Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers

Definitions

• Fatty Acid Binding Protein 4 (“FABP4") Gene and their Associations with Measures of Marbling and Subcutaneous Fat Depth in Beef Cattle INCORPORATION BY REFERENCE
• the present invention relates to the identification of single nucleotide polymorphisms (SNPs) within the bovine genes encoding fatty acid binding protein 4 ("FABP4") and their associations with economically relevant traits in beef production.
• SNPs single nucleotide polymorphisms
• the invention further relates to methods and systems, including network-based processes, to manage the SNP data and other data relating to specific animals and herds of animals, veterinarian care, diagnostic and quality control data and management of livestock which, based on genotyping, have predictable meat quality traits, husbandry conditions, animal welfare, food safety information, audit of existing processes and data from field locations.
• SNPs single nucleotide polymorphisms
• FABP4 fatty acid binding protein 4
• Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands (Kaikaus et al. 1990. Experientia, 46: 617-630). Their major functions include fatty acid uptake, transport, and metabolism. So far, 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 a major role in the regulation of lipid and glucose homeostasis through its interaction with perioxisome proliferator-activated receptors (PPARs), located in the cell nucleus.
• PPARs perioxisome proliferator-activated receptors
• the FABP4/fatty acid complex activates the PPAR- ⁇ isoform, which in turn, regulates transcription of F ABP 4 (Damcott et al. 2004. Metabolism, 53: 303-309).
• FABP 4 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 U S A, 96: 5528-5532), which is a primary enzyme involved in lipid catabolism (Tansey et al. 2003. J Biol Chem. 278: 8401-8406).
• FABP4 and FABP 5 were proposed as potential candidate genes for obesity as they are located within a quantitative trait loci (QTL) region 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 the regulation of food intake, energy expenditure, and whole- body energy balance (Jiang and Gibson 1999. Mamm Genome, 10: 191-193). All these factors indicate that FABP 4 may play an important role in lipid metabolism and homeostasis in adipocytes.
• the present invention relates to the identification of single nucleotide polymorphisms (SNPs) within the bovine genes encoding fatty acid binding protein 4 ("FABP4") and their associations with economically relevant traits in beef production.
• SNPs single nucleotide polymorphisms
• the invention encompasses a method for sub-grouping animals according to genotype wherein the animals of each sub-group have a similar polymorphism in a FABP 4 gene which may comprise determining the genotype of each animal to be sub-grouped by determining the presence of a single nucleotide polymorphism in the F ABP 4 gene, and segregating individual animals into sub-groups wherein each animal in a sub-group has a similar polymorphism in the FABP4 gene.
• the invention also encompasses a method for sub-grouping animals according to genotype wherein the animals of each sub-group have a similar genotype in the FABP 4 gene which may comprise determining the genotype of each animal to be sub-grouped by determining the presence of a single nucleotide polymorphism(s) of interest in the FABP 4 gene, and segregating individual animals into sub-groups depending on whether the animals have, or do not have, the single nucleotide polymorphism(s) of interest in the F ABP 4 gene.
• the single nucleotide polymorphism(s) of interest may be selected from the group consisting of a G to C substitution at the 7516 nucleotide position of the F ABP 4 gene and a G to C substitution at position 7713 of the F ABP 4 gene.
• the invention further relates to a method for sub-grouping animals according to genotype wherein the animals of each sub-group have a similar genotype in the FABP 4 gene which may comprise determining the genotype of each animal to be subgrouped by determining the presence of any one of the above SNPs, and segregating individual animals into sub-groups depending on whether the animals have, or do not have, any one of the above SNPs in the FABP4 gene.
• the invention also relates to method for identifying an animal having a desirable phenotype as compared to the general population of animals of that species, which may comprise determining the presence of a single nucleotide polymorphism in the FABP gene of the animal, wherein the presence of the SNP is indicative of a desirable phenotype.
• the animal may be a bovine.
• the FABP4 gene may be a bovine FABP gene.
• the invention also encompasses computer-assisted methods and systems for improving the production efficiency for livestock having marketable tender meat using multiple data, and in particular the genotype of the animals as it relates to F ABF 4 SNPs.
• Methods of the invention encompass obtaining a genetic sample from each animal in a herd of livestock, determining the genotype of each animal with respect to specific quality traits as defined by a panel of at least two single polynucleotide polymorphisms (SNPs), grouping animals with like genotypes, and optionally, further sub-grouping animals based on like phenotypes.
• SNPs single polynucleotide polymorphisms
• Methods of the invention may also encompass obtaining and maintaining data relating to the animals or to herds, their husbandry conditions, health and veterinary care and condition, genetic history or parentage, and providing this data to others through systems that are web-based, contained in a database, or attached to the animal itself such as by an implanted microchip.
• An advantageous aspect of the present invention therefore, is directed to a computer system and computer-assisted methods for tracking quality traits for livestock possessing specific genetic predispositions.
• the present invention advantageously encompasses computer-assisted methods and systems for acquiring genetic data, particularly genetic data as defined by the absence or presence of a SNP within the FABP 4 gene related to meat quality traits of the breed of animal and associating those data with other data about the animal or its herd, and maintaining those data in ways that are accessible.
• Another aspect of the invention encompasses a computer- assisted method for predicting which livestock animals possess a biological difference in meat quality, and which may include the steps of using a computer system, e.g., 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 through the input device data that includes a genotype of an animal as it relates to any one of the FABP SNPs described herein, (b) correlating meat quality predicted by the FABP 4 genotype using the processor and the data storage system and (c) outputting to the output device the meat quality correlated to the FABP4 genotype, thereby predicting which livestock animals possess a particular meat quality.
• a computer system e.g., 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 through the input device data that includes a genotype of an animal as it relates to any one of the FA
• Yet another aspect of the invention relates to a method of doing business for managing livestock comprising providing to a user computer system for managing livestock comprising physical characteristics and genotypes corresponding to one or more animals or a computer readable media for managing livestock comprising physical characteristics and genotypes corresponding to one or more animals or physical characteristics and genotypes corresponding to one or more animals, wherein a physical characteristic intake, growth or carcass merit in beef cattle and the genotype is a FABP 4 genotype.
• FIG. 1 depicts the sequence alignment between cDNA and genomic DNA to determine the genomic organization of the bovine F ABP 4 gene.
• FIG. 2 depicts two G/C substitutions detected at positions 7516 and 7713 in the bovine FABP4 gene.
• FIG. 3 depicts PCR-RFLP genotyping of the C/G substitution at position 7516 of the bovine FABP 4 gene.
• Lane 1 100 bp ladder.
• 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, CC animals do not have an MspAlI site and the 452 bp amplicon is not digested; Lanes 6 and 7, GG animals have one MspAlI site and reveal after complete digestion two bands: 352 bp and 100 bp.
• FIG. 4 depicts GenBank Accession No. AAFCOl 136716, Bos taurus Contl36721, whole genome shotgun sequence.
• FIG. 5 illustrates a flowchart of the input of data and the output of results from the analysis and correlation of the data pertaining to the breeding, veterinarian histories and performance requirements of a group of animals such as from a herd of cows and the interactive flow of data from the computer-assisted device to a body of students learning the use of the method of the invention.
• FIG. 6 illustrates potential relationships between the data elements to be entered into the system. Unidirectional arrows indicate, for example, that a barn is typically owned by only one farm, whereas a farm may own several barns. Similarly, a prescription may include veterinarian products.
• FIG. 7 A illustrates the flow of events in the use of the portable computer-based system for data entry on the breeding and rearing of a herd of cows.
• FIG. 7B illustrates the flow of events through the sub-routines related to data entry concerning farm management.
• FIG. 7C illustrates the flow of events through the sub-routines related to data entry concerning data specific to a company.
• FIG. 8 illustrates a flow chart of the input of data and the output of results from the analysis and the correlation of the data pertaining to the breeding, veterinarian histories, 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 explained fully in the literature. See, e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press; DNA Cloning, VoIs. I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J.
• the term “cow” or “cattle” is used generally to refer to an animal of bovine origin of any age. Interchangeable terms include “bovine”, “calf, “steer”, “bull”, “heifer” and the like. It also includes an individual animal in all stages of development, including embryonic and fetal stages. The animals as referred to herein may also include individuals or groups of individuals that are raised for other than food production such as, but not limited to, transgenic animals for the production of biopharmaceuticals including antibodies and other proteins or protein products.
• complementarity or “complementary” is meant, for the purposes of the specification or claims, a sufficient number in the oligonucleotide of complementary base pairs in its sequence to interact specifically (hybridize) with a target nucleic acid sequence of the gene polymorphism to be amplified or detected. As known to those skilled in the art, a very high degree of complementarity is needed for specificity and sensitivity involving hybridization, although it need not be 100%. Thus, for example, an oligonucleotide that is identical in nucleotide sequence to an oligonucleotide disclosed herein, except for one base change or substitution, may function equivalently to the disclosed oligonucleotides.
• a “complementary DNA” or “cDNA” gene includes recombinant genes synthesized by reverse transcription of messenger RNA ("mRNA").
• a "cyclic polymerase-mediated reaction” refers to a biochemical reaction in which a template molecule or a population of template molecules is periodically and repeatedly copied to create a complementary template molecule or complementary template molecules, thereby increasing the number of the template molecules over time.
• detecttable moiety is meant, for the purposes of the specification or claims, a label molecule (isotopic or non-isotopic) which is incorporated indirectly or directly into an oligonucleotide, wherein the label molecule facilitates the detection of the oligonucleotide in which it is incorporated, for example when the oligonucleotide is hybridized to amplified gene polymorphic sequences.
• “detectable moiety” is used synonymously with “label molecule”.
• Synthesis of oligonucleotides can be accomplished by any one of several methods known to those skilled in the art.
• Label molecules known to those skilled in the art as being useful for detection, include chemiluminescent, fluorescent or luminescent molecules.
• Various 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 upon the fluorescent molecule used. Such protocols are known in the art for the respective fluorescent molecule.
• DNA amplification refers to any process that increases the number of copies of a specific DNA sequence by enzymatically amplifying the nucleic acid sequence.
• PCR polymerase chain reaction
• PCR involves the use of a thermostable DNA polymerase, known sequences as primers, and heating cycles, which separate the replicating deoxyribonucleic acid (DNA), strands and exponentially amplify a gene of interest.
• a thermostable DNA polymerase known sequences as primers
• Any type of PCR such as quantitative PCR, RT-PCR, hot start PCR, LAPCR, multiplex PCR, touchdown PCR, etc.
• real-time PCR is used.
• the PCR amplification process involves a cyclic enzymatic chain reaction for preparing exponential quantities 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.
• extension product of the chain reaction will be a discrete nucleic acid duplex with a termini corresponding to the ends of the specific primers employed.
• enzymatically amplify or “amplify” is meant, for the purposes of the specification or claims, DNA amplification, i.e., a process by which nucleic acid sequences are amplified in number.
• DNA amplification i.e., a process by which nucleic acid sequences are amplified in number.
• PCR polymerase chain reaction
• LCR ligase chain reaction
• RNA ribonucleic acid
• SDA strand displacement amplification
• Q ⁇ RA Q ⁇ replicase amplification
• SSR self-sustained replication
• NASBA nucleic acid sequence-based amplification
• a “fragment” of a molecule such as a protein or nucleic acid is meant to refer to any portion of the amino acid or nucleotide genetic sequence.
• the term “genome” refers to all the genetic material in the chromosomes of a particular organism. Its size is generally given as its total number of base pairs.
• the term “gene” refers to an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (e.g., a protein or RNA molecule).
• an animal's genetic characteristics, as defined by the nucleotide sequence of its genome are known as its "genotype," while the animal's physical traits are described as its "phenotype.”
• heterozygous or “heterozygous polymorphism” is meant that the 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 at the same place in their sequences.
• homozygous or “homozygous polymorphism” is meant that the two alleles of a diploid cell or organism at a given locus are identical, that is, that they have the same nucleotide for nucleotide exchange at the same place in their sequences.
• hybridization or “hybridizing,” as used herein, is meant the formation of A-T and C-G base pairs between the nucleotide sequence of a fragment of a segment of a polynucleotide and a complementary nucleotide sequence of an oligonucleotide.
• complementary is meant that at the locus of each A, C, G or T (or U in a ribonucleotide) in the fragment sequence, the oligonucleotide sequenced has a T, G, C or A, respectively.
• the hybridized fragment/ oligonucleotide is called a "duplex.”
• a “hybridization complex”, such as in a sandwich assay, means a complex of nucleic acid molecules including at least the target nucleic acid and a sensor probe. It may also include an anchor probe.
• locus refers to the site of a gene on a chromosome. Pairs of genes, known as “alleles” control the hereditary trait produced by a gene locus. Each animal's particular combination of alleles is referred to as its "genotype”. Where both alleles are identical the individual is said to be homozygous for the trait controlled by that gene pair; where the alleles are different, the individual is said to be heterozygous for the trait.
• melting temperature is meant the temperature at which hybridized duplexes dehybridize and return to their single-stranded state. Likewise, hybridization will not occur in the first place between two oligonucleotides, or, herein, an oligonucleotide and a fragment, at temperatures above the melting temperature of the resulting duplex. It is presently advantageous that the difference in melting point temperatures of oligonucleotide-fragment duplexes of this invention be from about I 0 C to about 10°C so as to be readily detectable.
• nucleic acid molecule is intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), analogs of the DNA or RNA generated using nucleotide analogs, and derivatives, fragments and homologs thereof.
• the nucleic acid molecule can 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) in its either single stranded form, or a double-stranded helix.
• This term refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear DNA molecules (e.g., restriction fragments), viruses, plasmids, and chromosomes.
• sequences may be described herein according to the normal convention of giving only the sequence in the 5' to 3' direction along the nontranscribed strand of DNA (i.e., the strand having a sequence homologous to the mRNA).
• An "isolated" nucleic acid molecule is one that is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid.
• a “nucleoside” refers to a base linked 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 linked to a single phosphate group.
• oligonucleotide refers to a series of linked nucleotide residues, which oligonucleotide has a sufficient number of nucleotide bases to be used in a PCR reaction.
• a short oligonucleotide sequence may be based on, or designed from, a genomic or cDNA sequence and is used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue.
• 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 detection or identification of a target nucleic acid, including probes and primers.
• a “polymerase” is an enzyme that catalyzes the sequential addition of monomeric units to a polymeric chain, or links two or more monomeric units to initiate a polymeric chain.
• the "polymerase” will work by adding monomeric units whose identity is determined by and which is complementary to a template molecule of a specific sequence.
• 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, thereby synthesizing a nucleic acid that is complementary to the template molecule.
• thermostable polymerases may be used either to extend a primer once or repetitively 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 approaching 100 0 C.
• 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 variations and derivatives thereof.
• a “polynucleotide” refers to a linear chain of nucleotides connected by a phosphodiester linkage between the 3'-hydroxyl group of one nucleoside and the 5'-hydroxyl group of a second nucleoside which in turn is linked through its 3'-hydroxyl group to the 5'- hydroxyl group of a third nucleoside and so on to form a polymer comprised of 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 with modified nucleotides.
• a “primer” is an oligonucleotide, the sequence of at least of portion of which is complementary to a segment of a template DNA which is to be amplified or replicated.
• primers are used in performing the polymerase chain reaction (PCR).
• a primer hybridizes with (or “anneals” to) the template DNA and is used by the polymerase enzyme as the starting point for the replication/amplification process.
• the primers herein are selected to be “substantially” complementary to different strands of a particular target DNA sequence. This means that the primers must be sufficiently complementary to hybridize with their respective strands. Therefore, the primer sequence need not reflect the exact sequence of the template.
• 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 strand.
• non-complementary bases or longer sequences can be interspersed into the primer, provided that the primer sequence has sufficient complementarity with the sequence of the strand to hybridize therewith and thereby form the template for the synthesis of the extension product.
• Probes refer to oligonucleotides nucleic acid sequences of variable length, 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.
• polynucleotides a gene or gene fragment, exons, introns, mRNA, tRNA, rKNf A, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of 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 fluororibose and thiolate, and nucleotide branches.
• sequence of nucleotides may be further modified after polymerization, such as by conjugation, with a labeling component.
• modifications included in this definition are caps, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for attaching the polynucleotide to proteins, metal ions, labeling components, other polynucleotides or solid support.
• an “isolated" polynucleotide or polypeptide is one that is substantially pure of 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%, at 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%, most advantageously at least 98%, at least 99%, at least 99.5%, at least 99.9% free of these materials.
• nucleic acid molecule is a nucleic acid molecule separate and discrete from the whole organism with which the molecule is found in nature; or a nucleic acid molecule devoid, in whole or 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 therewith.
• polynucleotide encoding a protein refers to a DNA fragment or isolated 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.
• RNA sequences for use in the invention e.g., for use in RNA vectors, can be derived from DNA sequences, by thymidine (T) in the DNA 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 which 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 start codon at the 5' (amino) terminus and a translation stop codon at the 3' (carboxy) terminus.
• a coding sequence can 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 or two polypeptide moieties.
• Two DNA, or two polypeptide sequences are "substantially homologous" to each other when the sequences exhibit 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 the molecules.
• substantially homologous also refers to sequences showing complete identity (100% sequence identity) to the specified DNA or polypeptide sequence.
• Homology can be determined by hybridization of polynucleotides under conditions that form stable duplexes between homologous regions, followed by digestion with single- stranded-specific nuclease(s), and size determination of the digested fragments.
• DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al. supra; 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 a variant thereof or specifically priming a polymerase chain reaction: (i) under typical hybridization and wash conditions, as described, for example, in Sambrook et al.
• Stringent hybridization conditions typically permit the hybridization of nucleic acid molecules having at least 70% nucleic acid sequence identity with the nucleic acid molecule being used as a probe in the hybridization reaction.
• the first nucleic acid may be a test sample or probe
• the second nucleic acid may be the sense or antisense strand of a nucleic acid or a fragment thereof.
• Hybridization of the first and second nucleic acids may be conducted under stringent conditions, e.g., high temperature and/or low salt content that tend to disfavor hybridization of dissimilar nucleotide sequences.
• hybridization of the first and second nucleic acid may be conducted under reduced stringency conditions, e.g.
• Low stringency hybridization conditions may be followed by high stringency conditions or intermediate medium stringency conditions to increase the selectivity of the binding of the first and second nucleic acids.
• the hybridization conditions may further include reagents such as, but not limited to, dimethyl sulfoxide (DMSO) or formamide to disfavor still further the hybridization of dissimilar nucleotide sequences.
• DMSO dimethyl sulfoxide
• a suitable hybridization protocol may, for example, involve hybridization in 6 x SSC (wherein 1 x SSC comprises 0.015 M sodium citrate and 0.15 M sodium chloride), at 65° Celsius in an aqueous solution, followed by washing with 1 x SSC at 65° C.
• stringent conditions will be those in which the salt concentration is less than about 1.5 M sodium ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) from about pH 7.0 to about pH 8.3 and the temperature is at least about 30° Celsius for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C for long probes (e.g., greater than 50 nucleotides).
• Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
• Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° Celsius, and a wash in 1-2 x SSC at 50 to 55° Celsius.
• Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° Celsius, and a wash in 0.5-1 x SSC at 55 to 60° Celsius.
• Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° Celsius, and a wash in 0.1 x SSC at 60 to 65° Celsius.
• Methods and materials of the invention may be used more generally to evaluate a DNA sample from an animal, genetically type an individual animal, and detect genetic differences in animals.
• a sample of genomic DNA from an animal may be evaluated by reference to one or more controls to determine if a SNP, or group of SNPs, in a gene is present. Any method for determining genotype can be used for determining the genotype in the present invention.
• Such methods include, but are not limited to, amplimer sequencing, DNA sequencing, fluorescence spectroscopy, fluorescence resonance energy transfer (or "FRET")-based hybridization analysis, high throughput screening, mass spectroscopy, microsatellite 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 to one of skill in the art.
• FRET fluorescence resonance energy transfer
• restriction fragment refers to a fragment of a polynucleotide generated by a restriction endonuclease (an enzyme that cleaves phosphodiester bonds within a polynucleotide chain) that cleaves DNA in response to a recognition site on the DNA.
• the recognition site (restriction site) consists of a specific sequence of nucleotides typically about 4-8 nucleotides long.
• a "single nucleotide polymorphism” or "SNP” refers to a variation in the nucleotide sequence of a polynucleotide that differs from another polynucleotide by a single nucleotide difference. For example, without limitation, exchanging one A for one C, G or T in the entire sequence of polynucleotide constitutes a SNP. It is possible to have more than one SNP in a particular polynucleotide. For example, at one position in a polynucleotide, a C may be exchanged for a T, at another position a G may be exchanged for an A and so on. When referring to SNPs, the polynucleotide is most often DNA.
• 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 it should next incorporate into a growing strand to polymerize the complement of the naturally-occurring strand.
• a DNA strand may be single-stranded or it may be part of a double-stranded DNA template.
• the template strand itself may become modified by incorporation of modified nucleotides, yet still serve as a template for a polymerase to synthesize additional polynucleotides.
• a "thermocyclic reaction” is a multi-step reaction wherein at least two steps are accomplished by changing the temperature of the reaction.
• a “variance” is a difference in the nucleotide sequence among related polynucleotides. The difference may be the deletion of one or more nucleotides from the sequence of one 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 herein.
• the term “variance” in the singular is to be construed to include multiple variances; i.e., two or more nucleotide additions, deletions and/or substitutions in the same polynucleotide.
• a “point mutation” refers to a single substitution of one nucleotide for another.
• the terms “traits”, “quality traits” or “physical characteristics” or “phenotypes” refer to advantageous properties of the animal resulting from genetics. Quality traits include, but are not limited to, the animal's genetic ability to efficiently metabolize energy, produce meat or milk, put on intramuscular fat. Physical characteristics include, but are not limited to, marbled, tender or lean meats. The terms may be used interchangeably.
• a “computer system” refers to the hardware means, software means and data storage means used to compile the data of the present invention.
• the minimum hardware means 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 visualize structure data.
• 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 based, Linux, Windows NT, XP or IBM OS/2 operating systems.
• Computer readable media refers to any media which can be read and accessed directly by a computer, and includes, but is not limited to: magnetic storage media such as floppy discs, hard storage medium and magnetic tape; optical storage media such as optical discs or CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories, such as magnetic/optical media.
• magnetic storage media such as floppy discs, hard storage medium and magnetic tape
• optical storage media such as optical discs or CD-ROM
• electrical storage media such as RAM and ROM
• hybrids of these categories such as magnetic/optical media.
• data analysis module is defined herein to include any person or machine, individually or working together, which analyzes the sample and determines the genetic information contained therein.
• the term may include a person or machine within a laboratory setting.
• the term "data collection module” refers to any person, object or system obtaining a tissue sample from an animal or embryo.
• the term may define, individually or collectively, the person or machine in physical contact with the animal as the sample is taken, the containers holding the tissue samples, the packaging used for transporting the samples, and the like.
• the data collector is a person. More advantageously, the data collector is a livestock farmer, a breeder or a veterinarian
• 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 to be 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.
• breeding history refers to a record of the life of an animal or group of animals including, but not limited to, the location, breed, period of housing, as well as a genetic history of the animals, including parentage and descent therefrom, genotype, phenotype, transgenic history if relevant and the like.
• husbandry conditions refers to parameters relating to the maintenance of animals including, but not limited to, shed or housing temperature, weekly mortality of a herd, water consumption, feed consumption, ventilation rate and quality, litter condition and the like.
• veterinary history refers to vaccination data of an animal or group of animals, including, but not limited to, vaccine type(s), vaccine batch serial number(s), administered dose, target antigen, method of administering of the vaccine to the recipient animal(s), number of vaccinated animals, age of the animals and the vaccinator. Data relating to a serological or immunological response induced by the vaccine may also be included.
• Veterinary history as used herein is also intended to include the medication histories of the target animal(s) including, but not limited to drug and/or antibiotics administered to the animals including type of administered medication, quantity and dose rates, by whom and when administered, by what route, e.g., oral, subcutaneously and the like, and the response to the medication including desired and undesirable effects thereof.
• diagnostic data refers to data relating to the health of the animal(s) other than data detailing the vaccination or medication history of the animal(s).
• the diagnostic data may be a record of the infections experienced by the animal(s) and the response thereof to medications provided to treat such medications.
• Serological data including antibody or protein composition of the serum or other biofluids may also be diagnostic data useful to input in the methods of the invention.
• Surgical data pertaining to the animal(s) may be included, such as the type of surgical manipulation, outcome of the surgery and complications arising from the surgical procedure.
• “Diagnostic data” may also include measurements of such parameters as weight, morbidity, and other characteristics noted by a veterinary service such as the condition of the skin, feet, etc.
• welfare data refers to the collective accumulation of data pertaining to an animal or group of animals including, but not limited to, a breeding history, a veterinary history, a welfare profile, diagnostic data, quality control data, or any combination thereof.
• livestock profile refers to parameters such as weight, meat density, crowding levels in breeding or rearing enclosures, psychological behavior of the animal, growth rate and quality and the like.
• quality control refers to the desired characteristics of the animal(s).
• 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, breeding ability, and the like.
• performance parameters refers to such factors as meat yield, breeding yield, dairy form, meat quality and yield, productive life and the like that may be the desired goals from the breeding and rearing of the animal(s). Performance parameters may be either generated from the animals themselves, or those parameters desired by a customer or the market.
• fertilizer data refers to the composition, quantity and frequency of delivery of feed, including water, provided to the animal(s).
• food safety refers to the quality of the meat from a livestock animal, including, but not limited to, preparation time, place and manner, storage of the food product, transportation route, inspection records, texture, color, taste, odor, bacterial content, parasitic content and the like.
• the bovine FABP nucleotide sequence can be selected from, but is not limited to, the sequence corresponding to GenBank Accession No. AAFCOl 136716 (FIG. 4, SEQ ID NO: 1) or a fragment thereof or a region of the bovine genome that comprises this sequence.
• the present invention therefore, provides isolated nucleic acids that may specifically hybridize to the nucleotide sequence corresponding to GenBank Accession No. AAFCOl 136716 (FIG. 4, SEQ ID NO: 1) or the complement thereof, and which comprises the polymorphic site corresponding to nucleotide position a G to C substitution at the 7516 nucleotide position of the F ABP 4 gene and a G to C substitution at position 7713 of the FABP4 gene.
• the SNP advantageous in the present invention is associated with certain economically valuable and heritable traits relating to meat quality in bovines. 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 traits or other characteristics, and in particular by a panel or panels of SNPs. There are many methods known in the art for determining the sequence of DNA 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 performance of the methods of the present invention.
• the methods of the present invention allow animals with certain economically valuable heritable traits to be identified based on the presence of SNPs in their genomes and particularly with a SNP located within the FABP gene.
• the methods further allow, by computer-assisted methods of the invention, to correlate the SNP -associated traits with other data pertinent to the well-being and productive capacity of the animals, or group of animals.
• To determine the genotype of a given animal according to the methods of the present invention it is necessary to obtain a sample of genomic DNA from that animal. Typically, that sample of genomic DNA will be obtained from a sample of tissue or cells taken from that animal. A tissue or cell sample may be taken from an animal at any time in the lifetime of an animal but before the carcass identity is lost.
• the tissue sample can comprise hair, including roots, hide, bone, buccal swabs, blood, saliva, milk, semen, embryos, muscle or any internal organs.
• the source of the tissue sample, and thus also the source of the test nucleic acid sample is not critical.
• the test nucleic acid can be obtained from cells within a body fluid of the animal, or from cells constituting a body tissue of the animal.
• the particular body fluid from which cells are obtained is also not critical to the present invention.
• the body fluid may be selected from the group consisting of blood, ascites, pleural fluid and spinal fluid.
• the particular body tissue from which cells are obtained is also not critical to the present invention.
• the body tissue may be selected from the group consisting of skin, endometrial, uterine and cervical tissue. Both normal and tumor tissues can be used.
• the tissue sample is marked with an identifying number or other indicia that relates the sample to the individual animal from which the sample was taken.
• the identity of the sample advantageously remains constant throughout the methods and systems of the invention thereby guaranteeing the integrity and continuity of the sample during extraction and analysis.
• the indicia may be changed in a regular fashion that ensures 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 those skilled in the art and for example, can be determined by the subsequent steps used in the method and system of the invention and the specific methods of analysis used. Ideally, the size/volume of the tissue sample retrieved should be as consistent as possible within the type of sample and the species of animal.
• sample sizes/methods include non-fatty meat: 0.0002 gm-10.0 gm; hide: 0.0004 gm-10.0 gm; hair roots: at least one and advantageously greater than five; buccal swabs: 15 to 20 seconds of rubbing with modest pressure in the area between outer lip and gum using, for example, a cytology brush; bone: 0.0002 gm-10.0 gm; blood: 30 ⁇ l to 50 ml.
• the tissue sample is placed in a container that is labeled using a numbering system bearing a code corresponding to the animal, for example, to the animal's ear tag. Accordingly, 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 individual animals while simultaneously avoiding any cross-contamination of tissue. Accordingly, the size and volume of sample tissues derived from individual animals would be consistent.
• DNA can be isolated from the tissue/cells by techniques known to those skilled in the art (see, e.g., U.S. Patent Nos. 6,548,256 and 5,989,431; Hirota et al.
• DNA may be purified from cells or tissue using proteinase K extraction and ethanol precipitation. DNA, however, may be extracted from an animal specimen using any other suitable methods known in the art.
• the presence or absence of the SNP of any of the genes of the present invention may be determined by sequencing the region of the genomic DNA sample that spans the polymorphic locus.
• Many methods of sequencing genomic DNA are known in the art, and any such method can be used, see for example Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press.
• a DNA fragment spanning the location of the SNP of interest can be amplified using the polymerase chain reaction.
• the amplified region of DNA form can then be sequenced using any method known in the art, for example using an automatic nucleic acid sequencer.
• the detection of a given SNP can then be performed using hybridization of probes 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 specific nucleic acid sequences of the FABP 4 gene, advantageously of the region encompassing a F ABP 4 SNP. Such fragments should be of sufficient length to enable specific annealing or hybridization to the nucleic acid sample.
• the sequences typically will be about 8 to about 44 nucleotides in length. Longer sequences, e.g., from about 14 to about 50, may be advantageous for certain embodiments.
• the design of primers is well known to one of ordinary skill in the art.
• nucleic acid molecules include nucleic acid molecules having at least 70% identity or homology or similarity with a FABP 4 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 nucleotide sequence similarity or homology or identity can be determined using the "Align" program of Myers and Miller, ("Optimal Alignments in Linear Space", CABIOS 4, 11-17, 1988) and available at NCBI.
• the terms "similarity” or “identity” or “homology”, for instance, with respect to a nucleotide sequence is intended to indicate a quantitative measure of homology between two sequences.
• the percent sequence similarity can be calculated as (N re / - N ⁇ )* 100/Nr 8 /, wherein N ⁇ / is the total number of non- identical residues in the two sequences when aligned and wherein N n? / is the number of residues in one of the sequences.
• RNA sequences are said to be similar, or have a degree of sequence identity with 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 stretch of at least 8, preferably at least 10, more preferably at least 12, 13, 14, or 15, such as at least 20, e.g., at least 23 or 25, for instance at least 27 or 30 nucleotides in a FABP gene which are unique to a FABP gene.
• PCR or hybridization primers or probes and optimal lengths therefor 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 RNA sequences.
• the oligonucleotides can be produced by a conventional production process for general oligonucleotides. They can 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. Further, it is suitable to use a nucleic acid synthesizer.
• a nucleic acid synthesizer to label an oligonucleotide with the fluorescent dye, one of 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. Acids Res.
• the oligonucleotide may be labeled with a radiolabel e.g., 3 H, 125 1, 35 S, 14 C, 32 P, etc.
• a radiolabel e.g., 3 H, 125 1, 35 S, 14 C, 32 P, etc.
• Well-known labeling methods are described, for example, in Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press.
• the label is coupled directly or indirectly to a component of the oligonucleotide according to methods well known in the art. Reversed 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 one 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 on 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 respect.
• stringent conditions may be utilized, advantageously along with other stringency affecting conditions, to aid in the hybridization.
• Detection by differential disruption is particularly advantageous to reduce or eliminate slippage hybridization among probes and target, and to promote more effective hybridization.
• stringency conditions may be varied during the hybridization complex stability determination so as to more accurately or quickly determine whether a SNP is present in the target sequence.
• One method for determining the genotype at the polymorphic gene locus encompasses obtaining a nucleic acid sample, hybridizing the nucleic acid sample with a probe, and disrupting the hybridization to determine the level of disruption energy required wherein the probe has a different disruption energy for one allele as compared to another allele.
• This can be achieved where the probe has 100% homology with one allele (a perfectly matched probe), but has a single mismatch with the alternative allele. Since the perfectly matched probe is bound more tightly to the target DNA than the mis-matched probe, it requires more energy to cause the hybridized probe to dissociate.
• a second (“anchor”) probe may be used.
• the anchor probe is not specific to either allele, but hybridizes regardless of what 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 using with the first ("sensor") probe.
• Hybridization stability may be influenced by numerous factors, including thermoregulation, chemical regulation, as well as electronic stringency control, either alone or in combination with the other listed factors.
• stringency conditions include thermoregulation, chemical regulation, as well as electronic stringency control, either alone or in combination with the other listed factors.
• rapid completion of the process may be achieved. This is desirable to achieve properly indexed hybridization of the target DNA to attain the maximum number of molecules at a test site with an accurate hybridization complex.
• 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. Overall, the analytical process may be completed in less than half an hour.
• 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 detection device and method may include, but is not limited to, optical imaging, electronic imaging, imaging with a CCD camera, integrated optical imaging, and mass spectrometry.
• the amount of labeled or unlabeled probe bound to the target may 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 in toto.
• 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. Colormetric labeling, bioluminescent labeling and/or chemiluminescent labeling may further accomplish labeling. Labeling further may include energy transfer between molecules in the hybridization complex by perturbation analysis, quenching, electron transport between donor and acceptor molecules, the latter of which may be facilitated by double stranded match hybridization complexes. Optionally, if the hybridization complex is unlabeled, detection may be accomplished by measurement of conductance differential between double stranded and non-double stranded DNA.
• direct detection may be achieved by porous silicon-based optical interferometry or by mass spectrometry.
• mass spectrometry no fluorescent or other label is necessary. Rather detection is obtained by extremely high levels of mass resolution achieved by direct measurement, for example, by time of flight (TOF) or by electron spray ionization (ESI).
• TOF time of flight
• ESI electron spray ionization
• 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 un-amplified or amplified. Further, if the purified target is amplified and the amplification is an exponential method, it may be, for example, PCR amplified DNA or strand displacement amplification (SDA) amplified DNA. Linear methods of DNA amplification such as rolling circle or transcriptional runoff may also be used.
• SDA strand displacement amplification
• the forward and reverse primers may have contiguous stretches 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 any other length up to and including about 50 nucleotides in length.
• the sequences to which the forward and reverse primers anneal are advantageously located on either side of the particular nucleotide position that is substituted in the SNP to be amplified.
• a detectable label can be incorporated into a nucleic acid during at least one cycle of an amplification reaction.
• Spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means can detect such labels.
• Useful labels in the present invention include fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red, rhodamine, and the like), radiolabels (e.g., 3 H, 125 1, 35 S, 14 C, 32 P, etc.), enzymes (e.g. horseradish peroxidase, alkaline phosphatase etc.) colorimetric labels such as colloidal gold or colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads.
• fluorescent dyes e.g., fluorescein isothiocyanate, Texas red, rhodamine, and the like
• radiolabels e.g., 3 H, 125 1, 35 S, 14 C, 32 P
• the label is coupled directly or indirectly to a component of the assay according to methods well known in the art.
• a wide variety of labels are used, with the choice of label depending on sensitivity required, ease of conjugation with the compound, stability requirements, available instrumentation, and disposal provisions.
• Non-radioactive labels are often attached by indirect means.
• Polymerases can also incorporate fluorescent nucleotides during synthesis of nucleic acids.
• Reagents allowing the sequencing of reaction products can be utilized herein. For example, chain-terminating nucleotides will often be incorporated into a reaction product during one or more cycles of a reaction.
• Commercial kits containing the reagents most typically used for these methods of DNA sequencing are available and widely used.
• PCR exonuclease digestion methods for DNA sequencing can also be used.
• Many methods of sequencing genomic DNA are known in the art, and any such method can be used, see for example Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press.
• a DNA fragment spanning the location of the SNP of interest can 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.
• the nucleic acid sequencing is by automated methods (reviewed by Meldrum, (2000) Genome Res. 10: 1288- 303, the disclosure of which is incorporated by reference in its entirety), for example using a Beckman CEQ 8000 Genetic Analysis System (Beckman Coulter Instruments, Inc.).
• Methods for sequencing nucleic acids include, but are not limited to, automated fluorescent DNA sequencing (see, e.g., Watts & MacBeath, (2001) Methods MoI Biol.
• the sequencing can also be done by a commercial company. Examples of such companies include, but are not limited to, the University of Georgia Molecular Genetics Instrumentation Facility (Athens, Georgia) or SeqWright DNA Technologies Services (Houston, Texas).
• a SNP-specific probe can also be used in the detection of the SNP in amplified specific nucleic acid sequences of the target gene, such as the amplified PCR products generated using the primers described above.
• these SNP-specific probes consist of oligonucleotide fragments.
• the fragments are of sufficient length to provide specific hybridization to the nucleic acid sample.
• the use of a hybridization probe of between 10 and 50 nucleotides in length allows the formation of a duplex molecule that is both stable and selective. Molecules having complementary sequences over stretches greater than 12 bases in length are generally advantageous, in order to increase stability and selectivity of the hybrid, and thereby improve the quality and degree of particular hybrid molecules obtained.
• a tag nucleotide region may be included, as at the 5' end of the primer that may provide a site to which an oligonucleotide sequencing primer may hybridize to facilitate the sequencing of multiple PCR samples.
• the probe sequence must span the particular nucleotide position that may be substituted in the particular SNP to be detected.
• two or more different "allele-specific probes" may be used for analysis of a SNP, a first allele-specific probe for detection of one allele, and a second allele-specific probe for the detection of the alternative allele.
• this invention is not limited to the particular primers and probes disclosed herein and is intended to encompass at least nucleic acid sequences that are hybridizable to the nucleotide sequence disclosed herein, the complement or a fragment thereof, or are functional sequence analogs of these sequences. It is also contemplated that a particular trait of an animal may be determined by using a panel of SNPs associated with that trait. Several economically relevant traits may be characterized by the presence or absence of one or more SNPs and by 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 subject animal.
• Homologs i.e., nucleic acids derived from other species
• other related sequences e.g., paralogs
• the genetic markers, probes thereof, methods, and kits of the invention are also useful in a breeding program to select for breeding those animals having desirable phenotypes for various economically important traits, such as improved meat quality and yield, in particular meat tenderness.
• Continuous selection and breeding of animals, such as livestock, that are at least heterozygous and advantageously homozygous for desirable alleles of the FABP gene polymorphic sites associated with economically relevant traits of growth, feed intake, efficiency and carcass merit, would lead to a breed, line, or population having higher numbers of offspring with economically relevant traits of growth, feed intake, efficiency and carcass merit.
• the FABP SNPs of the present invention can be used as a selection tool.
• Desirable phenotypes include, but are not limited to, feed intake, growth rate, body weight, carcass merit and composition, and milk yield.
• Specific carcass traits with desirable phenotypes include, but are not limited to, additional carcass value (additional care value, $), average daily gain (ADG, lb/d), backfat thickness (BFAT, in), calculated live weight (CaIc Lv Wt, Ib), calculated yield grade (cYG), days on feed (DOF, d), dressing percentage (DP, %), dry matter intake (DMI, Ib), dry matter intake per day on feed (DMI per DOF, lb/d), hot carcass weight (HCW, Ib), hot carcass weight value (HCW value, $), intramuscular fat content (IMF%, %), marbling score (MBS, 10 to 99), marbling score divided by days on feed (MBS/DOF), quality grade, less than or equal to select versus greater than or equal to choice (QG, ⁇ Se vs,
• One aspect of the present invention provides for grouping animals and methods for managing livestock production comprising grouping livestock animals such as cattle according the genotype as defined by panels of SNPs, each panel comprising at least one SNP, one or more of which are in the FABP gene of the present invention.
• Other SNPs that may be included in panels of SNPs include, but not limited to, SNPs found in the calpastatin gene, GHR gene, ghrelin gene, leptin gene, NPY gene, ob gene, TFAM gene, UASMSl gene, UASMS2 gene, UASMS3 gene and/or the UCP2 gene.
• the genetic selection and grouping methods of the present invention can be used in conjunction with other conventional phenotypic grouping methods such as grouping animals by visible characteristics such as weight, frame size, breed traits, and the like.
• the methods of the present invention provide for producing cattle having improved heritable traits, 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 screening livestock to determine those more likely to develop a desired body condition by identifying the presence or absence of one or more gene polymorphisms correlated with meat quality.
• phenotypic traits with which the SNPs of the present invention may be associated.
• Each of the phenotypic and genetic traits can be tested using the methods described in the Examples, or using any suitable methods known in the art.
• a farmer, or feedlot 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 feeding behavior, as determined by SNP genotype.
• the cattle are tested to determine homozygosity or heterozygosity with respect to the SNP alleles of one or more genes so that they can be grouped such that each pen contains cattle with like genotypes.
• Each pen of animals is then fed and otherwise maintained in a manner and for a time determined by the feedlot operator, and then slaughtered.
• the individual genotypic data derived from a panel or panels of SNPs for each animal or a herd of animals can be recorded and associated with various other data of the animal, e.g. health information, parentage, husbandry conditions, vaccination history, herd records, subsequent food safety data and the like. Such information can be forwarded 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.
• the data 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 a microchip implanted in the animal.
• the methods of the invention may provide an analysis of the input data that may be compared with parameters desired by the operator. These parameters include, but are not limited to, such as breeding goals, egg laying targets, vaccination levels of a herd. If the performance or properties of the animals deviates from the desired goals, the computer-based 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 are associated with the individual animal or to the herd, in whole or in part, from which the sample was taken.
• the data are 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 may be stored in a database that can be integrated or associated with and/or cross-matched to other databases.
• the database along with the associated data allows information about the individual animal to be known through every stage of the animal's life, i.e., from conception to consumption of the animal product.
• the accumulated data and the combination of the genetic data with other types of data of the animal provides access to information about parentage, identification of herd, health information including vaccinations, exposure to diseases, feedlot location, diet and ownership changes. Information such as dates and results of diagnostic or routine tests are easily stored and attainable. Such information would be especially valuable to companies, particularly those who seek superior breeding lines.
• Each animal may be provided with a unique identifier.
• the animal can be tagged, as in traditional tracing programs or have implant computer chips providing stored and readable data or provided with any other identification method which associates the animal with its unique identifier.
• the database containing the SNP-based genotype results for each animal or the data for each animal can be associated or linked to other databases containing data, for example, which may be helpful in selecting traits for grouping or sub-grouping of an animal.
• data pertaining to animals having particular vaccination or medication protocols can optionally be further linked with data pertaining to animals having food from certain food sources.
• the ability to refine a group of animals is limited only by the traits sought and the databases containing information related to those traits. Databases that can usefully be associated with the methods of the invention include, but are not limited to, specific or general scientific data.
• Specific data includes, but is not limited to, breeding lines, sires, dames, and the like, other animals' genotypes, including whether or not other specific animals possess specific genes, including transgenic genetic elements, location of animals which share similar or identical genetic characteristics, and the like.
• General data includes, but is not limited to, scientific data such as which genes encode for specific quality characteristics, breed 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 swabs and tags useful for collecting samples from which genetic data may be obtained.
• the packaging is encoded with a bar code label.
• the tags are encoded with the same identifying indicia, advantageously with a matching bar code label.
• the packaging contains means for sending the tags to a laboratory for analysis.
• the optional packaging is also encoded with identifying indicia, advantageously with a bar code label.
• the method optionally includes a system wherein a database account is established upon ordering the sampling equipment.
• the database account identifier corresponds to the identifying indicia of the tags and the packaging. Upon shipment of the sampling equipment in fulfillment of the order, the identifying indicia are recorded in a database.
• the identifier is a bar code label which is scanned when the tags are sent.
• the tags are returned to the testing facility, the identifier is again recorded and matched to the information previously recorded in the database upon shipment of the vial to the customer.
• the information is recorded in the database and coded with the unique identifier.
• Test results are also provided to the customer or animal owner.
• the data stored in the genotype database can be integrated with or compared to other data or databases for the purpose of identifying animals based on genetic propensities.
• Other data or databases include, but are not limited to, those containing information related to SNP- based DNA testing, vaccination, Sure Health pre-conditioning program, estrus and pregnancy results, hormone levels, food safety/contamination, somatic cell counts, mastitis occurrence, diagnostic test results, milk protein levels, milk fat, vaccine status, health records, mineral levels, trace mineral levels, herd performance, and the like.
• the present invention encompasses computer-assisted methods for tracking the breeding and veterinary histories of livestock animals encompassing using a computer- based system comprising a programmed computer comprising a processor, a data storage system, an input device and an output device, and comprising the steps of generating a profile of a livestock animal by inputting into the programmed computer through the input device genotype data of the animal, wherein the genotype may be defined by a panel of at least two single nucleotide polymorphisms that predict at least one physical trait of the animal, inputting into the programmed computer through the input device welfare data of the animal, correlating the inputted welfare data with the phenotypic profile of the animal using the processor and the data storage system, and outputting a profile of the animal or group of animals to the output device.
• a computer- based system comprising a programmed computer comprising a processor, a data storage system, an input device and an output device, and comprising the steps of generating a profile of a livestock animal by inputting into the programmed
• the databases and the analysis thereof will be accessible to those to whom access has been provided. Access can be provided through rights to access or by subscription to specific portions of the data.
• the database can be accessed by owners of the animal, the test site, the entity providing the sample to the test site, feedlot personnel, and veterinarians.
• the data can be provided in any form such as by accessing a website, fax, email, mailed correspondence, automated telephone, or other methods for communication.
• These data can also be encoded on a portable storage device, such as a microchip, that can be implanted in the animal.
• information can be read and new information added without removing the microchip from the animal.
• the present invention comprises systems for performing the methods disclosed herein. Such systems comprise devices, such as computers, internet connections, servers, and storage devices for data.
• the present invention also provides for a method of transmitting data comprising transmission of information from such methods herein discussed or steps thereof, e.g., via telecommunication, telephone, video conference, mass communication, e.g., presentation such as a computer presentation (e.g., POWERPOINT), internet, email, documentary communication such as computer programs (e.g., WORD) and the like.
• presentation such as a computer presentation (e.g., POWERPOINT), internet, email, documentary communication such as computer programs (e.g., WORD) and the like.
• WORD computer programs
• Systems of the present invention may comprise a data collection module, which includes a data collector to collect data from an animal or embryo and transmit the data to 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 the data via a network to other sites, or to a storage device.
• a data collection module which includes a data collector to collect data from an animal or embryo and transmit the data to 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 the data via a network to other sites, or to a storage device.
• 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 the data via a network to other sites, and/or a storage device.
• the data collected by the data collection module leads to a determination of the absence or presence of a SNP of a gene in the animal or embryo, and for example, such data is transmitted when the feeding regimen of the animal is planned.
• the farmer can optimize the efficiency of managing the herd because the farmer is able to identify the genetic predispositions of an individual animal as well as past, present and future treatments (e.g., vaccinations and veterinarian visits).
• the invention therefore also provides for accessing other databases, e.g., herd data relating to genetic tests and data performed by others, by datalinks to other sites. Therefore, data from other databases can 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 a computer readable media for compiling data on an animal, the system containing inputted data on that animal, such as but not limited to, vaccination and medication histories, DNA testing, thyroglobulin testing, leptin, MMI (Meta Morphix Inc.), bovine spongiform encephalopathy (BSE) diagnosis, brucellosis vaccination, FMD (foot and mouth disease) vaccination, BVD (bovine viral diarrhea) vaccination, Sure Health pre-conditioning program, estrus and pregnancy results, tuberculosis, hormone levels, food safety/contamination, somatic cell counts, mastitis occurrence, diagnostic test results, milk protein levels, milk fat, vaccine status, health records, mineral levels, trace mineral levels, herd performance, and the like.
• the data of the animal can also include prior treatments as well as suggested tailored treatment depending on the genetic predisposition of that animal toward a particular disease.
• the invention also provides for a computer-assisted method for improving animal production comprising using a computer system, e.g., a programmed computer comprising a processor, a data storage system, an input device and an output device, the steps of inputting into the programmed computer through the input device data comprising a breeding, veterinary, medication, diagnostic data and the like of an animal, correlating a physical characteristic predicted by the genotype using the processor and the data storage system, outputting to the output device the physical characteristic correlated to the genotype, and feeding the animal a diet based upon the physical characteristic, thereby improving livestock production.
• a computer system e.g., a programmed computer comprising a processor, a data storage system, an input device and an output device, the steps of inputting into the programmed computer through the input device data comprising a breeding, veterinary, medication, diagnostic data and the like of an animal, correlating a physical characteristic predicted by the genotype using the processor and the data storage system, outputting to the output device the physical characteristic correlated to the genotype
• the invention further provides for a computer-assisted method for optimizing efficiency of feedlots for livestock comprising using a computer system, e.g., a programmed computer comprising a processor, a data storage system, an input device and an output device, and the steps of inputting into the programmed computer through the input device data comprising a breeding, veterinary history of an animal, correlating the breeding, veterinary histories using the processor and the data storage system, outputting to the output device the physical characteristic correlated to the genotype, and feeding the animal a diet based upon the physical characteristic, thereby optimizing efficiency of feedlots for livestock.
• a computer system e.g., a programmed computer comprising a processor, a data storage system, an input device and an output device, and the steps of inputting into the programmed computer through the input device data comprising a breeding, veterinary history of an animal, correlating the breeding, veterinary histories using the processor and the data storage system, outputting to the output device the physical characteristic correlated to the genotype, and feeding the animal
• the invention further comprehends methods of doing business by providing access to such computer readable media and/or computer systems and/or data collected from animals to users; e.g., the media and/or sequence data can be accessible to a user, for instance on a subscription basis, via the Internet or a global communication/computer network; or, the computer system can be available to a user, on a subscription basis.
• the invention provides for a computer system for managing livestock comprising physical characteristics and databases corresponding to one or more animals.
• the invention provides for computer readable media for managing livestock comprising physical characteristics and veterinary histories corresponding to one or more animals.
• the invention further provides methods of doing business for managing livestock comprising providing to a user the computer system and media described above or physical characteristics and veterinary histories corresponding to one or more animals.
• the invention further encompasses methods of transmitting information obtained in any method or step thereof described herein or any information described herein, e.g., via telecommunications, telephone, mass communications, mass media, presentations, internet, email, etc.
• kits useful for screening nucleic acid isolated from one or more bovine individuals for allelic variation of any one of the FABP genes, and in particular for any of the SNPs described herein wherein the kits may comprise at least one oligonucleotide selectively hybridizing to a nucleic acid comprising any one of the one or more of which are FABP sequences described herein and instructions for using the oligonucleotide to detect variation in the nucleotide corresponding to the SNP of the isolated nucleic acid.
• One embodiment of this aspect of the invention provides an an oligonucleotide that specifically hybridizes to the isolated nucleic acid molecule of this aspect of the invention, and wherein the oligonucleotide hybridizes to a portion of the isolated nucleic acid molecule comprising any one of the polymorphic sites in the FABP sequences described herein.
• Another embodiment of the invention is an oligonucleotide that specifically hybridizes under high stringency conditions to any one of the polymorphic sites of the FABP genes, wherein the oligonucleotide is between about 18 nucleotides and about 50 nucleotides.
• the oligonucleotide comprises a central nucleotide specifically hybridizing with a FABP 4 gene polymorphic site of the portion of the nucleic acid molecule.
• Another aspect of the invention is a method of identifying a FABP 4 polymorphism in a nucleic acid sample comprising isolating a nucleic acid molecule encoding FABP or a fragment thereof and determining the nucleotide at the polymorphic site.
• Another aspect of the invention is a method of screening cattle to determine those bovines more likely to exhibit a biological difference in meat quality comprising the steps of obtaining a sample of genetic material from a bovine; and assaying for the presence of a genotype in the bovine which is associated with meat quality, the genotype characterized by a polymorphism in any one of the FABP genes.
• the step of assaying is selected from the group consisting of: restriction fragment length polymorphism (RFLP) analysis, minisequencing, MALD-TOF, SINE, heteroduplex analysis, single strand conformational polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE).
• RFLP restriction fragment length polymorphism
• minisequencing minisequencing
• MALD-TOF minisequencing
• MALD-TOF minisequencing
• SINE heteroduplex analysis
• SSCP single strand conformational polymorphism
• DGGE denaturing gradient gel electrophoresis
• TGGE temperature gradient gel electrophoresis
• the method may further comprise the step of amplifying a region of the FABP gene or a portion thereof that contains the polymorphism.
• the amplification may include the step of selecting a forward and a reverse sequence primer capable of amplifying a region of the FABP gene.
• Another aspect of the invention is a computer-assisted method for predicting which livestock animals possess a biological difference in meat quality
• a computer system e.g., 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 through the input device data comprising a FABP genotype of an animal, (b) correlating a growth, feed intake, efficiency or carcass merit quality predicted by the FABP genotype using the processor and the data storage system and (c) outputting to the output device the meat quality correlated to the FABP genotype, thereby predicting which livestock animals possess a particular growth, feed intake, efficiency or carcass merit quality.
• a computer system e.g., 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 through the input device data comprising a FABP genotype of an animal, (b) correlating a growth, feed intake,
• Yet another aspect of the invention is a method of doing business for managing livestock comprising providing to a user computer system for managing livestock comprising physical characteristics and genotypes corresponding to one or more animals or a computer readable media for managing livestock comprising physical characteristics and genotypes corresponding to one or more animals or physical characteristics and genotypes corresponding to one or more animals.
• FABP4 fatty acid binding protein 4
• adipose tissue interacts with perioxisome proliferator-activated receptors and binds to hormone-sensitive lipase, thus playing an important role in lipid metabolism and homeostasis in adipocytes.
• the objective of this study was, therefore, to investigate associations of the bovine FABP4 gene with fat deposition in Waygu x Limousin F 2 crosses.
• cDNA (625 bp) and genomic DNA (803 lbp) sequences of the bovine FABP 4 gene were retrieved from the public databases and aligned to determine its genomic organization.
• Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands (Kaikaus et al. 1990). Their major functions include fatty acid uptake, transport, and metabolism. So far, 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 a major role in the regulation of lipid and glucose homeostasis through its interaction with perioxisome proliferator-activated receptors (PPARs), located in the cell nucleus.
• PPARs perioxisome proliferator-activated receptors
• the F ABP4/fatty acid complex activates the PP AR- ⁇ isoform, which in turn, regulates transcription of FABP4 (Damcott et al. 2004).
• 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), which is a primary enzyme involved in lipid catabolism (Tansey et al. 2003).
• FABP4 and FABP5 were proposed as potential candidate genes for obesity as they are located within a quantitative trait loci (QTL) region for serum leptin levels in mice (Ogino et al. 2003).
• QTL quantitative trait loci
• Leptin a 16-kDa protein secreted from white adipocytes, is involved in the regulation of food intake, energy expenditure, and whole-body energy balance (Jiang et al. 1999). All these factors indicate that FABP4 plays an important role in lipid metabolism and homeostasis in adipocytes.
• SFD subcutaneous fat depth
• the genomic sequence of the bovine FABP 4 gene has not been described.
• the cDNA sequence of the bovine FABP 4 gene (X89244), derived from the bovine mammary gland, was reported previously (Specht et al. 1996). Therefore, a BLAST search was performed using this cDNA sequence as a query to search for its genomic DNA sequence against the 3X bovine genome sequences that have been released to the public domain (http://www.hgsc.bcm.tmc.edu/projects/bovine/).
• the process retrieved Bos taurus contigl36721 (GenBank accession number AAFC01136716) that contains the 8,031 bp bovine FABP 4 gene sequence.
• the overall structure of the bovine FABP 4 gene was then determined by comparing the genomic DNA sequence with the complete cDNA sequence (FIG. 1).
• the genomic organization of the bovine FABP 4 gene consists of four exons and three introns (FIG. 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 human (NC_000008), pig (Y16039), mouse (NC_000069), rat (NC_005101) and chicken (NC_006089).
• the cDNA - genomic DNA alignment of the bovine FABP 4 gene showed 99% sequence identity in one aligned bock (Exon 3, FIG. 1) and 100% sequence identity in three blocks.
• the first primer pair (forward sequence, 5 'TCG TAA ACT TAG ATG AAG GTG CTC TGG 3 ' (SEQ ID NO: 1
• 5' ACG TAT CCA GCA GAA AGT CAT GGA G 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 sequence alignment between the cDNA and genomic DNA of the bovine FABP 4 gene.
• the second primer pair (forward sequence, 5' ATA TAG TCC ATA GGG TGG CAA AGA 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 tandem repeat of "CA".
• PCR conditions were carried out as follows: 94 0 C for 2 min, 32 cycles of 94 0 C for 30 sec, 63 0 C (for the first primer pair) or 56 0 C (for the second primer pair) for 30 sec and 72 0 C for 30 sec, followed by a further 5 min extension at 72 0 C. PCR products were examined by electrophoresis through a 1.5% agarose gel with IX TBE buffer to determine the quality and quantity of DNA for sequencing.
• DNA sequencing did not confirm the existence of a G/A substitution in exon 3 or a variation in the number of CA repeats in the 3 ' untranscribed region of the bovine FABP 4 gene between HMS and LMS pools. Instead, two single nucleotide polymorphisms (SNPs) were detected in the products amplified with the second primer pair, including a G/C substitution located at position 7516 (FIG. 2A) and a G/C substitution at 7713 bp within the CA repeat region (FIG. 2B).
• SNPs single nucleotide polymorphisms
• GG homozygous animals have one MspAl I site and reveal after complete digestion two bands: 100 bp and 352 bp.
• homozygous animals with C allele have lost the MspA 11 recognition site at this position and show only the 452 bp band.
• Heterozygous animals are identified by the presence of three bands after MspA II digestion (FIG. 3).
• 139 were homozygotes with allele C
• 21 were homozygotes with allele G
• the remaining 72 were heterozygotes with both alleles C and G (Table 1).
• Table 1 Associations of the bovine FABP 4 G/C SNP at position 7516 with marbling and SFD in Waygu X Limousin F2 crosses.
• the phenotypic data for marbling scores and SFD measurements were analyzed using the GLM (general linear model) procedure of SAS v9.1 (SAS institute Inc., Gary, NC).
• the fixed effects of the model included year of birth, gender, age at harvest (linear) and the genotype for a G/C substitution at 7516 bp of the FABP 4 gene. Pairwise comparisons of least-squares means were performed using a protected t-test.
• Genotypes for this microsatellite were significantly associated with the intramuscular fat content of the longissimus dorsi muscle of Duroc pigs (Gerbens et al. 1998) and longissimus lumborum muscle biopsies of crossbred barrows (Gerbens et al. 2001).
• Ye and coworkers (2002) indicated that a Bsml locus in the porcine FABP 4 gene near the microsatellite marker described by Gerbens et al. (1998) was significantly associated with intramuscular fat content.
• bovine chromosome 14 (BTAl 4) harbors significant or suggestive QTL for marbling (intramuscular fat content) and SFD in beef cattle.
• Taylor and Schnabel (2004) http://animalgenomics.missouri.edu/) recently developed a DNA repository from the semen of 1600 registered bulls representing 14 generations of the American Angus Association for an Angus Genome project and confirmed the existence of a marbling QTL with a similar location as the QTL identified by Casas and colleagues (2003).
• Example 2 This Example provides associations between TFAM-I, TFAM-2, and FABP4 markers and carcass traits in commercial feedlot steers and heifers.
• TFAM-I mitochondrial transcription factor A gene
• FBP4 fatty acid binding protein 4 gene
• the tested traits are: hot carcass weight (HCW, Ib), ribeye area (REA, in 2 ), ribeye area per hundred weight HCW (REA/cwt HCW, n ⁇ VlOO Ib hot carcass weight (HCW), hot carcass weight value (HCW value, $), calculated live weight (CaIc Lv Wt, Ib), dry matter intake (DMI, Ib), days on feed (DOF, d), dry matter intake per day on feed (DMI per DOF, lb/d), average daily gain (ADG, lb/d), dressing percentage (DP, %), backfat thickness (BFAT, in), calculated yield grade (cYG), quality grade, less than or equal to select versus greater than or equal to choice (QG, ⁇ Se vs, > Ch), intramuscular fat content (IMF%, %), marbling score (MBS, 10 to 99), marbling score divided by days on feed (MBS/DOF), additional carcass value (additional care value, $), adjusted net return
• the analysis models were genotype, wherein genotypes were fit as fixed effects and additive or allele substitution, which showed regression on allele number (0, 1, 2). Both models fit with 2-marker combinations.
• Another analysis model is haplotype, which shows regression on (expected) haplotype when fitting multiple TFAM markers. Significant single marker associations are presented in Table 2 and significant 2-marker combinations are presented in Table 3. Table 2: Single Marker Analyses for TFAM-I, TFAM-2, & FABP4
• Hot Carcass Wt 1539 5.929 2.402 .0137 .0478 5.894 2.504 .0187 -.172 3.476 .9606
• QG Ch(1, 2,5,9,20) implies Ch or better - includes Prime, Ch, CAB, Sterling Silver, & Angus Pride;
• TFAM-I TFAM-2 Adj NR w/o 1501 8.151 5.602 .1459 11.913 5.791 .0398 -2.564 5.312 .6294 .1528 .0868 .3998 init val
• QG Ch(1, 2,5,9,20) implies Ch or better - includes Prime, Ch, CAB, Sterling Silver, & Angus Pride;
• FIG. 5 shows a flowchart of the input of data and the output of results from the analysis and correlation of the data pertaining to the breeding, veterinarian histories and performance requirements of a group of animals such as from bovines.
• the flowchart illustrated in FIG. 5 further indicates the interactive flow of data from the computer-assisted device to a body of students learning the use of the method of the invention and the correlation of such interactive data to present an output as a pie-chart indicating the progress of the class.
• the flowchart further indicates modifications of the method of the invention in accordance with the information received from the students to advance the teaching process or optimize the method to satisfy the needs of the students.
• FIG. 6 illustrates potential relationships between the data elements to be entered into the system.
• Unidirectional arrows indicate, for example, that a barn is typically owned by only one farm, whereas a farm may own several barns.
• a prescription may include veterinarian products.
• FIG. 7 A illustrates the flow of events in the use of the portable computer-based system for data entry on the breeding and rearing of a herd of cows.
• FIG. 7B illustrates the flow of events through the sub-routines related to data entry concerning farm management.
• FIG. 7C illustrates the flow of events through the sub-routines related to data entry concerning data specific to a company.
• FIG. 8 illustrates a flow chart of the input of data and the output of results from the analysis and the correlation of the data pertaining to the breeding, veterinarian histories, and performance requirements of a group of animals.
• FABP4 gene comprising:
• a method for sub grouping animals according to genotype wherein the animals of each sub-group have a similar genotype in the FABP 4 gene comprising:
• a method for sub grouping animals according to genotype wherein the animals of each sub-group have a similar genotype in the FABP 4 gene comprising:
• a method for identifying an animal having a desirable phenotype as compared to the general population of animals of that species comprising determining the presence of a single nucleotide polymorphism in the FABP 4 gene of the animal, wherein the polymorphism is selected from the group consisting of G to C substitution at the 7516 nucleotide position of the FABP 4 gene and a G to C substitution at position 7713 of the FABP 4 gene single nucleotide polymorphism is indicative of a desirable phenotype.
• BFAT in
• calculated live weight CaIc Lv Wt, Ib
• calculated yield grade CYG
• days on feed DOF, d
• dressing percentage DP, %
• dry matter intake DI, Ib
• dry matter intake per day on feed DI per DOF, lb/d
• hot carcass weight HCW, Ib
• hot carcass weight value HW value, $
• intramuscular fat content IMF%, %)
• marbling score MS, 10 to 99
• marbling score divided by days on feed MS/DOF
• quality grade less than or equal to select versus greater than or equal to choice
• QG ⁇ Se vs, > Ch
• ribeye area REA, in 2
• SFD subcutaneous fat depth
• An interactive computer-assisted method for tracking the rearing of livestock bovines comprising, using a computer system comprising a programmed computer comprising a processor, a data storage system, an input device, an output device, and an interactive device, the steps of: (a) inputting into the programmed computer through the input device data comprising a breeding history of a bovine or herd of bovines, (b) inputting into the programmed computer through the input device data comprising a veterinary history of a bovine or herd of bovines, (c) correlating the veterinary data with the breeding history of the bovine or herd of bovines using the processor and the data storage system, and (d) outputting to the output device the breeding history and the veterinary history of the bovine or herd of bovines.
• the health data is selected from the group consisting of husbandry condition data, herd history, and food safety data.
• the method according to any one of paragraphs 10 to 14 further comprising at least one further step selected from the group consisting of inputting into the programmed computer data related to the quality control of the bovine or herd of bovines and correlating the quality control data to the breeding and veterinary histories of the cow or herd of cows, inputting into the programmed computer performance parameters of the cow or herd of cows; and correlating the required performance parameters of the bovine or herd of bovines to a specific performance requirement of a customer, correlating the vaccine data to the performance parameters of the bovine or herd of bovines, correlating herd to the performance parameters of the bovine or herd of bovines, correlating the food safety data to the performance parameters of the bovine or herd of bovines, correlating the husbandry condition data to the performance parameters of the bovine or herd of bo vines, inputting into the programmed computer data related to the quality control of the bovine or
• a method of transmitting data comprising transmission of information from such methods according to any one of paragraphs 10 to 16, selected from the group consisting of telecommunication, telephone, video conference, mass communication, a presentation, a computer presentation, a POWERPOINTTM presentation, internet, email, and documentary communication.
• An interactive computer system for tracking breeding and welfare histories of cows comprising breeding and veterinarian data corresponding to a bovine or herd of bovines, and wherein the computer system is configured to allow the operator thereof to exchange data with the device or a remote database.
• a method of doing business for tracking breeding and welfare histories of livestock comprising breeding and veterinarian data corresponding to one or more livestock animals comprising providing to a user the computer system of paragraph 19.
• a method of doing business for tracking breeding and welfare histories of livestock comprising breeding and veterinarian data corresponding to one or more livestock animals comprising providing to a user the computer system of paragraph 20.
• 23. The method of doing business according to paragraph 21 further comprising providing the animal owner or customer with sample collection equipment, such as swabs and tags useful for collecting samples from which genetic data may be obtained, and wherein the tags are optionally packaged in a container which is encoded with identifying indicia. 24.
• the computer system further comprises a plurality of interactive devices and wherein the method further comprises the steps of a receiving data from the interactive devices, compiling the data , outputting the data to indicate the response of a student or class of students to a question relating to the operation of the computer-assisted method, and optionally modifying the operation of the computer-assisted method in accordance with the indication of the response.

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