass value (additional carcass value, $), average daily gain (ADG, lb / d), dorsal fat thickness (BFAT, in), weight calculated live weight (Cale Lv Wt, lb), calculated yield (cYG), days in feed (DOF, d), seasoning percentage (SD,%), dry matter intake (DMI, lb), dry matter intake per day in ration (DMI by DOF, lb / d), hot carcass weight (HCW, lb), hot carcass weight value (HCV value, $), intramuscular fat content (MFI%,%), marbling (MBS, 10 to 99), marbling classification divided by days in feed (MBS / DOF), quality grade, less than or equal to select versus greater than or equal to choose (HQ, <Sc vs,> Ch), rib fillet area (REA, in2), rib fillet area by HCW percentage weight (REA / cwt HCW, in2 / 100 Ib hot carcass weight (HCW) and depth subcutaneous fat (SFD).

One aspect of the present invention provides animal grouping and methods for managing livestock production comprising grouping livestock, such as cattle, according to genotype as defined by SNP panels, each panel comprising at least one SNP, one or more of which is in the FABP gene of the present invention. Other SNPs, which may be included in SNP panels, include, but are not limited to, SNPs found on calpastatin gene, GHR gene, ghrelin gene, leptin gene, NPY gene, ob gene, TFAM gene, UASMS1 gene , UASMS2 gene, UASMS3 gene and / or UCP2 gene. The genetic selection and clustering methods of the present invention may be used in conjunction with other conventional phenotypic clustering methods, such as grouping animals by visible characteristics such as weight, frame size, racial characteristics, and the like. The methods of the present invention provide livestock production having improved hereditary characteristics, and can be used to optimize the performance of livestock herds in areas such as breeding, feed intake, carcass / meat quality and milk production. The present invention provides methods of selecting livestock to determine those most likely to develop a desired body condition by identifying the presence or absence of one or more gene polymorphisms correlated with meat quality.

As described above, and in the Examples, there are several phenotypic characteristics with which SNPs of the present invention may be associated. Each of the phenotypic and genetic characteristics may be tested using the methods described in the Examples, or using any suitable methods known in the art. Using the methods of the invention, a farmer, a fattening operator, or the like, can group cattle according to each animal's genetic propensity for a desired trait, such as growth rate, feed intake, or behavior. as determined by SNP genotype. Cattle are tested for homozygosity or heterozygosity with respect to SNP alleles of one or more genes, so that they can be grouped such that each pen contains cattle with similar genotypes. Each animal enclosure is then fed and otherwise maintained in a manner and for a time determined by the fattening operator, and then slaughtered.

Individual genotypic data derived from a panel or panels of SNPs for each animal or herd of animals may be recorded and associated with various other animal data, for example health information, kinship, livestock conditions, vaccination, herd records, subsequent food safety data and the like. Such information may be passed on to a government agency to provide traceability of an animal or meat product, or it may serve as the basis for breeding, feeding and marketing information. Once the data has or has not been associated with other data, the data is stored in an accessible database such as, but not limited to, a computer database or microchip implanted in the animal. The methods of the invention may provide an analysis of fed data that may be compared to parameters desired by the operator. These parameters include, but are not limited to, those such as breeding goals, egg laying goals, herd vaccination levels. If animal performance or properties deviate from desired objectives, computer-aided methods may trigger an alert to allow the operator to adjust vaccination doses, medications, feed, etc., accordingly.

The results of the analysis provide data that is associated with the individual animal or herd, in whole or in part, from those taken in the sample. The data is then kept in an accessible database, and may or may not be associated with other data from that particular individual or from other animals.

Data obtained from individual animals can be stored in a database that can be integrated or associated with and / or correlated with other databases. The database, together with associated data, provides information about the individual animal to be known through each stage of the animal's life, that is, from conception to consumption of the animal product.

Accumulated data and the combination of genetic data with other species of animal data provide access to kinship information, herd identification, health information including vaccinations, disease exposure, fattening park location, diet and ownership changes. . Information, such as dates and results of routine or diagnostic tests, is facially stored and accessible. Such information would be especially valuable to companies, particularly those seeking superior breeding lines.

Each animal may be provided with a unique identifier. The animal may be labeled, as in traditional tracking programs, or have computer chips implanted providing stored and readable data or provided with any other identification method that associates the animal with its unique identifier.

The database containing SNP-based genotype results for each animal or data for each animal may be associated with or linked to other databases containing data, for example, that may be useful in selecting traits for grouping or subgrouping of an animal. For example, and not by limitation, data pertinent to animals having particular medication or vaccination protocols may subsequently be linked with data relevant to animals having food from certain food sources. The ability to refine a group of animals is limited only by the characteristics sought and to databases containing information related to those characteristics.

Databases, which may be usefully associated with the methods of the invention, include, but are not limited to, breeding lineages, noble male ancestors, noble female ancestors, and the like, other animal genotypes, including whether or not the other specific animals have genes, including transgenic genetic elements, location of animals, which share similar or identical genetic characteristics, and similar ones. General data includes, but is not limited to, scientific data, such as which genes encode specific quality traits, breeding association data, feed data, breeding trends, and the like.

One method of the present invention includes providing the animal owner or customer with sample collection equipment, such as cotton swabs and labels, useful for collecting samples from which genetic data can be obtained. Advantageously, the package is encoded with a barcode label. Labels are encoded with the same identification indicia, advantageously with a compatibility bar code label.

Optionally, the package contains means for shipping the labels to an analysis laboratory. The optional package is also encoded with identification indicia, advantageously with a bar code label.

Optionally, the method includes a system in which a database account is established when ordering the sampling equipment. The database account identifier corresponds to the identification marks on the labels and packaging. Upon loading of the sampling equipment in compliance with the order, identification marks are recorded in a database.

Advantageously, the identifier is a barcode label which is scanned when tags are sent. When the labels are returned to the analysis facility, the identifier is re-registered and compared to the information previously recorded in the database when loading the vial to the customer. Once genotype typing is complete, information is recorded in the database and encoded with the unique identifier. Test results are also provided to the customer or the pet owner. Data stored in the genotype database may be integrated with or compared with other data or databases for the purpose of animal identification based on genetic propensities. Other data or databases include, but are not limited to, those containing information related to SNP-based DNA analysis, vaccination, Sure Health preconditioning program, estrus and pregnancy outcomes, hormone levels, safety / food contamination, somatic cell counts, mastitis occurrence, diagnostic test results, milk protein levels, milk fat, vaccination status, health records, mineral levels, trace mineral levels, herd performance, and similar.

Therefore, the present invention encompasses computer aided methods for tracking breeding and veterinary history of farmed animals, comprising the use of a computer based system comprising a programmed computer comprising a processor, a data storage system, a device and an output device, and comprising the steps of generating a profile of a farmed animal by inputting the animal's genotype data into the programmed computer via the input device, the genotype may be defined by a panel of at least two single nucleotide polymorphisms that predict at least one physical characteristic of the animal, the entry into the computer programmed by the animal welfare data input device, the correlation of the data fed the animal's phenotypic profile using the processor and data storage systems, and outputting a profile of the animal or group of animals to the output device.

The databases and their analysis will be accessible to those for whom access has been provided. Access can be provided through access rights or by subscription for specific portions of data. For example, the database may be accessed by animal owners, the test site, the entity providing the sample to the test site, fattening park staff, and veterinarians. Data may be provided in any form, such as by access to a website, fax, email, posted correspondence, automated telephone, or other communication methods. This data can also be encoded in a portable storage device such as a microchip that can be implanted in the animal. Advantageously, the information can be read and new information added without removing the microchip from the animal.

The present invention comprises systems for carrying out the methods disclosed herein. Such systems include devices such as computers, internet connections, servers, and data storage devices. The present invention also provides a data transmission method comprising transmitting information from such methods discussed herein or their steps, for example via telecommunications, telephone, video conferencing, mass communications, for example presentation, such. such as a computer presentation (eg, POWERPOINT), internet, email, document communication such as computer programs (eg, WORD), and the like.

Systems of the present invention may comprise a data collection module, which includes a data collector for collecting data from an animal or embryo and transmitting the data to a data analysis module, a network interface for receiving data from from the data analysis module, and optionally further adapted to combine multiple data from one or more individual animals, and to transmit the data via a network to other sites, or to a storage device. More particularly, systems of the present invention comprise a data collection module, a data analysis module, a network interface for receiving data from the data analysis module, and optionally further adapted to combine multiple data. from one or more individual animals, and to transmit data via a network to other sites, and / or a storage device. For example, the data collected by the data collection module leads to a determination of the absence or presence of a gene SNP in the animal or embryo, and, for example, such data is transmitted when the animal's feed diet is planned.

In an embodiment in which data is implanted in a microchip on a particular animal, the farmer can optimize herd management efficiency because the farmer is able to identify an individual animal's genetic predispositions as well as treatments (eg vaccinations). and veterinarian visits) past, present and future. Therefore, the invention also provides access to other databases, for example herd data relating to genetic testing and data performed by others, by linking data to other sites. Therefore, data from other databases may be transmitted to the central database of the present invention via a network interface for receiving data from the data analysis module of the other databases.

The invention relates to a computer system and computer readable media for compiling animal data, systems containing data fed on that animal, such as, but not limited to, vaccination and medication histories, DNA analysis, thyroglobulin, leptin, MMI (Meta Morphix Inc.) analysis, diagnosis of bovine spongiform encephalopathy (BSE), brucellosis vaccination, FMD (paw and mouth disease) vaccination, BVD (bovine viral diarrhea) vaccination ), Sure Health preconditioning program, heat and pregnancy outcomes, tuberculosis, hormone levels, food safety / contamination, somatic cell counts, mastitis occurrence, diagnostic test results, milk protein levels, milk fat , vaccination status, health records, mineral levels, trace mineral levels, herd performance, and the like. Animal data may also include prior treatments as well as tailored treatment suggested depending on the genetic predisposition of that animal in the face of a particular disease. The invention also provides a computer aided method for the improvement of animal production comprising the use of a computer system, for example, a programmed computer comprising a processor, a data storage system, an input device and an output device. , the steps of input into the programmed computer, via the input device, of data comprising rearing, veterinary, medication, diagnostics and the like, of an animal, of correlation of a physical trait predicted by the genotype using the processor and the data storage system, the output to the output device of the genotype-correlated physical trait, and the feeding of the animal from a diet based on the physical trait, thereby improving livestock production.

The invention further provides a computer aided method for optimizing the efficiency of animal feed lots comprising the use of a computer system, for example a programmed computer comprising a processor, a data storage system, a device input and output device, and the steps of input into the computer programmed, via the input device, data comprising a veterinary, breeding, animal history, correlation of veterinary, breeding histories using the processor and the data storage system, the output to the output device of the genotype-correlated physical trait, and the feeding of the animal to a diet based on the physical trait, whereby optimum feed efficiency is improved. farm animals.

The invention further comprises methods of doing business by providing access to such computer readable media and / or computer systems and / or data collected from animals to users; for example, streaming media and / or data may be accessible to a user, for example, on a subscription basis, via the internet or a global communications / computer network; or, the computer system may be available to a user on a subscription basis.

In one embodiment, the invention provides a farm animal mapping computer system comprising physical characteristics and databases corresponding to one or more animals. In another embodiment, the invention provides computer readable media for the management of farmed animals comprising veterinary physical and historical characteristics corresponding to one or more animals. The invention further provides methods of doing business for farm animal management comprising providing a user with the computer system and media described above or veterinary physical and historical characteristics corresponding to one or more animals. The invention further encompasses methods of transmitting information obtained by any method or steps thereof described herein or any information described herein, for example via telecommunications, telephone, mass communications, mass media, presentations, internet, email, etc.

The invention further encompasses kits useful for the selection of nucleic acid isolated from one or more individual cattle by allelic variation of any of the FABP genes, and in particular by any of the SNPs described herein, which kits may include. comprising at least one oligonucleotide that selectively hybridizes to a nucleic acid comprising any one or more of which are FABP sequences described herein, and instructions for using the oligonucleotide to detect nucleotide variation corresponding to nucleic acid SNP isolated.

One embodiment of this aspect of the invention provides an oligonucleotide that specifically hybridizes to the isolated nucleic acid molecule of this aspect of the invention, and the oligonucleotide hybridizes to a portion of the isolated nucleic acid molecule comprising any of the polymorphic sites on the FABP sequences described herein.

Another embodiment of the invention is an oligonucleotide, which specifically hybridizes under high stringency conditions to any of the FABP gene polymorphic sites, wherein the oligonucleotide is from about 18 nucleotides to about 50 nucleotides.

In another embodiment of the invention, the oligonucleotide comprises a central nucleotide that specifically hybridizes to a FABP4 gene polymorphic site of the nucleic acid molecule portion.

Another aspect of the invention is a method of identifying a FABP4 polymorphism in a nucleic acid sample comprising isolating a FABP-encoding nucleic acid molecule or fragment thereof, and determining the nucleotide at the polymorphic site.

Another aspect of the invention is a cattle selection method for determining those cattle most likely to exhibit a biological difference in meat quality comprising the steps of obtaining a sample of genetic material from a cattle; and evaluation by the presence of a genotype in cattle, which is associated with meat quality, the genotype characterized by a polymorphism in any of the FABP genes.

In other embodiments of this aspect of the invention, the evaluation step is selected from the group consisting of: restriction fragment length polymorphism (RFLP) analysis, mini-sequencing, MALD-TOF, SINE, heteroduplex analysis, conformational polymorphism Single-stranded (SSCP), Denaturation Gradient Gel Electrophoresis (DGGE) and Temperature Gradient Gel Electrophoresis (TGGE).

In various embodiments of the invention, the method may further comprise the step of amplifying a region of the FABP gene or a portion thereof containing the polymorphism. In other embodiments of the invention, amplification may include the step of selecting a forward sequence primer and a reverse sequence primer capable of amplifying a region of the FABP gene.

Another aspect of the invention is a computer aided method for predicting which livestock animals have a biological difference in meat quality, comprising: using a computer system, for example, a programmed computer comprising a processor, a storage system data input, an input device and an output device, the steps of: (a) entering the programmed computer, via the input device, comprising an FABP genotype of an animal, (b) correlating a quality growth, feed intake, efficiency or carcass merit predicted by the FABP genotype using the processor and data storage system and (c) output to the output device of genotype-correlated meat quality FABP, by predicting which livestock animals have a particular quality of growth, feed intake, housing cost.

Still another aspect of the invention is a method of doing business for managing livestock comprising providing a user with a computer system for managing livestock comprising physical characteristics and genotypes corresponding to one or more animals or animals. computer readable media for the management of farmed animals comprising physical characteristics and genotypes corresponding to one or more animals or physical characteristics and genotypes corresponding to one or more animals. The invention will now be further described by the following non-limiting examples. EXAMPLES

Example 1:

This Example demonstrates that the bovine fatty acid binding protein 4 (FABP4) gene is significantly associated with the marbling and depth of subcutaneous fat in Wagyu χ Limousin F2 crosses.

Evidence has been shown that fatty acid binding protein 4 (FABP4) gene, expressed in adipose tissue, interacts with peroxisome proliferator-activated receptors and binds to hormone-sensitive lipase, thus playing an important role in metabolism and metabolism. on lipid homeostasis in adipocytes. The aim of this study, therefore, was to investigate the associations of the bovine FABP4 gene with fat deposition at Wagyu χ Limousin F2 crosses. Sequences of both cDNA (625 bp) and genomic DNA (8031 bp) from the bovine FABP4 gene were retrieved from public databases and aligned to determine their genomic organization. Two primer pairs have been designed that target two gene regions, one from bases 5433 to 6106 and one from bases 7417 - 7868 (AAFC01136716). Direct sequencing of PCR products in two sets of DNA from high / low sparing animals revealed two G / C substitutions at positions 7516 and 7713, respectively. The first G / C substitution could be revealed by PCR-RFLP using the restriction enzyme MspAlI and had genotype typified in 246 F2 animals in the reference population. Statistical analysis showed that the bovine FABP4 gene genotype significantly affected intramuscular and subcutaneous fat deposition, as indicated by the marbling classification (P = 0.0321) and subcutaneous fat depth (P = 0.0246), respectively. The FABP4 gene falls within a suggestive / significant QTL interval for beef marbling, previously reported on bovine chromosome 14 in three other populations, which can be implemented immediately in beef breeding programs.

Fatty Acid Binding Proteins is a family of small, highly conserved, cytoplasmic proteins that bind to long chain fatty acids and other hydrophobic ligands (Kaikaus et al. 1990). Its main functions include assimilation, transport and metabolism of fatty acids. To date, nine distinct members have been identified in this gene family (Damcott et al., 2004), including adipocyte fatty acid binding protein or fatty acid binding protein 4 (FABP4). FABP4 plays an important role in the regulation of lipid and glucose homeostasis through its interaction with peroxisome proliferator activated receptors (PPARs) located in the cell nucleus.

Specifically, the FABP4 / fatty acid complex activates the PPAR-γ isoform, which in turn regulates FABP4 transcription (Damcott et al., 2004). In addition, FABP4 appears to be involved in lipid hydrolysis and intracellular fatty acid traffic through direct interaction and binding to hormone-sensitive lipase (Shen et al. 1999), which is a primary enzyme involved in lipid catabolism ( Tansey et al 2003). Recently, FABP4 and FABP5 have been proposed as potential candidate genes for obesity as they are located within a quantitative Ioci region (QTL) for serum leptin levels in mice (Ogino et al. 2003). Leptin, a 16 KDa protein secreted from white adipocytes, is involved in regulating whole body food intake, energy expenditure and energy balance (Jiang and Gibson 1999). All these factors indicate that FABP4 plays an important role in lipid metabolism and homeostasis in adipocytes. Here, the development of genetic markers in the bovine FABP4 gene and the significant association of the gene with marbling and subcutaneous fat depth (SFD) in Wagyu χ Limousin F2 crosses are reported.

The genomic sequence of the bovine FABP4 gene had not been described. However, the cDNA sequence of the bovine FABP4 gene (X89244), derived from the bovine mammary gland, has been previously reported (Specht et al. 1996). Therefore, a BLAST search was performed using this cDNA sequence as a key to fetching its genomic DNA sequence against 3X bovine genome sequences that had been released to the public domain (http: //www.hgsc.bcm.tmc .edu / projects / bovi ne /). The process recovered Bos taurus contigl36721 (GenBank Accession Number AAFC01136716) which contains the 8031 bp bovine FABP4 gene sequence. The overall structure of the bovine FABP4 gene was then determined by comparing the genomic DNA sequence with the complete cDNA sequence (Figure 1). The genomic organization of the bovine FABP4 gene consists of four exons and three introns (Figure 1), which is comparable to the gene structure in other members of the fatty acid binding protein family and is identical to the same gene structure in humans ( NC_000008), pigs (Y16039), mice (NC_000069), rats (NC_005101) and chickens (NC_006089). Genomic cDNA-DNA alignment of the bovine FABP4 gene showed 99% sequence identity in one aligned block (Exon 3, Figure 1) and 100% sequence identity in three blocks. These four aligned blocks represent the 5 'RTU (untranslated region), 4 exons and the 3' RTU. Therefore, this 8031 bp genomic sequence of bovine FABP4 could be tentatively distributed in the following organizational parts: 1819 bp for proximal promoter, 67 bp for 5 'UTR, 66 bp for exon 1, 2709 bp for intron 1, 173 bp for exon 2, 594 bp for intron 2, 102 bp for exon 3, 463 bp for exon 3, 51 bp for exon 4, 100 bp for 3 'RTU and 1887 bp for the non-transcribed sequence 3 'respectively (Figure 1).

The Wagyu χ Limousin reference population was jointly developed by Washington State University and the Fort Keogh Livestock and Range Research Laboratory, ARS, USDA. F1 crosses, including 6 F1 bulls and 113 ancestral females were bred at Washington State University and transferred to the USDA research station in the fall of 1998. Crossings between these F1 animals produced 71 F2 progenies in 2000, 90 in 2001 and 109. in 2002 respectively. Growth rate, carcass and meat quality data, including marbling and SFD classifications, were collected from all F2 calves. Marbling classification is a subjective measurement of the amount of intramuscular fat in the Iongissimusr muscle based on USDA standards (http://www.ams.usda.gov/). SFD was measured at the interface of the 12th and 13th ribs perpendicular to the outer surface, at a point three-quarters of the length of the longissimus muscle from its lumbar bone end. Marbling ratings ranged from 4 = Mild0 to 9.5 = Moderately Abundant50 (SD = 1.00) and SFD measurements ranged from 0.1 to 1.3 inches (SD = 0.18) in this F2 population. DNA was extracted from blood samples. Based on the availability of both data and DNA samples, 2460 observations were used in the present study. The two DNA sets were formed from the reference population, one from 20 individuals with the highest marbling ratings (HMS pool) and one from 20 individuals with the lowest marbling ratings (LMS pool), for an initial selection of marker association with characteristics.

Two primer pairs are designed to detect polymorphisms in the bovine FABP4 gene based on the genomic sequence contigl36721 (GenBank Accession Number AAFC01136716. All numbers in this descriptive report are based on this sequence). The first pair of primers (forward sequence, 5 'TCG TAA ACT TAG ATG AAG GTG CTC TGG 3 1 (SEQ ID NO: 2) and reverse sequence, 5' ACG TAT CCA GCA AGA CAT GGA G 3 '(SEQ ID NO: 3) targets a region from bases 5433 to 6106. This region includes exon 3, intron 3 and exon 4, and a putative G / A substitution was found in exon 3 based on the alignment of sequences between cDNA and bovine FABP4 genomic DNA The second pair of primers (forward sequence, 5 'ATA TAG TCC ATA GGG TGG CAA 3' (SEQ ID NO: 4) and reverse sequence, 5 'AAC CTC TCT TTG AAT TCT CCA TTC T 3 '(SEQ ID NO: 5) amplifies a region of 7417 - 7868 bp, which contains a short "CA" tandem repeat. Approximately 50 ng of genomic DNA from the HMS sets and LMS were amplified to a final volume of 10 μl; containing 12.5 ng of each primer, 150 μΜ dNTPS, 1.5 mM MgCl2, 50 mM KCl, 20 mM Tris-HCl and 0.25 U Platinum Taq polymerase (Inv Carlsbad, CA) PCR conditions were performed as follows: 940C for 2 minutes, 32 cycles of 940C for 30 seconds, 63 ° C (for the first pair of primers) or 56 ° C (for the second pair primers) for 30 seconds and 72 ° C for 30 seconds, followed by an additional 5 minute extension at 720C. PCR products were examined by electrophoresis through 1.5% agarose gel with IX TBE buffer to determine the quality and quantity of aDN for sequencing.

Direct sequencing of PCR products from two sets of DNA was performed on an ABI 3730 sequencer at the Biotechnology and Bioanalysis Laboratory (Washington State University) using a standard protocol. However, DNA sequencing did not confirm the existence of an exon 3 G / A substitution or a variation in the number of AC repeats in the 3 'non-transcribed region of the bovine FABP4 gene between the HMS and LMS sets. Instead, two single nucleotide polymorphisms (SNPs) were detected in products amplified with the second primer pair, including a G / C substitution located at position 7516 (Figure 2A) and a 7713 bp G / C substitution within the AC repeat region (Figure 2B). Restriction map analysis indicated that the 7516 bp G / C substitution could be genotyped by PCR-RFLP using the MspAlI restriction enzyme. This G / C SNP in the bovine FABP4 gene was then genotyped individually in DNA from Wagyu χ Limousin F2 animals with recorded marbling ratings and SFD measurements. After PCR amplification, the amplicons were digested at 37 ° C for three hours with 2 U MspAlI (New England Biolabs, Beverly, MA) followed by analysis on 1.5% agarose gels. The 452 bp amplicon with the 7516 bp C / G substitution contains a unique polymorphic site for the restriction enzyme MspAlI. However, GG homozygous animals have an MspAlI site and reveal, after complete digestion, two bands: 100 bp and 352 bp. In comparison, homozygous animals with the C allele lost the MspAlI recognition site at this position and show only the 452 bp band. Heterozygous animals are identified by the presence of three bands after MspAlI digestion (Figure 3). Of the 232 animals that had their genotype typed, 139 were C allele homozygotes, 21 were G allele homozygotes, and the remaining 72 were both C and G alleles (Table 1). Genotype distribution is Hardy-Weinberg equilibrium (χ2 = 2.82, P> 0.05).

Table 1. Associations of SNP with bovine FABP4 G / C at position 7516 with marbling and SFD in Wagyu x Limousin F2 crosses.

<table> table see original document page 95 </column> </row> <table> <table> table see original document page 96 </column> </row> <table>

abMedias within a line without common envelopes are

significantly different (P <0.05).

Phenotypic data for marbling classifications and SFD measurements were analyzed using the SAS v9.1 GLM (general linear model) procedure (SAS Institute Inc. Gary, NC). The fixed effects of the model included year of birth, gender, age of collection (linear) and genotype for a 7516 bp G / C substitution of the FABP4 gene. Least-square mean pair comparisons were performed using a protected t-test. Genotype significantly affected intramuscular and subcutaneous fat deposition (Table 1), as indicated by marbling classification (P = 0.0321) and SFD (P = 0.0246), respectively. Because the number of animals with the GG genotype was relatively low in the population, significant differences in SFD or marbling classifications were not detected. However, numerically, homozygous animals with the G allele had higher SFD and higher marbling ratings than homozygous animals with the C allele.

Animals with the heterozygous genotype had significantly higher marbling and SFD ratings (P <0.05) than animals with the CC genotype. Although these results are the first known report of an association between FABP4 genotype and either marbling or SFD classification in cattle, other researchers have reported significant polymorphisms in the porcine FABP4 gene that were related to lipid growth. Gerbens et al. (1998) detected a microsatellite marker on the porcine FABP4 gene, which was polymorphic in six pig litters. Genotypes for this microsatellite were significantly associated with intramuscular fat content of the longissimus dorsi muscle of Duroc pigs (Gerbens et al. 1988) and longissimus lumborum muscle biopsies of crossed wheelbarrows (Gerbens et al. 2001). Furthermore, Ye et al. (2002) indicated that the Bsml locus in the porcine FABP4 gene, close to the microsatellite marker described by Gerbens et al. (1998) was significantly associated with intramuscular fat content.

Several reports have shown that chromosome 14 (BTA14) houses significant or suggestive QTL for marbling (intramuscular fat content) and SFD in beef cattle. Casas and colleagues (2003) reported QTL suggested for marbling in a Bos indicus χ Bos taurus family located at 47 cM and QTL suggested for SFD at 16 cM in BTAl4. Taylor and Schnabel (2004) (http://animalgenomics.missouri.edu/) recently developed a DNA deposit from 1600 registered bulls representing 14 generations of the American Angus Association for an Angus Genome project and confirmed the existence of marbling QTL with a similar location as the QTL identified by Casas and colleagues (2003). In purebred Japanese black cattle QTL for marbling were found in the centromeric regions of BTA14 (Imai et al. 2004). The standardization of these marker locations based on the latest version of the bovine binding map (Ihara et al. 2004) demonstrated that these QTLs extend over a range of 59 cM to 70 cM in BTA14. The integration of both the genetic map (Ihara et al. 2004) and the RH map (Itoh et al. 2005) of BTAl 4 predicted that the FAB P 4 gene should be placed somewhere between 63,156 and 63,859 cM in the binding map of the BTAl 4. bovine chromosome. These data indicate that the FABP4 gene falls within a range of QTL for marbling reported in three different populations, as described above.

References:

Casas et al. 2003. Detection of quantitative trait Loci for growth and carcass composition in cattle. J Anim I know. 81: 2976-2983.

Damcott et al. 2004. Metabolism, 53: 303-309. De et al. 2004. Proceedings, Western Section, American Society of Animal Science, 55: 95-98. Gerbens et al. 2001. J Anim I know. 79: 347-354.

Gerbens et al. 1998. Mamm Genome, 9: 1022-1026. Ihara et al. 2004. Genome Res. 14: 1987-1998. Imai et al. 2004. Proceedings of the 29th International Conference on Animal Genetics, Tokyo, Japan, p.118.

Itoh et al. 2005. Genomics, 85: 413-424.

Jiang and Gibson 1999. Mamm Genome, 10: 191-193.

Kaikaus et al. 1990. Experientia, 46: 617-630.

Shen et al. 1999. Proc Natl Acad Sci USA, 96: 5528-5532.

Specht et al. 1996. J Biol Chem. 271: 19943-19949. Tansey et al. 2003. J Biol Chem. 278: 8401-8406.

Thaller et al. 2003. Anim Genet. 34: 354-357.

Ye et al. 2002. 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, 31: 359-362.

Example 2

This Example provides associations between TFAM-I, TFAM-2 and FABP4 markers and carcass characteristics in commercial fattening steers and heifers.

The following markers were evaluated: (1) a substitution of C for A at nucleotide position 1220 in the mitochondrial transcription factor A gene promoter (TFAM-I), (2) a substitution of C for T at nucleotide position 1212 at the TFAM-2 promoter and (3) a G-C substitution at nucleotide position 7516 of the fatty acid binding protein 4 (FABP4) gene. Previous results indicate that markers affect marbling and dorsal fat.

Initially, there were 1589 records from heifers and heifers. The target end point was 12.2 mm dorsal fat. The collection date was the optimal economic end point predicted by animal. Contemporary groups included source and gender. It was assumed that the type of race was confused with the source. The final dataset included the number of records based on phenotypes and genotypes available for each trait.

The characteristics tested are: hot carcass weight (HCW, lb), rib fillet area (REA, in2), rib fillet area by HCW percentage weight (REA / cwt HCW, in2 / 100 Ib carcass weight (HCW), warm carcass weight value (HCW value, $), calculated live weight (Cale Lv Wt, lb), dry matter intake (DMI, lb), days in feed (DOF, d), dietary intake. daily dry matter intake (DMI by DOF, lb / d), average daily gain (ADG, lb / d), seasoning percentage (SD,%), back fat thickness (BFAT, in), yield grade (cYG), quality grade, less than or equal to select versus greater than or equal to choose (HQ, <Se vs,> Ch), intramuscular fat content (MFI%,%), marbling classification ( MBS, 10 to 99), daytime split marbling classification (MBS / DOF), additional carcass value (additional carcass value, $), adjusted net return - all costs removed (net return to just - all costs removed, $) and adjusted net return - initial animal value not removed (adjusted net return, - initial animal value not removed, $).

The analysis models were genotype, and genotypes were adjusted as fixed and additive effects or allele substitution, which showed regression in number <table> table see original document page 102 </column> </row> <table> <table> table see original document page 103 </column> </row> <table> <table> table see original document page 104 </column> </row> <table> table see original document page 105 </column> </row> <table> <table> table see original document page 106 </column> </row> <table> <table> table see original document page 107 </column> </row> <table> <table> table see original document page 108 </column> </row> <table> <table> table see original document page 109 </column> </row> <table> table see original document page 110 </column> </row> <table> Adjusting allele replacement markers: A for TFAMl; C for TFAM2 & FABP4

Marbling ratings range from 10 to 99; 10 = RFQ = Std. 99 = A90 = Initiator

GG Ch (1,2,5,9,20) implies Ch or better - includes Initiator, Ch, CAB, Sterling Silver & Angus Pride; Alternative included Se, No Roll, Dark cutter & Hard bone Example 3

Figure 5 shows a flowchart of data input and output from analysis and correlation of data pertaining to breeding, veterinary history and performance requirements of a group of animals, such as from cattle. The flowchart illustrated in Figure 5 further indicates the interactive flow of data from the computer aided device to a student body learning to use the method of the invention and the correlation of such interactive data to present an output as a pie chart indicating the class progress. The flowchart further indicates modifications of the method of the invention according to information received from students to advance the teaching process or to optimize the method to meet student needs. Figure 6 illustrates the potential relationships between data elements to be fed to the system. One-way arrows indicate, for example, that a stable typically belongs to a single farm, while a farm may own several stables. Similarly, a prescription may include veterinary products.

Figure 7A illustrates the flow of events in the use of the laptop-based system for data entry on rearing and maintaining a herd of cows.

Figure 7B illustrates the flow of events through data entry-related subroutines that pertain to farm management.

Figure 7C illustrates the flow of events through data entry-related subroutines that pertain to company-specific data.

Figure 8 illustrates a flowchart of data input and output from analysis and correlation of data pertaining to the breeding, veterinary history and performance requirements of a group of animals.

The invention is further described by the following numbered paragraphs:

1. A method for subgrouping animals according to genotype, with animals from each subgroup having a similar polymorphism in the fatty acid binding protein 4 ("FABP4") gene, comprising:

(a) determining the genotype of each animal to be subgrouped by determining the presence of single nucleotide polymorphism in the FABP4 gene, and

(b) segregation of individual animals into subgroups, with each animal in a subgroup having a similar polymorphism in the FABP4 gene.

2. A method for subgrouping animals according to genotype, with animals from each subgroup having a similar polymorphism in the FABP4 gene, comprising:

(a) determining the genotype of each animal to be subgrouped by determining the presence of single nucleotide polymorphism (s) of interest in the FABP4 gene, and

(b) the segregation of individual animals into subgroups depending on whether or not the animals have the single nucleotide polymorphism (s) of interest in the FABP4 gene.

3. The method according to paragraphs -1 or 2, wherein the single nucleotide polymorphism (s) of interest is selected from the group consisting of one substitution. of G by C at nucleotide position 7516 of the FABP4 gene and at a G-C substitution at position 7713 of the FABP4 gene.

4. The method for subgrouping animals according to genotype, with animals from each subgroup having a similar genotype in the FABP4 gene comprising:

(a) determining the genotype of each animal to be subgrouped by determining the presence of a G-C substitution at nucleotide position 7516 of the FABP4 gene and a G-C substitution at position 7713 of the FABP4 gene,

and

(b) the segregation of individual animals into subgroups depending on whether or not animals have G to C substitution at nucleotide position 7516 of the FABP4 gene and a substitution of G to C at position 7713 of the FABP4 gene.

5. A method for identifying an animal having a desirable phenotype as compared to the general animal population of that species, comprising determining the presence of a single nucleotide polymorphism in the animal's FABP4 gene, the polymorphism being selected from the In the group consisting of G-C substitution at nucleotide position 7516 of the FABP4 gene and a G-C substitution at position 7713 of the FABP4 gene, single nucleotide polymorphism is indicative of a desirable phenotype.

6. The method according to paragraph 5, wherein the desirable phenotype is feed intake, growth rate, body weight, merit and carcass composition, milk yield or a combination thereof.

7. The method according to paragraphs 5 or 6, wherein the desirable phenotype is additional carcass value (additional carcass value, $), average daily gain (ADG, lb / d), dorsal fat thickness (BFAT, in), calculated live weight (Cale Lv Wt, lb), calculated yield (cYG), days in feed (DOF, d), seasoning percentage (SD,%), dry matter intake (DMI, lb), dry matter intake per day in feed (DMI by DOF, lb / d), hot carcass weight (HCW, lb), hot carcass weight value (HCV value, $), intramuscular fat content (MFI%,% ), marbling classification (MBS, 10 to 99), marbling classification divided by days in feed (MBS / DOF), quality grade, less than or equal to select versus greater than or equal to choose (HQ, < Sc vs,> Ch), rib fillet area (REA, in2), rib fillet area by HCW percentage weight (REA / cwt HCW, in2 / 100 lb hot carcass weight (HCW), subeutaneous fat depth ( SFD ) or any combination thereof.

8. The method according to any of paragraphs 1 to 7, wherein the animal is a bovine animal.

The method according to any of paragraphs 1 to 8, wherein the FABP4 gene is a bovine FABP gene.

10. An interactive computer aided method for tracking livestock rearing comprising the use of a computer system comprising a programmed computer comprising a processor, a data storage system, an input device, a and an interactive device, the steps of: (a) entering the programmed computer via the input device comprising a history of rearing a bovine or herd of cattle, (b) entering the programmed computer via the input device, comprising a veterinary history of a bovine or herd of cattle, (c) the correlation of veterinary data with the history of rearing of the bovine or herd using the processor and data storage system, and (d) the exit to the exit device of the breeding history and veterinary history of the bovine or herd.

11. The method according to paragraph 10, wherein the computer system is an interactive system whereby modifications to the output of the computer aided method may be correlated according to input from the interactive device.

12. The method according to paragraph 10 or 11, further comprising the steps in entering the programmed computer of diagnostic data related to cow or cow herd health; and the correlation of diagnostic data with the breeding and veterinary history of the cow or herd of cows.

13. The method according to any of paragraphs -10 to 12, wherein the veterinary data comprises a vaccination record for a cow or herd of cows.

14. The method according to any of paragraphs -10 to 13, wherein health data is selected from the group consisting of livestock condition data, herd history and food safety data.

15. The method according to any of paragraphs -10 to 14, further comprising at least one additional step selected from the group consisting of input to the programmed computer of data related to the quality control of the bovine or cattle herd and the correlation of quality control data to cow and herd herding and veterinary histories, programmed computer input of cow or herd herd performance parameters; and the correlation of the required performance parameters of the bovine or herd to a customer-specific performance requirement, the correlation of vaccination data to the performance parameters of the bovine or herd, the correlation of the herd to the performance parameters of the cattle. bovine or cattle herd, the correlation of food safety data with the performance parameters of the bovine or cattle herd, the correlation of livestock condition data with the performance parameters of the bovine or cattle herd, programmed computer data entry nutritional data of cattle or herd of cattle; and the correlation of nutritional data with performance parameters of cattle or cattle herd, and the warning of undesirable changes in performance parameters of cattle or cattle herd.

16. The method according to any of paragraphs -10 to 15, further comprising the steps of entering the computer programmed by means of the input device comprising a genotype of a bovine; the correlation of a physical trait predicted by the genotype using the processor and data storage system; and the output to the output device of the genotype-correlated physical trait for a bovine or bovine population, and feeding the animal (s) to a diet based on physical trait, whereby the cattle production.

17. The computer-aided method according to any of paragraphs 10 to 16 for optimizing the efficiency of farmed fattening farms including the output of the bovine breeding and veterinary history to the exit device herd of cattle and feed the animal (s) with a diet based on their breeding and veterinary histories, thereby optimizing the efficiency of fattening farms for the cattle or herd.

18. A data transmission method comprising transmitting information from methods such according to any one of paragraphs 10 to 16, selected from the group consisting of telecommunication, telephone, video conferencing, mass communication, a presentation , a computer presentation, a POWERPOINT ™ presentation, the internet, email and document communication.

19. An interactive computer system according to any one of paragraphs 10 to 16 for tracking cow breeding and welfare histories comprising breeding and veterinary data corresponding to a bovine or herd of bovine animals, and The computer system is configured to allow your operator to exchange data with the device or a remote database.

20. The interactive computer system according to paragraph 19, wherein the input and output devices are a personal digital assistant or a pocket computer.

21. A business method for tracking breeding and welfare history of farmed animals, comprising farmed and veterinary data corresponding to one or more farmed animals, comprising providing a user with the system computer in accordance with paragraph 19.

22. A business method for tracking breeding and welfare history of farmed animals, comprising farmed and veterinary data corresponding to one or more farmed animals, comprising providing a user with the system computer in accordance with paragraph 20.

23. The method of doing business in accordance with paragraph 21, further comprising providing the animal owner or customer with sample collection equipment, such as cotton rods and useful sample collection labels, from from which genetic data can be obtained, and the tags being optionally packaged in a container that is encoded with identification indicia.

24. The method of doing business according to any of paragraphs 10 to 16, wherein the computer system further comprises a plurality of interactive devices and the method further comprising the steps of receiving data from the devices. data compilation, data output to indicate a student or class response to a question regarding the operation of the computer aided method, and optionally the modification of the operation of the computer aided method according to indication of the answer.

25. The method according to any of paragraphs -10 to 24, wherein the data comprises the presence or absence of one or more single nucleotide polymorphism (s) of interest in the FABP gene.

26. The method according to paragraph 25, wherein the single nucleotide polymorphism (s) is selected from the group consisting of substitution of G for C at nucleotide position 7516 of the FABP4 gene and one substitution of G by C at position 7713 of the FABP4 gene.

Therefore, having described in detail the preferred embodiments of the present invention, it should be understood that the invention defined by the above paragraphs should not be limited to the particular details described in the above descriptive report, since many obvious variations thereof are possible without deviating. object or scope of the present invention.

Claims (19)

1. Method for identification of an animal having a desirable calculated live weight (Cale Lv Wt, lb), calculated yield (cYG), feeding days (DOF, d), dry matter intake (DMI, lb), intake dry matter intake per day (DMI by DOF, lb / d), fresh carcass weight (HCW, lb), fresh carcass weight value (HCV value, $), intramuscular fat content (MFI%,%) , marbling rating (MBS, 10 to 99), marbling rating divided by feeding days (MBS / DOF), quality grade, less than or equal to select versus greater than or equal to choose (HQ, <Se vs, > Ch), rib fillet area (REA, in2), rib fillet area per cent HCW weight (REA / cwt HCW, in2 / 100 Ib fresh carcass weight (HCW), or a combination thereof, when compared to the general population of animals of that species characterized by the determination of the presence of a single nucleotide polymorphism in a fatty acid binding protein 4 ("FABP4") gene, the presence of a single nucleotide polymorphism in the animal's FABP4 gene, the only nucleotide polymorphism being indicative of desirable calculated body weight (Cale Lv Wt , lb), calculated degree of yield (cYG), days in feed (DOF, d), dry matter intake (DMI, lb), daily dry matter intake in feed (DMI by DOF, lb / d), weight fresh carcass weight (HCW, lb), fresh carcass weight value (HCV value, $), intramuscular fat content (MFI%,%), marbling rating (MBS, 10 to 99), marbling rating divided by days in feed (MBS / DOF), quality grade, less than or equal to select versus greater than or equal to choose (HQ, <Se vs,> Ch), rib fillet area (REA, in2), fillet area per cent HCW weight (REA / cwt HCW, in2 / 100 Ib fresh carcass weight (HCW), or a combination thereof. Method according to claim 1, characterized in that it further comprises subgrouping animals according to genotype, with animals in each subgroup having a similar polymorphism in the FABP4 gene, the method comprising: (a) a determining the genotype of each animal to be subgrouped by determining the presence of a single nucleotide polymorphism in the FABP4 gene, and (b) segregating individual animals into subgroups depending on whether or not the animals have the only nucleotide polymorphism. of interest in the FABP4 gene. Method according to claim 1, characterized in that the single nucleotide polymorphism (s) of interest is selected from the group consisting of a G-substitution. by C at the position of nucleotide 7516 of the FABP4 gene and a substitution of G for C at position 7713 of the FABP4 gene. Method according to claim 1, characterized in that the animal is a bovine animal. Method according to claim 1, characterized in that the FABP4 gene is a bovine FABP4 gene. 6. Interactive computer aided method for tracking cattle breeding characterized in that it comprises the use of a computer system comprising a programmed computer comprising a processor, a data storage system, an input device, a device output and an interactive device, the steps of: (a) entering the programmed computer, via the input device, comprising a history of rearing a bovine or cattle herd and a genotype of a bovine; the correlation of a physical characteristic predicted by the phenotype using the processor and data storage system; (b) input to the programmed computer by means of the input device comprising a veterinary history of a bovine or herd of bovine animals; (c) the correlation of veterinary data with the breeding history of the bovine or herd using the processor and data storage system, and (d) the output device's breeding history bovine or herd herd and the genotype-correlated physical trait for a bovine or bovine population, the physical trait being desirable calculated live weight (Cale Lv Wt, lb), calculated yield grade (cYG), days in feed (DOF, d), dry matter intake (DMI, lb), daily dry matter intake (DMI by DOF, lb / d), fresh carcass weight (HCW, lb), ditch r fresh carcass weight (HCV value, $), intramuscular fat content (IMF%,%), marbling classification (MBS, 10 to 99), marbling classification divided by days in feed (MBS / DOF), degree less than or equal to select versus greater than or equal to choose (HQ, <Se vs,> Ch), rib fillet area (REA, in2), rib fillet area HCW weight percent ( REA / cwt HCW, in2 / 100 Ib fresh carcass weight (HCW), or a combination of these when compared to the general cattle population, and the phenotype is a single nucleotide polymorphism in a FABP4 gene. Method according to claim 6, characterized in that the computer system is an interactive system, whereby modifications to the output of the computer-aided method can be correlated according to input from the device. interactive. Method according to claim 6, characterized in that it further comprises the steps in entering the programmed computer of diagnostic data related to cow health or herd of cows and the correlation of diagnostic data to the breeding and veterinary history of the cow. or herd of cows. Method according to claim 6, characterized in that the veterinary data comprises a vaccination record for a cow or herd of cows. Method according to claim 6, characterized in that health data are selected from the group consisting of livestock condition data, herd history and food safety data. Method according to claim 6, characterized in that it further comprises at least one additional step selected from the group consisting of input to the programmed computer of data related to the quality control of the bovine or cattle herd and the correlation of quality control data to the breeding and veterinary history of the cow or herd of cows, the programmed entry of cow or cow herd performance parameters and the correlation of the required performance parameters of the cattle or herd to a requirement specific performance of a client, the correlation of vaccination data to performance parameters of cattle or herd, the correlation of herd to performance parameters of cattle or herd, the correlation of food safety data to performance parameters bovine herd or herd, the correlation of livestock condition data to the performance parameters of the bovine or cattle herd, input to the programmed computer of data related to the nutritional data of the bovine or cattle herd; and the correlation of nutritional data with performance parameters of cattle or cattle herd, and the warning of undesirable changes in performance parameters of cattle or cattle herd. Method according to claim 6, characterized in that the single nucleotide polymorphism (s) of interest is selected from the group consisting of a G-substitution. by C at the position of nucleotide 7516 of the FABP4 gene and a substitution of G for C at position 7713 of the FABP4 gene. Data transmission method comprising the transmission of information from the methods according to claim 6 selected from the group consisting of telecommunication, telephone, video conferencing, mass communication, a presentation, a computer presentation, a POWERPOINT ™ presentation, the internet, email and document communication. Interactive computer system according to claim 6, characterized in that it serves to track poultry rearing and welfare histories, comprising rearing and veterinary data corresponding to a bovine or herd of cattle; and the computer system is configured to allow its operator to exchange data with the device or a remote database. The interactive computer system according to claim 14, characterized in that the input and output devices are a personal digital assistant or a pocket computer. 16. Business method for tracking breeding and welfare history of domestic animals, comprising understanding livestock and veterinary data corresponding to one or more domestic animals, including providing a user with the system described in claim -14. 17. Business method for tracking pet breeding and welfare history characterized by comprising livestock and veterinary data corresponding to one or more domestic animals, comprising providing a system to a user described in claim -14. Business method according to claim 16, characterized in that it further comprises providing the owner of the animal or the customer with sample collection equipment, such as cotton rods and labels useful for sample collection. , from which genetic data can be obtained, and the tags being optionally packaged in a container that is encoded with identification indicia. Business method according to claim 16, characterized in that the computer system further comprises a plurality of interactive devices and the method further comprising the steps of receiving data from the interactive devices, data compilation, data output to indicate a student or class response to a question regarding the operation of the computer aided method, and optionally the modification of the operation of the computer aided method as indicated by the answer.