WO2007065206A1 - Marqueurs de sélection pour la prise alimentaire nette - Google Patents

Marqueurs de sélection pour la prise alimentaire nette Download PDF

Info

Publication number
WO2007065206A1
WO2007065206A1 PCT/AU2006/001842 AU2006001842W WO2007065206A1 WO 2007065206 A1 WO2007065206 A1 WO 2007065206A1 AU 2006001842 W AU2006001842 W AU 2006001842W WO 2007065206 A1 WO2007065206 A1 WO 2007065206A1
Authority
WO
WIPO (PCT)
Prior art keywords
seq
sequence
animal
bovine
contiguous sequence
Prior art date
Application number
PCT/AU2006/001842
Other languages
English (en)
Inventor
Ben Hayes
Michael Goddard
Iona Macleod
Amanda Chamberlain
Original Assignee
Commonwealth Scientific And Industrial Research Organisation
Department Of Primary Industries For And On Behalf Of The State Of New South Wales
Meat And Livestock Australia Limited
The State Of Queensland Through Its Department Of Primary Industries And Fisheries
The University Of New England
Department Of Primary Industries For And On Behalf Of The State Of Victoria
The University Of Adelaide
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Commonwealth Scientific And Industrial Research Organisation, Department Of Primary Industries For And On Behalf Of The State Of New South Wales, Meat And Livestock Australia Limited, The State Of Queensland Through Its Department Of Primary Industries And Fisheries, The University Of New England, Department Of Primary Industries For And On Behalf Of The State Of Victoria, The University Of Adelaide filed Critical Commonwealth Scientific And Industrial Research Organisation
Publication of WO2007065206A1 publication Critical patent/WO2007065206A1/fr

Links

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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/027—New or modified breeds of vertebrates
    • 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
    • C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
    • 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
    • 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
    • C12Q2600/172—Haplotypes

Definitions

  • the present invention relates to methods and reagents for determining the feeding efficiency of an animal.
  • nucleotide and amino acid sequence information prepared using Patentln Version 3.3.
  • Each nucleotide sequence is identified in the sequence listing by the numeric indicator ⁇ 210> followed by the sequence identifier (e.g. ⁇ 210>l, ⁇ 210>2, ⁇ 210>3, etc).
  • the length and type of sequence (DNA, protein (PRT), etc), and source organism for each nucleotide sequence are indicated by information provided in the numeric indicator fields ⁇ 211>, ⁇ 212> and ⁇ 213>, respectively.
  • Nucleotide sequences referred to in the specification are defined by the term "SEQ ID NO:", followed by the sequence identifier (e.g., SEQ ID NO: 1 refers to the sequence in the sequence listing designated as ⁇ 400>l).
  • nucleotide residues referred to herein are those recommended by the IUPAC-IUB Biochemical Nomenclature Commission, wherein A represents Adenine, C represents Cytosine, G represents Guanine, T represents thymine, Y represents a pyrimidine residue, R represents a purine residue, M represents Adenine or Cytosine, K represents Guanine or Thymine, S represents Guanine or Cytosine, W represents Adenine or Thymine, H represents a nucleotide other than Guanine, B represents a nucleotide other than Adenine, V represents a nucleotide other than Thymine, D represents a nucleotide other than Cytosine and N represents any nucleotide residue.
  • derived from shall be taken to indicate that a specified integer may be obtained from a particular source albeit not necessarily directly from that source.
  • the present invention is performed without undue experimentation using, unless otherwise indicated, conventional techniques of molecular biology, microbiology, virology, recombinant DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology. Such procedures are described, for example, in the following texts that are incorporated by reference:
  • Meat from animals accounts for almost 20 percent of the world's food consumption. As a consequence, animal-based food products are a major source of revenue throughout the world. In the United States alone, beef production is the fourth largest manufacturing industry and accounts for nearly 25 percent of the farm sector cash receipts and seven percent of supermarket sales each year.
  • Profitability in the production of feed animals is a function of both inputs (e.g., providing feed to animals, fertilizer, irrigation and/or pasture improvement) and outputs (e.g., liveweight, fertility and/or carcass traits).
  • Genetic screening has been used to determine those animals carrying alleles that are associated with, or causative of a trait associated with feed animal output, e.g., an improved meat or carcass quality.
  • alleles of the calpastatin gene have been found to be associated with improved tenderness and/or marbling in meat from pigs or beef (Ciobanu et ah, J. Anim. Sd. 52:2829-2839, 2004 and Barandse et ah, Beef Quality CRC Marbling Symposium, Coffs Harbour pp. 52-57, 2001).
  • These alleles are detected using the commercially available GeneSTAR assay from Genetic Solutions (Queensland, Australia).
  • Gross efficiency is defined as the ratio between production outputs (e.g., weight gain of growing animals or gain in lean tissue) and feed inputs.
  • Gross efficiency is phenotypically and genotypically correlated with aspects of meat production.
  • Buttazoni and Mao describe high phenotypic and genetic correlations between milk yield and gross efficiency of milk production in cows.
  • Brelin and Brannang ⁇ Swedish Journal of Agricultural Research, 12: 29-34, 1982) review a number of studies that demonstrate strong genetic correlations between growth rate and feed conversion ratio.
  • selection for improved feed conversion ratio may improve efficiency during the growth and/or finishing phase of feed animal production, it will not necessarily improve the efficiency or profitability of the entire production system.
  • NFI Residual Feed Intake
  • RFI Residual Feed Intake
  • NFI Net Feed Intake
  • NFI is generally expressed as a deviation from a mean of zero, whereby a negative result indicates that an animal consumes less feed than expected (i.e., has improved feeding efficiency). Conversely, a positive result indicates that an animal has reduced or poor feeding efficiency.
  • mice (Archer et ah, Anim. ScL (57:171-82, 1998); poultry (Luiting and Urff, Br. Poult. ScL 52:763-782, 1991); pigs (Foster et ah, Anim. Prod. 57:387-393, 1983); and cattle (reviewed by Archer et al, Aust. J. Agric. Res. 50:147-161, 1999).
  • NFI is a heritable trait indicating that NFI may be selected.
  • testing of animals for a negative " NFI value facilitates the selection of animals that eat less than expected for their bodyweight and average daily weight gain (Herd et al, J, Anim. ScL, 81: E9-E17).
  • a study by Basarab ⁇ Canadian Journal of Animal Science, 83: 189-204, 2003 monitored animals for individual animal feed intake over a period ranging from 71 to 183 days. On average, animals grew at 1.52kg/day and had an actual feed intake of 12.3 kg/day.
  • NFI provides a useful measure of feed efficiency
  • the methods currently used to determine NFI are both time consuming and expensive (Herd et ah, J. Anim. ScL, 81: E9-E17).
  • individual feed intakes are measured over a set period of 70 days (following a 21 day pre-test adjustment period).
  • animals are fed a standard diet ad libitum using automated self-feeding equipment.
  • Test cattle are weighed regularly and the amount of food intake measured compared to predicted food intake for their weight. Accordingly, this form of testing requires specialized equipment and is performed over a period of about 13 weeks.
  • the inventors analyzed polymorphisms in DNA from selection lines of cattle having positive NFI (low feed efficiency) or negative NFI values (high feed efficiency).
  • the inventors identified a large number of polymorphisms associated with positive or negative NFI. Sequence comparison between fragments comprising SNPs permitted alleles associated with positive or negative NFI to be determined.
  • Use of selection lines increased the power of the experiment by magnifying the genetic differences among the cattle so that these differences were more readily apparent against the background noise created by environmental effects on NFI.
  • the selection of individual animals to assay for SNPs also increased the power of the experiment by selecting the most informative animals and animals in which haplotypes of markers could be deduced.
  • the present inventors also sought to identify clusters of markers and/or haplotypes associated with NFI.
  • bovine, ovine and porcine genome sequence data are incomplete and poorly annotated, the inventors considered that the location of a bovine, ovine or porcine marker can be preferably mapped to a homeologous position of each marker in the human genome or bovine genome.
  • the inventors identified homeologous regions in the human genome to those regions comprising bovine SNPs. This analysis was made possible by the synteny between bovine and human genomes as determined using software of the National Center for Biotechnology Information, Bethesda, MD, USA.
  • the present invention provides an isolated genetic marker associated with net feed intake (NFI) of an animal wherein said marker is positioned within a contiguous sequence of nucleotides in the genome of the animal and wherein said sequence is homeologous to:
  • any reference to an "animal” shall be taken to include a post-partum animal, a fetus or an embryo unless the context requires otherwise or specifically stated otherwise.
  • the term "genetic marker” shall be taken to mean a nucleic acid that comprises a nucleotide sequence associated with a polymorphism associated with NFI.
  • the term "marker” shall be taken to refer to genomic DNA or an expression product of a gene or an allele of a gene that is associated with NFI, such as, for example, a pre-mRNA molecule, a 5'capped mRNA, a polyadenylated mRNA and/or a mature or processed mRNA.
  • the genetic marker is associated with a negative NFI value.
  • an animal having a negative NFI value consumes less feed than is predicted on the basis of mean requirements for body-weight maintenance and level of production for that animal.
  • Suitable genetic markers associated with a negative NFI value will be apparent to the skilled artisan based on the description herein. It follows from the foregoing that a genetic marker associated with a positive NFI value is also useful in the context of a negative screen, in which case the skilled artisan would select against the genetic marker when determining feed efficiency. Accordingly, a genetic marker associated with a positive NFI value is also preferred.
  • a genetic marker of the invention associated with NFI is preferably detectable using a standard procedure, for example, by nucleic acid hybridization or polymerase chain reaction (PCR). Accordingly, a nucleic acid marker is preferably at least about 8 nucleotides in length (e.g., for detection using a locked nucleotide analogue (LNA) probe).
  • LNA locked nucleotide analogue
  • a marker is preferably at least about 15 nucleotides in length or more preferably at least 20 to 30 nucleotides in length.
  • markers are particularly amenable to detection by nucleic acid hybridization-based assays, such as, for example, any known format of PCR or ligase chain reaction.
  • nucleic acid hybridization-based assays such as, for example, any known format of PCR or ligase chain reaction.
  • it will be apparent to the skilled artisan that such a marker is detectable with one or more probes of shorter length (e.g. at least about 8 to about 20 nucleotides in length, more preferably, about 12 to about 20 nucleotides in length, and, even more preferably, about 15 to about 20 nucleotides in length).
  • genetic markers are within an intergenic region of the genome of an animal.
  • intergenic region shall be taken to mean nucleic acid located between genes or nucleic acid capable of being transcribed into RNA.
  • the genetic marker comprises a polymorphism.
  • polymorphism shall be taken to mean a difference in the nucleotide sequence of the genome that occurs in a normal population of individuals.
  • the marker is or comprises a single nucleotide polymorphism (SNP).
  • the term "marker associated with NFI” shall be taken to mean that the presence of a marker in the genome or an expression product thereof is significantly correlated with NFI of an animal. For example, one or more specific markers or alleles is/are associated with a negative or positive NFI.
  • the presence of the marker in the genome or an expression product thereof is significantly correlated with NFI of a plurality of animals. Even more preferably, the presence of the marker is significantly correlated with the NFI of a plurality of animals from different breeds and/or different strains and/or different species.
  • the term "animal” shall be taken to mean any non-human animal or an embryo thereof.
  • the animal is a feed animal, i.e., the animal that is used as a source of meat for consumption, e.g., by a human.
  • the animal is a bovine animal, an ovine animal, a porcine animal, a capran animal or an avian animal (e.g., a chicken or a turkey).
  • the animal is a bovine animal, such as, Bos taurus or Bos indica or other beef-producing species.
  • the bovine is a beef-producing bovine breed selected from Angus, Jersey and Limousin and hybrids and progeny thereof.
  • the bovine may be a beef-producing bovine of a breed selected from Angus, Jersey and Limousin or a beef-producing bovine hybrid or other progeny produced from an animal of Angus and/or Jersey and/or Limousin
  • homeologous chromosomes are generally partially homologous or comprise regions of homology (e.g., synteny) as a result of ancestral homology.
  • the present inventors have identified regions of human chromosomes that are homeologous to regions of bovine chromosomes comprising markers associated with NFI.
  • Information from the homeologous human and bovine chromosomes enables the skilled artisan to, for example, determine and/or identify a haplotype of markers for determining the feeding efficiency of any animal, especially those animals having a high degree of synteny with humans and/or bovines.
  • a SNP allele in a contiguous sequence of nucleotides in the genome of the animal being tested can be the same as a SNP allele, or the same as a plurality of SNP alleles or all SNP alleles, in a homeologous sequence of the bovine genome shown in Table 4 or 5 or at nucleotide residue at position 251 of any one of SEQ ID NOs: 1-124, with related (i.e., homologous) flanking sequences.
  • the flanking sequences may be more divergent than the SNP allele due to genetic distance of the animal from bovines notwithstanding a high level of synteny, however the SNP allele will be conserved.
  • flanking sequences In the case of a bovine animal being tested, there will naturally be a higher level of conservation of flanking sequences (albeit not necessarily absolute due to genetic variation between animals), in addition to conservation of the SNP allele(s), such that a single SNP, a plurality of SNPs or all SNPs in a contiguous sequence of nucleotides in the genome of the animal is a SNP allele of the bovine genome shown in Table 4 or 5 or at nucleotide residue at position 251 of any one of SEQ ID NOs: 1-124, with related flanking sequences.
  • the homeologous region in the bovine genome to which the animal is compared comprises a sequence set forth in any one of SEQ ID NOs: 1-124 or sequences complementary thereto or a fragment of one or more of said sequences.
  • the contiguous sequence of nucleotides in the animal genome comprises a sequence at least about 80% identical to a bovine sequence set forth in any one of more of SEQ ID NOs: 1-124 or sequences complementary thereto or a fragment of one or more of said sequences.
  • Preferred fragments include, for example, a nucleotide sequence comprising nucleotides 1-251 or nucleotides 251-500 of any one of SEQ ID NOs: 1-124.
  • the present invention also provides an isolated genetic marker associated with net feed intake (NFI) comprising or within a nucleic acid comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1
  • chromosome segments carrying one or more genetic markers, e.g., polymorphisms, described herein are identifiable as clusters of alleles or haplotypes. Chromosome segments that carry the same haplotype are likely to be identical-by-descent from a common ancestor and therefore will be identical at all genes within the segment. Therefore these haplotypes, as exemplified herein, are a more accurate means to select animals for high or low NFI than the individual markers. For example, the effect of a cluster on NFI may have greater significance than the effect of an individual allele within the cluster.
  • the "accuracy" of a marker or cluster of markers (i.e. haplotype) for predicting NFI is the correlation between the NFI predicted from the marker or haplotype and the actual NFI of the animal.
  • the "accuracy” of a marker or haplotype for predicting the breeding value of an animal for NFI is the correlation between the NFI predicted from the marker or haplotype and the actual breeding value for NFI of the animal.
  • the term "feed efficiency” or “feed conversion efficiency” or “FCE” shall be taken to mean the ratio of output (e.g., weight of meat recovered from the animal) per unit of feed inputs (e.g., the weight of feed consumed by an animal during a set period). For example, an animal having improved feed efficiency or feed conversion efficiency may consume less food than an animal having average or poor feed efficiency or feed conversion efficiency and produce a similar amount of meat.
  • the present invention provides an isolated nucleic acid comprising a cluster of genetic markers associated with net feed intake (NFI) of an animal wherein said cluster of genetic markers is positioned within a contiguous sequence of nucleotides in the genome of the animal and wherein said contiguous sequence of nucleotides is homeologous to:
  • NFI net feed intake
  • the contiguous sequence of nucleotides is also homeologous to a region of the bovine genome selected from the group consisting of:
  • the genetic markers in a cluster of genetic markers are in linkage disequilibrium.
  • a genetic marker associated with NFI of an animal is a single nucleotide polymorphism (SNP).
  • SNP single nucleotide polymorphism
  • a SNP in a contiguous sequence of nucleotides in the genome of the animal is the same as a SNP allele in a homeologous sequence of the bovine genome shown in Table 4 or 5 or at nucleotide residue at position 251 of any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110.
  • a contiguous sequence of nucleotides in the genome of the animal comprises a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110 or a sequence complementary thereto or a fragment thereof.
  • a SNP in a contiguous sequence of nucleotides in the genome of the animal is a SNP allele of the bovine genome shown in Table 4 or 5 or at nucleotide residue at position 251 of any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110.
  • a contiguous sequence of nucleotides in the genome of the animal comprises a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ID NOs: 1-99 or a sequence complementary thereto or a fragment thereof.
  • a plurality of the genetic markers associated with NFI of an animal are single nucleotide polymorphisms (SNPs).
  • SNPs single nucleotide polymorphisms
  • a plurality of SNPs in a contiguous sequence of nucleotides in the genome of the animal are the same as a plurality of SNP alleles in homeologous sequences of the bovine genome shown in
  • SEQ ID NO: 110 a plurality of SNPs in a contiguous sequence of nucleotides in the genome of the animal are SNP alleles of the bovine genome shown in Table 4 or 5 or at nucleotide residue at position 251 of any one of
  • a contiguous sequence of nucleotides in the genome of the animal may comprise a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110 or a sequence complementary thereto or a fragment thereof.
  • a genetic marker is associated with NFI in a feed animal, for example a bovine animal, an ovine animal, a porcine animal, a capran animal or an avian animal.
  • a feed animal is a bovine animal, such as, for example, Bos taurus or Bos indica.
  • Suitable feed animals include a beef-producing bovine of a breed selected from Angus, Jersey and Limousin or a beef-producing bovine hybrid or other progeny produced from an animal of Angus and/or Jersey and/or Limousin.
  • cluster shall be taken to refer to a grouping of different markers within a region of a chromosome, e.g., based on an alignment to the human genome or bovine animal or a genome of the animal from which the allele is derived.
  • clusters may comprise markers showing linkage disequilibrium as described in the examples.
  • the bovine genome coordinates provided herein are particularly useful for determining the NFI (and/or breeding value) of a bovine animal.
  • the present invention also provides an isolated nucleic acid of a bovine animal comprising a cluster of single nuclear polymorphisms (SNPs) in linkage disequilibrium wherein said cluster of SNPs is associated with net feed intake (NFI) of a bovine animal and is positioned within a contiguous sequence of nucleotides in the bovine genome selected from the group consisting of:
  • a SNP is a SNP allele of the bovine genome shown in Table 4 or 5 or at nucleotide residue at position 251 of any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110.
  • a contiguous sequence of nucleotides comprises a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ED NOs: 1-99 or SEQ ID NO: 110 or a sequence complementary thereto or a fragment thereof.
  • a plurality of SNPs are the same as a plurality of SNP alleles of the bovine genome shown in Table 4 or 5 or at nucleotide residue positions 251 of any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110.
  • a contiguous sequence of nucleotides comprises a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ID NOs: 1 -99 or SEQ ID NO: 110 or a sequence complementary thereto or a fragment thereof.
  • Exemplary bovines belong to the species Bos Taurus, including, for example, a beef- producing bovine of a breed selected from Angus, Jersey and Limousin or a beef- producing bovine hybrid or other progeny produced from an animal of Angus and/or Jersey and/or Limousin.
  • the present invention also provides an isolated nucleic acid comprising a cluster of genetic markers associated with net feed intake (NFI) positioned within a nucleic acid comprising a nucleotide sequence selected from the group consisting of:
  • NFI net feed intake
  • the component SEQ ID NOs or portions thereof may overlap e.g., if the cluster is small, especially if the cluster is less than about 2.0kb in length.
  • the skilled artisan will know that a standard alignment of the sequences using publicly available software will identify the overlapping sequence(s) thereby permitting the cluster sequence to be derived.
  • the markers within the clusters referred to herein above are short i.e., less than 10 Mbp in length, and span short regions of the bovine or human chromosome from about 170 to about 7.45 x 10 6 nucleotides in length.
  • the relatively short genetic distances covered by the cluster regions of the present invention means that recombination between the markers in each cluster is reduced compared to markers that are more widely distributed over a chromosome e.g., more than about 10 Mbp.
  • Preferred clusters within the scope of the present invention contain markers that span regions of the bovine or human chromosome up to about 1.0 x 10 6 nucleotides in length , more preferably up to about 1.0 x 10 5 nucleotides in length [including e.g., between about 4.0 x 10 4 to about 5.0 x 10 4 nucleotides in length (e.g., clusters numbered (iv), (xix) and (xx) supra)], even more preferably up to about 1.0 x 10 nucleotides in length [including e.g., between about 1.0 x 10 3 to about 1.0 x 10 nucleotides in length (e.g., clusters numbered (vi), (vii), (xi), (xii) and (xiii) supra)] and still more preferably less than about 1.5 x 10 4 in length [e.g., clusters numbered (ii), (vi), (vii), (viii), (xi), (xii), (xi
  • the effect of a specific cluster on NFI is determined and subsequently selected for or against in a breeding population.
  • a "within cluster haplotype" associated with NFI is used.
  • the effects of one or more alleles within one or more clusters or between clusters is determined, e.g., for breeding purposes. In such cases a "between clusters haplotype" associated with NFI is used.
  • haplotype shall be taken to refer to a selection of one or more alleles, e.g., within or between clusters.
  • haplotype shall be taken to encompass a within cluster haplotype, i.e., a haplotype comprising a plurality of alleles selected from one cluster as defined herein, in addition to a between clusters haplotype, i.e., comprising one or more alleles selected from different clusters. Other combinations of alleles are not to be excluded.
  • Suitable within cluster haplotypes are exemplified herein, e.g., in Table 4 and/or Table 5.
  • Suitable between cluster haplotypes comprise a combination of markers set forth, for example, in Table 6.
  • the genetic markers, clusters thereof and haplotypes comprising said markers described herein are preferably used for determining feed efficiency in an animal, or a number of different breeds or species or genera. It is particularly preferred that these markers, clusters and haplotypes are conserved across breeds, species or genera, especially with respect to their association with NFI. That is, they provide an advantage of being useful for breeding programs and in hybridization programs by virtue of providing high population coverage.
  • population coverage is meant the proportion of individuals in a mixed population or complex population of subjects (e.g., comprising animals have mixed levels of feeding efficiency or FCE) that are detected as having a desired feeding efficiency or FCE. Accordingly, the population coverage of a marker is related to the frequency at which the marker occurs in a selected population or absent from a population selected against the marker.
  • the present invention also provides an isolated nucleic acid comprising a sequence of nucleotides capable of specifically hybridizing to an isolated nucleic acid comprising a cluster of genetic markers associated with net feed intake (NFI) of an animal, including a bovine animal, according to any embodiment described herein.
  • NFI net feed intake
  • the present invention provides an isolated nucleic acid hybridization probe or amplification primer comprising a sequence of nucleotides capable of specifically detecting (i.e., hybridizing to or amplifying) a genetic marker associated with NFI as described herein according to any embodiment.
  • the probe or primer comprises a sequence that hybridizes to any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110 or a complementary sequence thereto.
  • the probe or primer comprises a sequence having at least about 80% identity to at least about 20 contiguous nucleotides of any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110 or a sequence complementary thereto.
  • the present invention also provides a solid substrate or surface comprising a plurality of nucleic acids immobilized thereon wherein said nucleic acids each comprise one or more single nuclear polymorphisms (SNPs) associated with net feed intake (NFI) of an animal as shown in Table 4 or 5 or at nucleotide residue positions 251 of any one of SEQ ID NOs: 1-124.
  • SNPs single nuclear polymorphisms
  • NFI net feed intake
  • one or a plurality of nucleic acids can comprise a cluster of single nuclear polymorphisms (SNPs) in linkage disequilibrium as shown in Table 4 or 5 or at nucleotide residue positions 251 of any one of SEQ ID NOs: 1-99 or 110.
  • the nucleic acids each comprise a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ID NOs: 1- 124 or a sequence complementary thereto or a fragment thereof.
  • the nucleic acids each comprise a sequence at least about 80% identical to a bovine sequence set forth in any one of SEQ ID NOs: 1-99 or 110 or a sequence complementary thereto or a fragment thereof.
  • the nucleic acids are from one or more feed animals e.g., a bovine animal (Bos taurus or Bos indic ⁇ ), an ovine animal, a porcine animal, a capran animal or an avian animal.
  • a preferred feed animal is a bovine animal such as Bos taurus including a a breed selected from Angus, Jersey and Limousin or a beef-producing bovine hybrid or other progeny produced from an animal of Angus and/or Jersey and/or Limousin, however the invention is clearly applicable to other feed animals.
  • the present invention also provides a solid substrate comprising a plurality of isolated nucleic acids each comprising a cluster of genetic markers associated with net feed intake (NFI) of an animal, including a bovine animal, according to any embodiment described herein.
  • NFI net feed intake
  • the present invention also provides a solid substrate comprising a plurality of isolated nucleic acids each capable of hybridizing to a nucleic acid comprising a cluster of genetic markers associated with net feed intake (NFI) of an animal, including a bovine animal, according to any embodiment described herein.
  • NFI net feed intake
  • the present invention provides a solid substrate or surface comprising a plurality of isolated genetic markers and/or isolated nucleic acid comprising a cluster of said genetic markers according to any embodiment herein immobilized thereon (e.g., a microchip).
  • the plurality of isolated genetic markers and/or isolated nucleic acids consists of SEQ ID NOs: 1-99 or SEQ ID NO: 110, selections and combinations thereof immobilized thereon.
  • the present invention provides a solid substrate or surface comprising one or more isolated probes or primers according to any embodiment immobilized thereon (e.g., a microchip).
  • a solid substrate or surface comprising one or more isolated probes or primers according to any embodiment immobilized thereon (e.g., a microchip).
  • said solid substrate or surface has a plurality of probes or primers according to any embodiment immobilized thereon.
  • the present invention also provides a kit for determining the feed efficiency or FCE of an animal, said kit comprising one or more isolated nucleic acids that hybridize to a nucleic acid comprising a cluster of genetic markers associated with net feed intake (NFI) of an animal, including a bovine animal, according to any embodiment described herein.
  • the kit is packaged with instructions for use.
  • the nucleic acids of the kit are arrayed on a solid substrate.
  • kits for determining the feed efficiency or FCE of an animal comprising one or more isolated probes or primers described herein according to any embodiment.
  • kits comprise a plurality of probes or primers as described herein according to any embodiment.
  • the plurality of probes or primers preferably comprises the probes or primers arrayed on a solid substrate, e.g., a microchip.
  • the kit is also packed with instructions for use.
  • the kit additionally comprises a means for detecting hybridization of the probe or primer to a nucleic acid in a sample.
  • the kit comprises a detectable marker, optionally linked to the probe or primer.
  • the kit comprises enzymatic means for amplifying nucleic acid e.g., a thermostable polymerase or other DNA polymerase enzyme.
  • the present invention also provides a method for identifying a single nuclear polymorphism (SNP) associated with net feed intake (NFI) in an animal, said method comprising:
  • each selection line comprises a breeding population selected for one or more generations on the basis of their high NFI or low NFI;
  • selection line shall be taken to mean a population of animals selected as having high and/or low NFI.
  • said population of animals is a breeding population of animals that has been selected for one or more generations on the basis of high or low NFI, thereby creating divergent selection lines that differ significantly in NFI.
  • the population of animals comprises genetically similar animals.
  • animals in the population are derived from (e.g., are progeny of one or more of the same parental animals (e.g., the same sire).
  • the population of animals is derived from many individual animals, hi one example, the method further comprises producing the population of near-isogenic animals, hi another example, the method further comprises determining a sequence of nucleic acid comprising a SNP identified at (ii). In another example, the method further comprises determining a plurality of SNPs identified at (ii) that are in linkage disequilibrium and thereby form a cluster of SNPs. hi another example, the method further comprises determining a haplotype effect of the SNP.
  • the method further comprises determining a haplotype effect of the cluster of SNPs.
  • the method further comprises positioning a region of a chromosome of the animal comprising the plurality of SNPs to a region of a homeologous chromosome from another animal.
  • the present invention also provides a method for identifying a marker associated with net feed intake (NFI) in the genome of an animal, said method comprising: (i) hybridizing a first nucleic acid to nucleic acid from the animal under at least moderate stringency hybridization conditions wherein the first nucleic acid is capable of hybridizing to a cluster of genetic markers associated with net feed intake (NFI) of an animal, including a bovine animal, according to any embodiment described herein;
  • the present invention also provides a method for identifying a marker associated with net feed intake (NFI) in the genome of an animal, said method comprising:
  • the present invention also provides a method for identifying a cluster of markers and/or a haplotype of markers associated with NFI, said method comprising:
  • linkage disequilibrium shall be taken to mean that two or more markers or polymorphisms are non-randomly associated. For example, the two or more markers or polymorphisms are inherited together significantly more regularly than would be expected were the markers or polymorphisms randomly associated. In one example, the methods supra are performed to determine feed efficiency or feed conversion efficiency (FCE) of an animal.
  • FCE feed conversion efficiency
  • the first nucleic acid or solid substrate is hybridized to nucleic acid from an animal under at least moderate stringency hybridization conditions and the hybridization detected using a detection means, wherein hybridization is indicative of the presence of one or a plurality of single nuclear polymorphisms (SNPs) or one or more SNP haplotypes associated positively or negatively with net feed intake (NFI) thereby indicating the feeding efficiency or FCE of the animal.
  • hybridization is indicative of one or more SNP haplotypes associated positively or negatively with net feed intake (NFI) thereby indicating the feeding efficiency or FCE of the animal.
  • a SNP haplotype is within a cluster of SNPs as shown in Table 4 or 5.
  • a SNP haplotype is between SNPs of two or more clusters of SNPs as shown in Table 4 or 5.
  • the detection means is a polymerase chain reaction (PCR), however other detection means are not excluded.
  • the nucleic acid from the animal comprises genomic DNA.
  • the nucleic acid from the animal comprises RNA.
  • the nucleic acid from the animal can be in a sample selected from the group consisting of whole blood, saliva, urine, skin, hair follicle and semen and combinations thereof.
  • the nucleic acid can also be in a fraction of a body fluid from the animal, such as a fraction of blood.
  • the nucleic acid can also be in a sample comprising epidermal cells.
  • the nucleic acid can also be in a sample of fetal cells, embryonic cells or amniotic fluid.
  • the method comprises positioning the region of a chromosome of the animal comprising the plurality of polymorphisms to a region of a homeologous chromosome from an animal having high synteny with the animals forming the population.
  • the method additionally comprises positioning the plurality of polymorphisms to a region of a chromosome of the animal such that the plurality forms a cluster and/or haplotype.
  • the method further comprises determining a haplotype effect of the cluster of markers on NFI.
  • the present invention also provides a method for identifying a marker associated with NFI of an animal, said method comprising:
  • this method further comprises isolating the hybridized nucleic acid.
  • the identified marker comprises a different nucleotide sequence to the sequence set forth in any one of SEQ ID NOs: 1-99 or SEQ ID NO: 110 or a complement thereof.
  • such a process further comprises selecting a detected animal having improved feeding efficiency or FCE for breeding and/or finishing.
  • such a process further comprises breeding a detected animal by a conventional and/or an assisted breeding program.
  • such a process further comprises finishing or slaughtering a detected animal or providing a detected animal for finishing or slaughter.
  • such a process further comprises providing an isolated cell, gamete or embryo from the detected animal.
  • such a process further comprises providing an isolated cell, gamete or embryo from the selected animal. In one example, such a process further comprises providing an isolated cell, gamete or embryo from the bred animal. In one example, such a process further comprises genotyping the detected animal or a cell or gamete or embryo thereof and optionally providing information on the genotype of the animal or cell or gamete or embryo.
  • such a process further comprises selecting a detected animal having improved feeding efficiency or FCE for breeding and/or finishing.
  • such a process further comprises breeding a detected animal by a conventional and/or an assisted breeding program.
  • such a process further comprises finishing or slaughtering a detected animal or providing a detected animal for finishing or slaughter.
  • such a process further comprises providing an isolated cell, gamete or embryo from the detected animal.
  • such a process further comprises providing an isolated cell, gamete or embryo from the selected animal. In one example, such a process further comprises providing an isolated cell, gamete or embryo from the bred animal. In one example, such a process further comprises genotyping the detected animal or a cell or gamete or embryo thereof and optionally providing information on the genotype of the animal or cell or gamete or embryo.
  • animals having an improved or reduced feed efficiency or FCE comprise one or more of the genetic markers of the invention.
  • the markers in each cluster being in linkage disequilibrium, one or a plurality of markers in a cluster described herein, or one or a plurality of markers in a plurality of clusters, may be used to determine feed efficiency or feed conversion efficiency of an animal.
  • the present invention additionally provides a method for determining feed efficiency or feed conversion efficiency of an animal comprising detecting the presence or absence of a genetic marker associated with NFI as described herein according to any embodiment, wherein the presence or absence of said marker is indicative of feed efficiency or feed conversion efficiency of the animal.
  • an assay that detects a plurality of genetic markers of the invention is also useful for screening a population of animals as a result of its improved accuracy.
  • the present invention also provides a method for determining feeding efficiency or FCE of an animal comprising detecting the presence or absence of a haplotype of genetic markers associated with NFI as described herein according to any embodiment of the invention, wherein the presence or absence of said haplotype is indicative of the feeding efficiency or FCE of the animal.
  • this embodiment of the invention clearly encompasses detecting the presence or absence of a within cluster haplotype (i.e., a cluster of genetic markers) or a between cluster haplotype.
  • the marker, cluster of markers and or haplotype is detected using a nucleic acid hybridization reaction or amplification reaction.
  • the marker, cluster of markers and/or haplotype may be identified and/or detected by hybridizing a nucleic acid probe or primer comprising the sequence of the marker to a marker linked to nucleic acid from an animal under at least moderate, or preferably high stringency hybridization conditions and detecting the hybridization using a detection means, wherein hybridization of the probe to the sample nucleic acid is indicative of the feeding efficiency or FCE of the animals.
  • the detection means is a polymerase chain reaction (PCR).
  • the invention preferably comprises detecting the marker in a sample obtained from the animal, and more preferably, the provision of a sample from the animal.
  • the sample has been obtained previously from the animal.
  • Any sample that comprises genomic DNA (e.g., a nucleated cell) or RNA is preferred for detecting a genetic marker associated with positive or negative NFI.
  • Exemplary samples include whole blood, saliva, urine, a hair follicle or semen.
  • the sample is a fraction of a body fluid, such as, for example, serum, plasma, buffy-coat fraction, Fraction II+III obtainable by ethanol fractionation of Cohn (E. J. Cohn et al., J. Am. Chem. Soc, 68, 459 (1946), Fraction II obtainable by ethanol fractionation of Cohn (E. J. Cohn et al., J. Am. Chem. Soc, 68, 459 (1946) or an albumin fraction of blood.
  • a body fluid such as, for example, serum, plasma,
  • the sample is a blood sample.
  • the sample comprises or consists of plasma.
  • the sample comprises or consists of epidermal cells, e.g., a hair follicle sample.
  • the present invention also provides a method for identifying an animal having an improved feeding efficiency or improved FCE, said method comprising detecting the presence of a genetic marker associated with negative NFI as described herein according to any embodiment of the invention, wherein the detection of said marker indicates that the animal has improved feeding efficiency or improved FCE.
  • the present invention provides a method for identifying an animal having an improved feeding efficiency or improved FCE, said method comprising detecting and/or identifying a haplotype of genetic markers associated with negative NFI as described herein according to any embodiment of the invention, wherein the detection of said haplotype indicates that the animal has improved feeding efficiency or improved FCE.
  • an animal having improved feed efficiency or improved FCE is useful for, for example, finishing for meat production prior to slaughter, and/or for breeding to thereby produce stock having improved feed efficiency or improved FCE. Accordingly, it is desirable in any event to select an animal having improved feed efficiency or improved FCE.
  • the method of identifying an animal having improved feed efficiency or improved FCE additionally comprises selecting the identified animal.
  • the invention additionally provides a method for selecting an animal suitable for finishing or suitable for breeding, said method comprising:
  • Such a selected animal may then be bred or finished, or, alternatively, the animal may be sold, for example, to a feed-lot for finishing or sold for breeding.
  • the foregoing method may additionally comprise selecting an animal having negative NFI and optionally determining the NFI of the selected animal or recommending that the NFI of the selected animal is determined, e.g., using a traditional method.
  • a method of the invention is used to pre-select an animal likely to have an improved feeding efficiency or improved FCE prior to conventional testing. Such pre-selection is useful for, for example, reducing the number of animals tested to determine NFI and, as a consequence, the cost of testing.
  • Methods for determining NFI are known in the art and/or described herein.
  • a method of identification and/or selection of an animal having improved feed efficiency or improved FCE is also useful for screening one or more embryos produced using an assisted breeding technique, e.g., in vitro fertilization, to identify an animal embryo likely to give rise to an animal having improved feeding efficiency or improved FCE.
  • an assisted breeding technique e.g., in vitro fertilization
  • Such selection is important, for example, for industries, such as, for example, the cattle industry, where assisted breeding techniques may be used to breed cattle with reduced fertility.
  • assisted breeding techniques are used to accelerate the selection of animals having a desired trait, e.g., improved feeding efficiency or improved FCE.
  • the present invention also provides a method for breeding an animal having improved feed efficiency or improved FCE, said method comprising:
  • the method may additionally comprise selecting the animal identified at (i).
  • the method additionally comprises identifying an offspring of the animal having an improved feeding efficiency or improved FCE (e.g., by performing a method described herein according to any embodiment).
  • identifying an offspring of the animal having an improved feeding efficiency or improved FCE e.g., by performing a method described herein according to any embodiment.
  • Such a method is useful for, for example, improving the feeding efficiency or FCE of a herd or group of animals.
  • the present invention clearly encompasses a method for identifying and/or selecting and/or breeding an animal having improved feeding efficiency or improved FCE additionally comprising providing an isolated cell, gamete or embryo from the identified and/or selected and/or bred animal.
  • the method for identifying and/or selecting and/or breeding an animal having improved feeding efficiency or improved FCE additionally comprises genotyping the animal or cell or gamete or embryo and optionally providing information on the genotype of the animal or cell or gamete or embryo.
  • the animal or cell or gamete or embryo is genotyped using a method described herein according to any embodiment.
  • the present invention also provides an animal having improved feeding efficiency produced by a process described herein according to any embodiment of the invention, or reproductive material thereof that produces a progeny having improved feeding efficiency.
  • the present invention extends to a progeny animal of the animal or reproductive material, wherein said progeny has improved feeding efficiency.
  • an animal having improved feeding efficiency or improved FCE identified by the method of the invention consumes less feed than animals with standard or reduced feeding efficiency or FCE.
  • the present invention is also useful for reducing the cost of producing animals for meat production.
  • the present invention also provides a process for reducing the cost of producing feed animals, said process comprising:
  • the method additionally comprises breeding the animals or a subset of the animals selected at (ii) to produce offspring of the animals and identifying and selecting offspring having improved feeding efficiency or improved FCE by performing a method described herein according to any embodiment.
  • the drawings Brief description of the drawings
  • Figure Ia is a graphical representation showing the number of SNPs detected at different significant thresholds.
  • the test statistic was calculated for the bovine SNPs as described in Example 1, and was converted into a P value (significance threshold) using the chi square 1 degree of freedom distribution.
  • the log (P values) are plotted vs the number of SNPs detected (closed diamonds).
  • Figure Ib is a graphical representation showing the false detection rate (FDR) for the SNPs of Figure Ia detected at different significant thresholds. FDR was calculated for the bovine SNPs as described in Example 1 and is plotted vs the log (P values) (open triangles).
  • Figure 2a is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 1 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles).
  • Figure 2b is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 10 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2c is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 11 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles).
  • Figure 2d is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 12 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2e is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 13 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2f is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 16 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2g is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 2 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2h is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 3 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2i is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 4 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2j is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 5 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2k is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 6 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 21 is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 7 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2m is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 8 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles).
  • Figure 2n is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome 9 of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r 2 values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • Figure 2o is a graphical representation showing the physical position of significant bovine SNPs when aligned to chromosome X of the human genome.
  • the x axis of each graph shows the physical position across the human chromosome; the y axis shows the test statistic of significant SNPs (closed triangles). Pairs of adjacent SNPs which have r values > 0.25 belong to clusters and are indicated by closed squares underneath each of the SNPs in the pair.
  • the present inventors have identified a plurality of markers associated with net feed intake (NFI) positioned within a contiguous sequence of nucleotides in the genome of an animal that is homeologous to a contiguous sequence of nucleotides in the bovine and/or human genome.
  • the contiguous sequence of nucleotides in the human genome described supra comprises one or more sequences at least about 80% identical to a sequence set forth in any one of more of SEQ ID NOs: 1-124 from the bovine genome, or sequences complementary thereto or a fragment of one or more of said sequences.
  • nucleotide identities and similarities are calculated using software of the Computer Genetics Group, Inc., University Research Park, Maddison, Wisconsin, United States of America, e.g., using the GAP program of Devereaux et at, Nucl. Acids Res. 12, 387-395, 1984, which utilizes the algorithm of Needleman and Wunsch, J. MoI. Biol. 48, 443-453, 1970.
  • the CLUSTAL W algorithm of Thompson et al, Nucl. Acids Res. 22, 4673-4680, 1994 is used to obtain an alignment of multiple sequences, wherein it is necessary or desirable to maximize the number of identical/similar residues and to minimize the number and/or length of sequence gaps in the alignment.
  • Nucleotide sequence alignments can also be performed using a variety of other commercially and/or publicly available sequence analysis programs, such as, for example, the BLAST program available from NCBI.
  • the phragment assembly program (PHRAP) program is also useful for determining percentage identity between different sequences (Ewing, B. and Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. (1998) 8: 186-194.)
  • the degree of sequence identity is at least about 85% or 90% or 95% or 98% or 99%.
  • the marker is a simple nucleotide polymorphism.
  • simple nucleotide polymorphism shall be taken to mean a polymorphism that comprises or consists of one or more small changes (i.e., an insertion, a deletion, a transition or a transversion) to the genome of a subject or an expression product thereof.
  • a simple nucleotide polymorphism comprises or consists of, a single nucleotide insertion or deletion, insertion or deletion of two, three or four or more nucleotides, transition of one or more nucleotides, or transversion of one or more nucleotides.
  • a marker associated with NFI comprises or consists of a single nucleotide polymorphism (SNP).
  • SNP single nucleotide polymorphism
  • the marker associated with NFI comprises or consists of one or more SNPs selected from the group consisting of:
  • the SNP is associated with a negative NFI value e.g., a SNP selected from the group consisting of:
  • the SNP associated with negative NFI comprises or consists of a cytosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 3.
  • the SNP comprises or consists of a guanine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 16.
  • the SNP comprises or consists of a guanine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 26.
  • the SNP comprises or consists of a guanine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 2.
  • the SNP comprises or consists of a guanine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 29.
  • the SNP comprises or consists of an adenosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 33.
  • the SNP comprises or consists of an adenosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ TD NO: 38.
  • the SNP comprises or consists of a thymine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ TD NO: 39.
  • the SNP comprises or consists of a cytosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 42.
  • the SNP comprises or consists of a cytosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 50.
  • the SNP comprises or consists of a thymine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 54.
  • the SNP comprises or consists of a thymine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 68.
  • the SNP comprises or consists of a thymine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 76.
  • the SNP comprises or consists of a cytosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 78.
  • the SNP comprises or consists of an adenosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 79.
  • the SNP comprises or consists of a cytosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 86.
  • the SNP comprises or consists of an adenosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 87.
  • the SNP comprises or consists of a cytosine in a nucleic acid at a position corresponding to nucleotide position 251 of SEQ ID NO: 96.
  • the present invention also provides methods comprising detecting and/or identifying a plurality of markers of NFI to thereby determine the NFI of an animal.
  • the method of the invention comprises detecting or identifying a plurality of markers in a chromosome region described herein in respect of any embodiment of the invention.
  • the present inventors have determined markers that are in linkage disequilibrium to thereby determine a cluster of markers (or a within cluster haplotype of markers).
  • Methods for determining linkage disequilibrium are known in the art and/or described herein. For example, linkage disequilibrium is determined using a method described by Hill (Genetical Research, 38: 209-216, 1981).
  • a and B are on the same chromosome.
  • freq (A1J31) is the frequency of the A1_B1 haplotype in the population, and likewise for the other haplotypes.
  • linkage disequilibrium is determined using the method described by Hill and Robertson (Theor. Appl. Genet, 38: 226-231, 1968). In this respect the measure of linkage disequilibrium (r 2 ) is determined using the formula:
  • freq(Al) is the frequency of the Al allele in the population, and likewise for the other alleles in the population (e.g., the Bl allele or the B2 allele).
  • the method of the invention comprises detecting a marker in a nucleic acid comprising a sequence set forth in Table 6.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 39, a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 46 and an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 25.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 39, a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 46 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 25.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 66 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 53 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 110.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 59, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 10, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 8 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 52.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 59, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 10, a guanine at a position corresponding to nucleotide position 251 of SEQ ED NO: 8 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 52.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 59, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 10, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 8 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 52.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 71, a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 70, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 38 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 50.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 71, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 70, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 38 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 50.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 71, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 70, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 38 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 50.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 95 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 84.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 96, an adenosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 79, a cytosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 78 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 3.
  • the method of the invention comprises a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 22 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 60.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ED NO: 35, a guanine at a position corresponding to nucleotide position 251 of SEQ ED NO: 12 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 33.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 44, a thymine at a position corresponding to nucleotide position 251 of SEQ ED NO: 54 and an adenosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 87.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 44, a cytosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 54 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 87.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 44, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 54 and an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 87.
  • the method of the invention comprises detecting an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 18, a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 11, a thymine at a position corresponding to nucleotide position 251 of SEQ ED NO: 88 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 63.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ED NO: 18, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 11, a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 88 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ED NO: 63.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ED NO: 18, an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 11, a thymine at a position corresponding to nucleotide position 251 of SEQ ED NO: 88 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 63.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 29, a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 27, a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 26 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 73.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 67 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 16.
  • the method of the invention comprises detecting an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 17, a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 97, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 98 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 14.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 15, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 56 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 90.
  • the method of the invention comprises detecting an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 31 and an adenosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 1.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 80, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 94 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 28.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 82 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 69.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 82 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 69.
  • the method of the invention comprises detecting 'a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 82 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 69.
  • the method of the invention comprises detecting a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 61 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 45.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 92, a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 55 and a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 51.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 92, a cytosine at a position corresponding to nucleotide position 251 of SEQ ID NO: 55 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 51.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 99 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 93.
  • the method of the invention comprises detecting a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO: 99 and a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 93.
  • the method of the invention comprises detecting a guanine at a position corresponding to nucleotide position 251 of SEQ ID NO: 99 and a thymine at a position corresponding to nucleotide position 251 of SEQ ID NO : 93.
  • the method of the invention comprises detecting one or more markers in a plurality of chromosome regions and/or nucleic acids described herein with respect to any one of more embodiments of the invention.
  • the method of the invention comprises detecting one or more markers in a plurality of haplotypes described herein in respect of any embodiment of the invention.
  • the present invention is preferably used to determine the level of feeding efficiency or FCE in an animal that is used as a source of food and preferably for meat production, e.g., cattle, sheep, goat, poultry, etc. Suitable animals will be apparent to the skilled artisan and/or described herein.
  • the animal is an ungulate, for example, a bovine animal, e.g., beef cattle or dairy cattle.
  • the animal is of the genus Bos.
  • the animal is of the genus and species Bos taurus or Bos indica.
  • the animal may be any breed or cross of beef cattle.
  • the animal is a breed or a cross of beef cattle used to produce meat for consumption.
  • the animal is a bull, cow or calf from a breed or cross of cattle selected from the group consisting of Angus, Ankole-Watusi, Ayrshire, Bazadaise, Beefalo, Beeftnaster, Belgian Blue, Blonde d'Aquitaine, Bonsmara, Braford, Brahman, Brahmousin, Brangus, Braunvieh, British White, American Brown Swiss, BueLingo, Charolais, Chianina, Corriente, American Devon, Dexters, Droughtmaster, Galloway, Gelbvieh, Guernsey, Hereford, Highland, Holstein, Jersey, Limousin, Lowline, Maine- Anjou, Marchigiana, Milking Shorthom, Montbeliarde, Murray Grey, Normande, Parthenaise, Piedmontese, Pinzgauer, Romagnola, Salers, Salorn, Santa Gertrude, Shetland, Shorthorn, Simmental, South Devons, Tarentaise,
  • the animal is a bull, cow or calf from a breed of cattle selected from the group consisting of Africander, Angus, Beef Shorthorn , Belmont Red, Boran, Braford, Brahman, Brangus, Charolais, Chiangus, Chianina, Devon, Droughtmaster, Galloway, Gelbvieh, Hereford, Limousin, Maine-Anjou, Murray Grey, Poll Hereford, Romagnola, Santa Gertrudis, Shorthorn, Simmental, South Devon and TuIi.
  • a marker of the invention is associated with NFI in an Angus bull, cow or calf. Accordingly, a preferred animal for performance of the invention is an Angus bull, cow or calf.
  • a preferred sample for performing the method of the invention is a readily accessible sample that comprises genomic DNA.
  • genomic DNA for example, genetic testing of cattle is often performed using a hair follicle, for example, isolated from the tail of an animal to be tested.
  • readily accessible samples include, for example, bodily fluids or an extract thereof or a fraction thereof.
  • a readily accessible bodily fluid includes, for example, whole blood, saliva, semen or urine.
  • Exemplary whole blood fractions are selected from the group consisting of buffy-coat fraction, Fraction II+III obtainable by ethanol fractionation of Cohn (E. J. Cohn et al., J. Am. Chem. Soc, 68, 459 (1946), Fraction II obtainable by ethanol fractionation of Cohn (E. J. Cohn et al., J. Am. Chem. Soc, 68, 459 (1946), albumin fraction, an immunoglobulin-containing fraction and mixtures thereof.
  • a biological sample comprises a cell or cell extract or mixture thereof derived from a tissue such as, for example, skin.
  • a biological sample has been isolated or derived previously from a subject by, for example, surgery, or using a syringe or swab.
  • Cell preparations or nucleic acid preparation derived from such tissues or cells are not to be excluded.
  • the sample can be prepared on a solid matrix for histological analyses, or alternatively, in a suitable solution such as, for example, an extraction buffer or suspension buffer, and the present invention clearly extends to the testing of biological solutions thus prepared.
  • a marker associated with NFI is detected using a probe or primer that selectively hybridizes to said marker in a sample from an animal under moderate, and preferably, high stringency conditions.
  • a low stringency is defined herein as being a hybridization and/or a wash carried out in 6 x SSC buffer, 0.1% (w/v) SDS at 28 0 C, or equivalent conditions.
  • a moderate stringency is defined herein as being a hybridization and/or washing carried out in 2 x SSC buffer, 0.1% (w/v) SDS at a temperature in the range 45 0 C to 65 0 C, or equivalent conditions.
  • a high stringency is defined herein as being a hybridization and/or wash carried out in 0.1 x SSC buffer, 0.1% (w/v) SDS, or lower salt concentration, and at a temperature of at least 65°C, or equivalent conditions. Reference herein to a particular level of stringency encompasses equivalent conditions using wash/hybridization solutions other than SSC known to those skilled in the art.
  • the stringency is increased by reducing the concentration of SSC buffer, and/or increasing the concentration of SDS and/or increasing the temperature of the hybridization and/or wash.
  • concentration of SSC buffer and/or increasing the concentration of SDS and/or increasing the temperature of the hybridization and/or wash.
  • the conditions for hybridization and/or wash may vary depending upon the nature of the hybridization matrix used to support the sample DNA, or the type of hybridization probe used.
  • a probe or primer capable of specifically detecting a marker that is associated with NFI is any probe or primer that is capable of specifically hybridizing to the region of the genome that comprises said marker.
  • selective hybridizes means that the polynucleotide used as a probe is used under conditions where a target polynucleotide is found to hybridize to the probe at a level significantly above background.
  • the background hybridization may occur because of other polynucleotides present, for example, in genomic DNA being screening.
  • background implies a level of signal generated by interaction between the probe and non-specific DNA which is less than 10 fold, preferably less than 100 fold as intense as the specific interaction observed with the target DNA. The intensity of interaction are measured, for example, by radiolabelling the probe, e.g. with 32 P.
  • a preferred probe or primer comprises, consists of or is within a nucleic acid comprising nucleotide sequence at least about 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 1-99 and a sequence complementary thereto.
  • a probe or primer comprises a nucleic acid comprising a nucleotide sequence at least about 80% identical to a sequence of 20 contiguous nucleotides from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-99 and a sequence complementary thereto.
  • probe or primer used in an assay of the present invention will depend upon the assay format used. Clearly, a probe or primer that is capable of selectively hybridizing to or detecting the marker of interest is preferred.
  • Methods of designing probes and/or primers for, for example, PCR or hybridization are known in the art and described, for example, in Dieffenbach and Dveksler (Eds) (In: PCR Primer: A Laboratory Manual, Cold Spring Harbour Laboratories, NY, 1995).
  • Eds Dieffenbach and Dveksler
  • PCR Primer A Laboratory Manual, Cold Spring Harbour Laboratories, NY, 1995.
  • several software packages are publicly available that design optimal probes and/or primers for a variety of assays, e.g. Primer 3 available from the Center for Genome Research, Cambridge, MA, USA.
  • Probes and/or primers useful for detection of a marker associated with feeding efficiency are preferably assessed to determine those that do not form hairpins, self-prime or form primer dimers (e.g. with another probe or primer used in a detection assay).
  • a probe or primer (or the sequence thereof) is preferably assessed to determine the temperature at which it denatures from a target nucleic acid (i.e. the melting temperature of the probe or primer, or Tm). Methods of determining Tm are known in the art and described, for example, in Santa Lucia, Proc. Natl. Acad. Sci. USA, 95: 1460-1465, 1995 or Bresslauer et al, Proc. Natl. Acad. Sci. USA, 83: 3746- 3750, 1986.
  • a primer or probe useful for detecting a SNP in an allele specific PCR assay or a ligase chain reaction assay is designed such that the 3' terminal nucleotide hybridizes to the site of the SNP.
  • the 3' terminal nucleotide may be complementary to any of the nucleotides known to be present at the site of the SNP.
  • complementary nucleotides occur in both the probe or primer and at the site of the polymorphism the 3' end of the probe or primer hybridizes completely to the marker of interest and facilitates, for example, PCR amplification or ligation to another nucleic acid. Accordingly, a probe or primer that completely hybridizes to the target nucleic acid produces a positive result in an assay.
  • a primer useful for a primer extension reaction is designed such that it specifically hybridizes to a region adjacent to a specific nucleotide of interest, e.g., a SNP. While the specific hybridization of a probe or primer may be estimated by determining the degree of homology of the probe or primer to any nucleic acid using software, such as, for example, BLAST, the specificity of a probe or primer can only be determined empirically using methods known in the art.
  • a locked nucleic acid (LNA) or protein-nucleic acid (PNA) probe or a molecular beacon useful for, for example, detection of a SNP by hybridization is at least about 8 to 12 nucleotides in length.
  • the nucleic acid, or derivative thereof, that hybridizes to the site of the SNP is positioned at approximately the centre of the probe, thereby facilitating selective hybridization and accurate detection.
  • oligonucleotide synthesis is described, in Gait (Ed) (In: Oligonucleotide Synthesis: A Practical Approach, IRL Press, Oxford, 1984); LNA synthesis is described, for example, in Nielsen et al, J. Chem. Soc. Perkin Trans., 1: 3423, 1997; Singh and Wengel, Chem. Commun. UAl, 1998; and PNA synthesis is described, for example, in Egholm et al, Am. Chem.
  • Methods for detecting nucleic acids include for example, hybridization based assays, amplification based assays and restriction endonuclease based assays.
  • a change in the sequence of a region of the genome or an expression product thereof such as, for example, an insertion, a deletion, a transversion, a transition, is detected using a method, such as, polymerase chain reaction (PCR), strand displacement amplification, ligase chain reaction, cycling probe technology or a DNA microarray chip amongst others.
  • PCR polymerase chain reaction
  • ligase chain reaction strand displacement amplification
  • cycling probe technology or a DNA microarray chip amongst others.
  • PCR Methods of PCR are known in the art and described, for example, in Dieffenbach (ed) and Dveksler (ed) (In: PCR Primer: A Laboratory Manual, Cold Spring Harbour Laboratories, NY, 1995).
  • two non-complementary nucleic acid primer molecules comprising at least about 15 nucleotides, more preferably at least 20 nucleotides in length are hybridized to different strands of a nucleic acid template molecule, and specific nucleic acid molecule copies of the template are amplified enzymatically.
  • PCR products may be detected using electrophoresis and detection with a detectable marker that binds nucleic acids.
  • one or more of the oligonucleotides is/are labeled with a detectable marker (e.g. a fluorophore) and the amplification product detected using, for example, a lightcycler (Perkin Elmer, Wellesley, MA, USA).
  • a detectable marker e.g. a fluorophore
  • the present invention also encompasses quantitative forms of PCR, such as, for example, Taqman assays.
  • Strand displacement amplification utilizes oligonucleotides, a DNA polymerase and a restriction endonuclease to amplify a target sequence.
  • the oligonucleotides are hybridized to a target nucleic acid and the polymerase used to produce a copy of this region.
  • the duplexes of copied nucleic acid and target nucleic acid are then nicked with an endonuclease that specifically recognizes a sequence at the beginning of the copied nucleic acid.
  • the DNA polymerase recognizes the nicked DNA and produces another copy of the target region at the same time displacing the previously generated nucleic acid.
  • SDA Strand displacement amplification
  • Ligase chain reaction uses at least two oligonucleotides that bind to a target nucleic acid in such a way that they are adjacent. A ligase enzyme is then used to link the oligonucleotides. Using thermocycling the ligated oligonucleotides then become a target for further oligonucleotides. The ligated fragments are then detected, for example, using electrophoresis, or MALDI-TOF. Alternatively, or in addition, one or more of the probes is labeled with a detectable marker, thereby facilitating rapid detection.
  • RNA-DNA duplex formed is a target for RNase H thereby cleaving the probe.
  • the cleaved probe is then detected using, for example, electrophoresis or MALDI-TOF.
  • a SNP that introduces or alters a sequence that is a recognition sequence for a restriction endonuclease is detected by digesting DNA with the endonuclease and detecting the fragment of interest using, for example, Southern blotting (described in Ausubel et al (In: Current Protocols in Molecular Biology. Wiley Interscience, ISBN 047 150338, 1987) and Sambrook et al (In: Molecular Cloning: Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Third Edition 2001)).
  • a nucleic acid amplification method described supra is used to amplify the region surrounding the SNP. The amplification product is then incubated with the endonuclease and any resulting fragments detected, for example, by electrophoresis, MALDI-TOF or PCR.
  • the direct analysis of the sequence of polymorphisms of the present invention can be accomplished using either the dideoxy chain termination method or the Maxam- Gilbert method (see Sambrook et al, Molecular Cloning, A Laboratory Manual (2nd Ed., CSHP, New York 1989); Zyskind et al, Recombinant DNA Laboratory Manual, (Acad. Press, 1988)).
  • a region of genomic DNA comprising one or more markers of NFI described herein with respect to any embodiment of the invention is amplified using an amplification reaction, e.g., PCR.
  • the amplified nucleic acid is used in a sequencing reaction to determine the sequence of one or both alleles at the site of a SNP of interest.
  • a SNP is detected using single stranded conformational polymorphism (SSCP) analysis.
  • SSCP analysis relies upon the formation of secondary structures in nucleic acids and the sequence dependent nature of these secondary structures.
  • an amplification method such as, for example, a method described supra, is used to amplify a nucleic acid that comprises a SNP.
  • the amplified nucleic acids are then denatured, cooled and analyzed using, for example, non-denaturing polyacrylamide gel electrophoresis, mass spectrometry, or liquid chromatography (e.g., HPLC or dHPLC).
  • Regions that comprise different sequences form different secondary structures, and as a consequence migrate at different rates through, for example, a gel and/or a charged field.
  • a detectable marker may be incorporated into a probe/primer useful in SSCP analysis to facilitate rapid marker detection.
  • any nucleotide changes may be detected using, for example, mass spectrometry or capillary electrophoresis.
  • amplified products of a region of DNA comprising a SNP from a test sample are mixed with amplified products from a subject having a known genotype at the site of the SNP.
  • the products are denatured and allowed to re-anneal.
  • Those samples that comprise a different nucleotide at the position of the SNP will not completely anneal to a nucleic acid molecule from the control sample thereby changing the charge and/or conformation of the nucleic acid, when compared to a completely annealed nucleic acid.
  • Such incorrect base pairing is detectable using, for example, mass spectrometry.
  • Allele specific PCR (as described, for example, In Liu et al, Genome Research, 7: 389-398, 1997) is also useful for determining the presence of one or other allele of a
  • An oligonucleotide is designed, in which the most 3' base of the oligonucleotide hybridizes to a specific form of the SNP of interest (i.e., allele).
  • the 3' end of the oligonucleotide does not hybridize to a target sequence that does not comprise the particular form of the SNP detected. Accordingly, little or no PCR product is produced, indicating that a base other than that present in the oligonucleotide is present at the site of SNP in the sample.
  • PCR products are then detected using, for example, gel or capillary electrophoresis or mass spectrometry.
  • oligonucleotide is used that hybridizes to the region of a nucleic acid adjacent to the SNP.
  • This oligonucleotide is used in a primer extension protocol with a polymerase and a free nucleotide diphosphate that corresponds to either or any of the possible bases that occur at the site of the SNP.
  • the nucleotide-diphosphate is labeled with a detectable marker (e.g. a flurophore).
  • a detectable marker e.g. a flurophore
  • primer extension products are detected using mass spectrometry
  • the present invention extends to high-throughput forms of primer extension analysis, such as, for example, minisequencing (Sy Vamen et al, Genomics 9: 341- 342, 1995).
  • a probe or primer or multiple probes or primers
  • a solid support e.g. a glass slide
  • a biological sample comprising nucleic acid is then brought into direct contact with the probe/s or primer/s, and a primer extension protocol performed with each of the free nucleotide bases labeled with a different detectable marker.
  • the nucleotide present at a SNP or a number of SNPs is then determined by determining the detectable marker bound to each probe and/or primer.
  • LNA and PNA molecules Fluorescently labeled locked nucleic acid (LNA) molecules or fluorescently labeled protein-nucleic acid (PNA) molecules are useful for the detection of SNPs (as described in Simeonov and Nikiforov, Nucleic Acids Research, 30(17): 1-5, 2002).
  • LNA and PNA molecules bind, with high affinity, to nucleic acid, in particular, DNA.
  • Flurophores in particular, rhodomine or hexachlorofluorescein conjugated to the LNA or PNA probe fluoresce at a significantly greater level upon hybridization of the probe to target nucleic acid compared to a probe that has not hybridized to a target nucleic acid.
  • the level of increase of fluorescence is not enhanced to the same level when even a single nucleotide mismatch occurs. Accordingly, the degree of fluorescence detected in a sample is indicative of the presence of a mismatch between the LNA or PNA probe and the target nucleic acid, such as, in the presence of a SNP.
  • fluorescently labeled LNA or PNA technology is used to detect a single base change in a nucleic acid that has been previously amplified using, for example, an amplification method described supra.
  • LNA or PNA detection technology is amenable to a high-throughput detection of one or more markers immobilizing an LNA or PNA probe to a solid support, as described in Oram et al., CUn. Chem. 45: 1898-1905, 1999.
  • Molecular Beacons are useful for detecting SNPs directly in a sample or in an amplified product (see, for example, Mhlang and Malmberg, Methods 25: A ⁇ 2s-Al ⁇ , 2001).
  • Molecular beacons are single stranded nucleic acid molecules with a stem-and- loop structure.
  • the loop structure is complementary to the region surrounding the SNP of interest.
  • the stem structure is formed by annealing two "arms" complementary to each other, that are on either side of the probe (loop).
  • a fluorescent moiety is bound to one arm and a quenching moiety that suppresses any detectable fluorescence when the molecular beacon is not bound to a target sequence bound to the other arm.
  • the arms Upon binding of the loop region to its target nucleic acid the arms are separated and fluorescence is detectable. However, even a single base mismatch significantly alters the level of fluorescence detected in a sample. Accordingly, the presence or absence of a particular base at the site of a SNP is determined by the level of fluorescence detected.
  • a single nucleotide polymorphism is identified or detected by hybridization to nucleic acid arrays, an example of which are described in WO 95/11995.
  • WO 95/11995 also describes subarrays that are optimized for detection of a variant form of a precharacterized polymorphisms.
  • Such a subarray contains probes designed to be complementary to a second reference sequence, which is an allelic variant of the first reference sequence.
  • the second group of probes is designed by the same principles, except that the probes exhibit complementarity to the second reference sequence.
  • a second group (or further groups) can be particularly useful for analyzing short subsequences of the primary reference sequence in which multiple mutations are expected to occur within a short distance commensurate with the length of the probes (e.g., two or more mutations within 9 to 21 bases).
  • the present invention encompasses other methods of detecting a SNP that is associated with NFI, such as, for example, SNP microarrays (available from Affymetrix, or described, for example, in US 6,468,743 or Hacia et al, Nature Genetics, 14: 441, 1996), Taqman assays (as described in Livak et al, Nature Genetics, 9: 341-342, 1995), solid phase minisequencing (as described in Syvamen et al, Genomics, 13: 1008-1017, 1992), minisequencing with FRET (as described in Chen and Kwok , Nucleic Acids Res. 25: 347-353, 1997) or pyrominisequencing (as reviewed in Landegren et al, Genome Res., 8(8): 169-11 ⁇ , 1998).
  • SNP microarrays available from Affymetrix, or described, for example, in US 6,468,743 or Hacia et al, Nature Genetics, 14: 44
  • polymorphism or marker occurs in a region of nucleic acid that encodes RNA
  • said polymorphism or marker is detected using a method such as, for example, RT-PCR, NASBA or TMA.
  • RT-PCR Methods of RT-PCR are known in the art and described, for example, in Dieffenbach (ed) and Dveksler (ed) ⁇ In: PCR Primer: A Laboratory Manual, Cold Spring Harbour Laboratories, NY, 1995).
  • Methods of TMA or self-sustained sequence replication use two or more oligonucleotides that flank a target sequence, a RNA polymerase, RNase H and a reverse transcriptase.
  • One oligonucleotide (that also comprises a RNA polymerase binding site) hybridizes to an RNA molecule that comprises the target sequence and the reverse transcriptase produces cDNA copy of this region.
  • RNase H is used to digest the RNA in the RNA-DNA complex, and the second oligonucleotide used to produce a copy of the cDNA.
  • the RNA polymerase is then used to produce a RNA copy of the cDNA, and the process repeated.
  • NASBA systems relies on the simultaneous activity of three enzymes (a reverse transcriptase, RNase H and RNA polymerase) to selectively amplify target mRNA sequences.
  • the mRNA template is transcribed to cDNA by reverse transcription using an oligonucleotide that hybridizes to the target sequence and comprises a RNA polymerase binding site at its 5' end.
  • the template RNA is digested with RNase H and double stranded DNA is synthesized.
  • the RNA polymerase then produces multiple RNA copies of the cDNA and the process is repeated.
  • the hybridization to and/or amplification of a marker feeding efficiency using any of these methods is detectable using, for example, electrophoresis and/or mass spectrometry.
  • one or more of the probes/primers and/or one or more of the nucleotides used in an amplification reactions may be labeled with a detectable marker to facilitate rapid detection of a marker, for example, a fluorescent label (e.g. Cy5 or Cy3) or a radioisotope (e.g. 32 P).
  • amplification of a nucleic acid may be continuously monitored using a melting curve analysis method, such as that described in, for example, US 6,174,670. Such methods are suited to determining the level of an alternative splice form in a biological sample.
  • the method of the present invention provides a useful screen to identify animals that are likely to have a NFI of interest (e.g., a negative NFI).
  • a NFI of interest e.g., a negative NFI
  • an animal identified by the method of the present invention as likely having an NFI of interest is tested to determine its NFI.
  • y is daily feed intake (e.g., dry matter)
  • ⁇ 0 is the regression intercept
  • ⁇ i is the partial regression of daily intake on average daily gain (ADG)
  • ⁇ 2 is the partial regression of daily intake on body weight (WT).
  • the weight of the 5 animal is expressed as average or midweight on test, and may further be transformed to a so-called metabolic equivalent by raising midweight to the power of 0.75 or 0.73.
  • NFI ⁇ N(O, ⁇ «f') 10. property (i.e., NFI ⁇ N(O, ⁇ «f')) showing that NFI has zero mean.
  • Properties of linear regression can be used to show that NFI is independent of the partial regression terms in the estimation model including both ADG and (metabolic) body weight. Efficient animals (i.e., with NFI values below zero) have daily intakes less than would be predicted given their own level of production and body weight, whereas the converse
  • the method of the invention provides the means for selecting and/or producing an animal having
  • a method for determining the feeding efficiency or FCE of an animal as described herein in respect of any embodiment of the invention is used to test an animal or a plurality of animals and that or those animals comprising one or more markers associated with negative NFI are selected. Such an animal may then be used, for example, for breeding, e.g., to produce
  • the method of the invention is used to screen the likelihood of a calf having improved feeding efficiency. Those calves having improved feeding
  • animals having improved feeding efficiency also reduces the cost associated with breeding animals. For example, as animals consume less feed, they may be maintained, for example, in the same pasture for a longer period of time than animals having average or positive NFI values.
  • an animal having improved feeding efficiency is selected using a method of the invention for breeding. Such an animal may then be mated with, for example, an unselected animal to thereby produce offspring, some of which may have improved feeding efficiency.
  • the selected animal is mated with an animal that has been shown to have a improved feeding efficiency (e.g., screened using a method of the invention). In this manner, the likelihood of offspring produced from this mating having improved feeding efficiency is increased.
  • a improved feeding efficiency e.g., screened using a method of the invention.
  • the mated animals may comprise the same one or more markers associated with negative NFI of the invention. Such a mating will then produce offspring animals comprising that or those markers thereby increasing the probability of the offspring having negative NFI.
  • the mated animals comprise different markers associated with negative NFI of the invention. Such a mating will then produce offspring comprising one or more of the markers of the invention from one or both of the parent animals.
  • the selected animals may be used to produce offspring using, for example, in vitro fertilization.
  • ova are harvested from a cow comprising one or more markers associated with negative NFI of the invention by, for example, by transvaginal ovum pick-up (OPU) or by laparoscopic aspiration.
  • OOU transvaginal ovum pick-up
  • the recovered ovum are then matured prior to fertilization using, for example, sperm recovered from a bull comprising one or more markers associated with negative NFI of the invention.
  • Zygotes are then cultured for a time and under conditions suitable for embryo development. For example, zygotes are cultured in a ligated oviduct of a temporary recipient (sheep or rabbit). Alternatively, zygotes are co-cultured in vitro with somatic cells (e.g., oviduct epithelial cells, granulosa cells, etc.) in a defined medium.
  • somatic cells e.g., oviduct epi
  • zygotes are cultured in vitro in a simple medium such as synthetic oviductal fluid without any somatic cell support.
  • one or more cells is/are isolated there from and screened, for example, using the method of the invention to determine feeding efficiency of the embryo.
  • An embryo having or likely to have a improved feeding efficiency is then selected and implanted into a suitable recipient. In this manner, animals having or likely to have improved feeding efficiency are produced.
  • the method described supra is amenable to screening embryos produced using any assisted breeding technology and/or for screening embryos produced using an ovum and/or sperm from an animal that has net been screened using the method of the invention.
  • Each of the methods described supra are useful, for example, for breeding animals to thereby reduce the average feeding efficiency of a herd or group of animals and/or to produce a herd or group of animals having improved feeding efficiency.
  • Such animals are useful for reducing the costs associated with feeding and, as a consequence, the cost of producing, for example, meat for consumption.
  • the present inventors have also identified a large number of markers that are associated with positive NFI. Such a marker is useful, for example, for selecting against an animal having or likely to have an reduced or poor feeding efficiency. For example, such an animal may be selected to prevent it from breeding.
  • an animal is additionally screened, for example, to identify the presence of a marker associated with a further desirable characteristic.
  • the animal may be screened to detect a marker associated with increased marbling and/or increased meat tenderness.
  • an animal is screened for an allele of the calpastatin gene that is associated with improved tenderness and/or marbling in meat (e.g., as described in Ciobanu et al, J. Anim. ScI 52:2829-2839, 2004 and Barandse et al, Beef Quality CRC Marbling Symposium, Coffs Harbour pp. 52-57, 2001).
  • the allele(s) are detected using the commercially available GeneSTAR assay from Genetic Solutions (Queensland, Australia).
  • the present invention provides the means for selecting an animal capable of producing meat with improved quality and improved feeding efficiency. Such an animal will produced improved meat at a lower cost than an animal with increased or average NFI.
  • the inventors have developed an assay for determining genotypes associated with improved feed conversion in beef cattle by genotyping selected cattle using single nucleotide polymorphisms (SNPs) and estimating the effect of the SNPs on net feed intake (NFI).
  • SNPs single nucleotide polymorphisms
  • NFI net feed intake
  • the inventors selected animals from a beef research project based at Trangie Agricultural Research Centre in NSW, Australia. All animals were Angus breed with sire and dam pedigree records, and from 1993 to 2000 had been selected for high or low post-weaning feed efficiency, or were part of a control herd. The selection criteria used are described by Arthur et al (Proceedings of the Australian Society of Animal Production 27:107-110, 1996). The inventors performed the feed efficiency test on these cattle essentially as described by Arthur et al (Journal of Animal Science 79(11): 2805-2811, 2001). Expected feed intake of animals was calculated by using all the data to model feed intake on metabolic weight and average daily gain in a linear regression.
  • the inventors then selected approximately equal numbers of the extreme highest and lowest feed efficiency animals for SNP genotyping. Care was taken to ensure that, where possible, animals were in half sib-groups of 2 or more and not exceeding 10, so at least 30 sire groups were sampled from. Also where possible, half sibs groups were chosen so that they represented both ends of the feed efficiency distribution. A total of 225 animals were selected in this way, and where available, their sire and/or dam DNA was also submitted for SNP genotyping, to increase the accuracy of haplotyping. This resulted in the selection of 379 animals. The inventors prepared DNA from these 379 animals and submitted the DNA for SNP genotyping.
  • DNA was extracted from ImI of Blood using the Puregene® Genomic DNA Extraction Kit for Blood (Gentra Systems, Inc., Minneapolis MN, USA). DNA samples were quantified using PicoGreen® nucleic acid stain and fluorometer (Turner BioSystems Inc., Sunnyvale, CA, USA). All samples were diluted to 30ng/ul and lOul aliquoted into 96 well plates. Plates were stored at -2O 0 C until assayed. Genotyping was performed by ParAllele BioScience Inc. on each of the DNA samples using an array of 9323 SNPs, randomly distributed across the bovine genome. Data set preparation
  • genotyping and pedigree errors were removed from the data by using the pedigree structure of the population to check for Mendelian segregation. Thus, all suspected pedigree and genotyping errors were removed.
  • the inventors then estimated the effect of each of the 8326 polymorphic SNPs on NFI. These analyses were performed by ASREML (Gilmour et. at, NSW Agriculture Biometric Bulletin, 5:210) using the following model:
  • NFIhij k i ⁇ + contempary group h + start ageic + allel ⁇ i + allel ⁇ j + animalk + eyki
  • NFI h i jkh the phenotypic record for net food intake for "animal k " with SNP alleles "i” and "j”
  • ⁇ is a fixed effect of the mean
  • contempary group h is defined as "all animals from the same herd
  • start ag ⁇ k was the age at which animal "k” began the NFI test, and was fitted as a covariate.
  • the effects of animal and SNP alleles were treated as random effects, with the following (co) variance matrix: allele ⁇ allele */ 0 0
  • Table 1 shows a list of 124 SNPs showing significant associations with NFI.
  • the inventors have identified 124 statistically significant SNP genotypes associated with NFI, thereby influencing feed conversion efficiency in beef cattle, as described in Example 1.
  • the inventors have determined the haplotypes and mapped the position of a subset of these SNPs to the bovine genome.
  • the inventors determined the physical location of 99 SNPs relative to each other on the bovine genome by taking advantage of both the ongoing bovine genome sequencing project (Human Genome Sequencing Center, Baylor College of Medicine) and the high degree of synteny between the bovine and human genomes (e.g. Gautier et al, Mamm. Genome, 14:111-121, 2003). From the bovine genome sequencing project, 250 bases of sequence to the left and 250 bases of sequence to the right of each SNP genotyped was available. The inventors used these 500 bases of sequence to determine the contig (bovine genome build 1.1) to which each SNP belonged, using BLASTN tool from the National Center for Biotechnology Information (NCBI, Bethesda, MD). The inventors then took these bovine contigs and positioned them on the sequenced human genome using the Human Genome Resources of NCBI (Bethedsa, MD).
  • NCBI National Center for Biotechnology Information
  • the inventors determined which of the 99 significant SNPs showed correlations between their alleles with respect to linkage disequilibrium. High levels of linkage disequilbrium are indicative of physical linkage which can be represented by the r 2 parameter (Hill and Robertson, Theor. Appl. Genet. 38:226-231 1968).
  • the inventors used the Idmax procedure of the GOLD program from the Genome- Wide Linkage Disequilibrium Project (University of Oxford, UK) to calculate the r 2 measure of linkage disequilbrium between all possible pairs of the 99 loci.
  • the Idmax procedure uses the algorithm of Slatkin and Excoffier (MoI. Biol. Evol 12:921-921, 1995) to calcuate r 2 for pairs of loci from genotype data.
  • the SNP pairs with r 2 levels > 0.25 were extracted from the output.
  • the authors then grouped the pairs of SNPs into "clusters", where r 2 between all loci in the cluster was >0.25.
  • r 2 between all loci in the cluster was >0.25.
  • 55 pairs had an r 2 value of greater than 0.25.
  • These 55 pairs of SNPs were grouped into 21 clusters, based on their r 2 value as shown in Table 3. From the data it was found that the clusters generally consisted of between 2 and 4 SNPs.
  • the inventors then compared the physical location of the SNPs on the human genome to the clustering results.
  • the human chromosome position of each SNP was plotted vs its test statistic as shown in Figures 2a-2o. Pairs of adjacent SNPs (within 1 megabase) which had r 2 values >0.25 and thus belonged to clusters were identified. These pairs are indicated by closed squares on the graphs shown in Figures 2a-2o. Twenty of the 21 clusters from the r 2 data contained SNPs that had physical locations, when mapped to the human genome, which were within a megabase ( Figures 2a-2o). Haplotype construction
  • haplotypes of the SNPs within the cluster by extracting the genotypes of the SNPs from the data and using the PHASE program (Stephens et al, Am. J. of Human Genet. 55:978-989 2001). Using this program, both the haplotypes in the data and the most likely haplotype pair was determined for each animal. When the SNP data were sorted into haplotypes using this program, there were between 2 and 8 haplotypes per cluster as shown in Table 4 and/or Table 5. Estimation of haplotype effects
  • NFIhijki ⁇ + contempary grouph + start age + haplotypei + haplotypej + animalk + ⁇ yki
  • the parameter "NFI h ijk h " is the phenotypic record for net food intake for "animal k " with haplotypes "i” and "j” representing haplotypes calculated by the PHASE program and the most likely haplotype pairs
  • the parameter " ⁇ ” is a fixed effect of the mean
  • "contemporary grouph” is defined as "all animals from the same herd
  • the inventors then performed a likelihood ratio test to evaluate if the haplotypes had significant effects on NFI.
  • This test was performed as follows: let “L 0 " be the likelihood value for the model under "H 0 ", where the haplotype is not included in the model; then “L 1 " is the likelihood value for the alternative model, that is, the haplotype is included in the model; the test statistic was then defined as ⁇ n o ⁇ in i) an( j this equation was used to determine the haplotype test statistic of the cluster.
  • haplotype 3 of cluster 1 on chromosome 5 The largest favourable effect of a haplotype on NFI was for haplotype 3 of cluster 1 on chromosome 5, with an effect of -0.693 kg, which is a large effect considering the phenotypes of the animals in the data set for NFI ranged from -4.41 kg to 3.13kg.
  • identical-by-descent chromosome segments carrying genetic markers can be identified in the current population by unique haplotypes of SNP alleles.
  • a haplotype of SNPs is more likely to identify these identical-by-descent chromosome segments uniquely than a single SNP.
  • the results shown in this example reflect this.
  • the effect of the haplotypes, as measured by the test statistic were considerably more significant than the effect of the individual SNPs comprising the haplotypes.
  • the haplotypes of cluster 2 on chromosome 12 have a test statistic of 33.5, while the maximum significance value of an individual SNP within this cluster is 25.2.
  • SEQ ID NO. SNP data
  • SNP list SNP statistic, SNP allele
  • haplotype allele data haplotype, haplotype test statistic, haplotype alleles, haplotype frequencies and haplotype effects on NFI
  • SEQ ED NO. Sequence cross-references (SEQ ED NO.), SNP data (SNP list; SNP statistic, SNP allele) and haplotype allele data (haplotype, haplotype test statistic, haplotype alleles, haplotype frequencies and haplotype effects on NFI) for bovine alleles described herein; and start and stop positions of clusters of bovine haplotypes on bovine chromosomes.
  • DNA samples are genotyped using a microarray of the 99 significant SNPs to determine which of the SNPs are present in the Jersey/Limousin herd.
  • the effect(s) of the SNPs present in the Jersey/Limousin herd on NFI is determined.
  • the allele effects of each of the SNPs are determined essentially as described in Example 1.
  • the haplotype effect for the SNPs present in the Jersey/Limousin herd is determined.
  • the haplotype effect and test statistic is determined essentially as described in Example 2.
  • Example 4 The data identified from this Example using the Jersey/Limousin cross are preferably compared to the data obtained from the Angus herd of Example 1 and Example 2. AU significant SNPs of single haplotypes and clustered haplotypes that have a negative NFI effect are identified for use as a marker for screening other herds. EXAMPLE 4
  • DNA samples are preferably genotyped using a PCR based test of the 99 significant SNPs identified in Angus beef, to determine which of these SNPs are also present in the Jersey/Limousin herd.
  • primers are designed using the known 250 bp of sequence upstream and 250 bp of sequence downstream of each of the 99 SNPs. Primer design is performed using software, such as, for example, OligoPerfectTM Designer (Invitrogen Corporation). The PCR reaction is performed by standard methods using the following reaction:
  • genomic DNA MgCl 2 0.5 ⁇ l genomic DNA MgCl 2 is included in each reaction. The concentration OfMgCl 2 is determined for each reaction.
  • Samples are cycled in a thermocycler using standard conditions determined for each primer pair, such as, for example, 5 minutes at 95 0 C; 39 cycles of [94 0 C for 30 seconds, 62 0 C for 30 seconds, 72 0 C for 2 minutes], 5 minutes at 72 0 C.
  • the sequence at the position of each SNP is then determined using heat dissociation analysis. Essentially this method comprises adding 2x SYBR® Green 1 Master mix (Applied Biosystems) to the PCR following completion of initial thermal cycling. The reactions are then cycled at 95°C for 15 sees, 60 0 C for 20 sees, with the temperature increasing gradually from 60°C to 9O 0 C and the melting dissociation trace analyzed using the ABI Prism 7700HT Sequence Detection System.
  • nucleic acid from a sample known to be homozygous for either form of the SNP is included.
  • a sample known to be heterozygous for each form of the SNP is also included where possible.
  • Each control is then used to produce a heat dissociation curve to thereby determine the allele present in each test sample.
  • the inventors estimate the haplotype effect for the SNPs present in the Jersey/Limousin herd.
  • the haplotype effect and test statistic is determined essentially as described in Example 2.
  • the data identified from this Example using the Jersey/Limousin cross are preferably compared to the data obtained from the Angus herd of Example 1 and Example 2.
  • AU significant SNPs of single haplotypes and clustered haplotypes that have an NFI effect less than -0.2 kg are identified for use as a marker for screening other herds.
  • SEQ ID NO: 59 SEQ ID NO: 10, SEQ ID NO: 8 and SEQ ID NO: 52 and a sequence comprising SEQ ID NO: 71, SEQ ID NO: 70, SEQ ID NO: 38 and SEQ ID NO: 50
  • SEQ ID NO: 96 SEQ ID NO: 79, SEQ ID NO: 78 and SEQ ID NO: 3 and a sequence comprising SEQ ID NO: 22 and SEQ ID NO: 60
  • SEQ ID NO: 35 SEQ ID NO: 12 and SEQ ID NO: 33 and a sequence comprising SEQ ID NO: 35, SEQ ID NO: 12 and SEQ ID NO: 33
  • SEQ ID NO: 35 SEQ ID NO: 12 and SEQ ID NO: 33 and a sequence comprising SEQ ID NO: 18, SEQ ID NO: 11, 88 and SEQ ID NO: 63
  • SEQ ID NO: 18 SEQ ID NO: 11, 88 and SEQ ID NO: 63 and a sequence comprising SEQ ID NO: 44, SEQ ID NO: 54 and SEQ ID NO: 87
  • SEQ ID NO: 44 SEQ ID NO: 54 and SEQ ID NO: 87 and a sequence comprising SEQ ID NO: 80, SEQ ID NO: 94 and SEQ ID NO: 28
  • SEQ ID NO: 17 SEQ ID NO: 97, SEQ ID NO: 98 and SEQ ID NO: 14 and a sequence comprising SEQ ID NO: 15, SEQ ID NO: 56 and SEQ ID NO: 90
  • SEQ ID NO: 15 SEQ ID NO: 56 and SEQ ID NO: 90 and a sequence comprising SEQ ID NO: 31 and SEQ ID NO: 1
  • SEQ ID NO: 29 SEQ ID NO: 27, SEQ ID NO: 26 and SEQ ID NO: 73 and a sequence comprising SEQ ID NO: 67 and SEQ ID NO: 16
  • SEQ ID NO: 96 SEQ ID NO: 79, SEQ ID NO: 78 and SEQ ID NO: 3 and a sequence comprising SEQ ID NO: 22 and SEQ ID NO: 60 and a sequence comprising SEQ ID NO: 35, SEQ ID NO: 12 and SEQ ID NO: 33
  • SEQ ID NO: 33 and a sequence comprising SEQ ID NO: 35, SEQ ID NO: 12 and SEQ ID NO: 33
  • SEQ ID NO: 18 SEQ ID NO: 11, 88 and SEQ ID NO: 63 and a sequence comprising SEQ ID NO: 44, SEQ ID NO: 54 and SEQ ID NO: 87 and a sequence comprising SEQ ID NO: 80, SEQ ID NO: 94 and SEQ ID NO: 28
  • SEQ ID NO: 17 SEQ ID NO: 97, SEQ ID NO: 98 and SEQ ID NO: 14 and a sequence comprising SEQ ID NO: 15, SEQ ID NO: 56 and SEQ ID NO: 90 and a sequence comprising SEQ ID NO: 31 and SEQ ID NO: 1
  • SEQ ID NO: 15 comprising SEQ ID NO: 15, SEQ ID NO: 56 and SEQ ID NO: 90 and a sequence comprising SEQ ID NO: 31 and SEQ ID NO: 1 and a sequence comprising SEQ ID NO: 29, SEQ ID NO: 27, SEQ ID NO: 26 and SEQ ID NO: 73

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Environmental Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Animal Behavior & Ethology (AREA)
  • Animal Husbandry (AREA)
  • Biodiversity & Conservation Biology (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne des polymorphismes nucléotidiques simples (SNP) associés à la prise alimentaire nette (NFI) d'un animal dans les positions 251 des séquences nucléotidiques de SEQ ID N° 1 à 124, ainsi que des séquences complémentaires et des fragments desdites séquences comprenant les SNP. Des coordonnées chromosomiques dans les régions synténiques du génome de chromosomes humains et bovins ont été affectées à plusieurs SNP en déséquilibre de liaison afin d'obtenir ainsi des segments chromosomiques contigus comprenant des groupes d'amas de SNP. La présente invention concerne également des acides nucléiques comprenant les SNP individuels, des amas de SNP, ainsi que des acides nucléiques complémentaires et s'hybridant à ceux-ci, et des procédés d'utilisation des acides nucléiques dans la détection et/ou la sélection et/ou l'élevage d'animaux ayant une efficacité de conversion alimentaire améliorée en tant que reproducteurs ou pour la production de viande.
PCT/AU2006/001842 2005-12-05 2006-12-05 Marqueurs de sélection pour la prise alimentaire nette WO2007065206A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US74239205P 2005-12-05 2005-12-05
US60/742,392 2005-12-05

Publications (1)

Publication Number Publication Date
WO2007065206A1 true WO2007065206A1 (fr) 2007-06-14

Family

ID=38122401

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/AU2006/001842 WO2007065206A1 (fr) 2005-12-05 2006-12-05 Marqueurs de sélection pour la prise alimentaire nette

Country Status (1)

Country Link
WO (1) WO2007065206A1 (fr)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110093406A (zh) * 2019-05-27 2019-08-06 新疆农业大学 一种盘羊及其杂交后代遗传基因研究方法
CN116334243A (zh) * 2023-03-21 2023-06-27 湖北省农业科学院畜牧兽医研究所 基于SASH1基因的猪繁殖性状相关的InDel分子标记、引物及应用
CN116397033A (zh) * 2023-03-23 2023-07-07 湖北省农业科学院畜牧兽医研究所 与猪繁殖性状基因nck1相关的snp分子标记、引物对及其应用
CN116790764A (zh) * 2023-06-30 2023-09-22 湖北省农业科学院畜牧兽医研究所 Atp11a基因中与公猪精液质量性状相关的snp分子标记、引物对及其应用

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003078651A2 (fr) * 2002-03-15 2003-09-25 Iowa State University Research Foundation, Inc. Alleles de hmga, et leur utilisation comme marqueurs genetiques pour controler la croissance, l'adiposite, la qualite de la viande et l'efficacite nutritionnelle

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003078651A2 (fr) * 2002-03-15 2003-09-25 Iowa State University Research Foundation, Inc. Alleles de hmga, et leur utilisation comme marqueurs genetiques pour controler la croissance, l'adiposite, la qualite de la viande et l'efficacite nutritionnelle

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
LIEFERS S.C. ET AL.: "Associations between Leptin Gene Polymorphisms and Production, Live Weight, Energy Balance, Feed Intake, and Fertility in Holstein Heifers", JOURNAL OF DAIRY SCIENCE, vol. 85, June 2002 (2002-06-01), pages 1633 - 1638, XP008072978 *
MURANI E. ET AL.: "Association of corticotropin-releasing hormone gene variation with performance and meat quality traits in commercial pig lines", ANIMAL GENETICS, vol. 37, October 2006 (2006-10-01), pages 509 - 512, XP003014233 *
NKRUMAH J.D. ET AL.: "Polymorphisms in the bovine leptin promoter associated with serum concentration, growth, feed intake, feeding behaviour, and measures of carcass merit", JOURNAL OF ANIMAL SCIENCE, vol. 83, no. 1, January 2005 (2005-01-01), pages 20 - 28, XP003014232 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110093406A (zh) * 2019-05-27 2019-08-06 新疆农业大学 一种盘羊及其杂交后代遗传基因研究方法
CN116334243A (zh) * 2023-03-21 2023-06-27 湖北省农业科学院畜牧兽医研究所 基于SASH1基因的猪繁殖性状相关的InDel分子标记、引物及应用
CN116397033A (zh) * 2023-03-23 2023-07-07 湖北省农业科学院畜牧兽医研究所 与猪繁殖性状基因nck1相关的snp分子标记、引物对及其应用
CN116790764A (zh) * 2023-06-30 2023-09-22 湖北省农业科学院畜牧兽医研究所 Atp11a基因中与公猪精液质量性状相关的snp分子标记、引物对及其应用

Similar Documents

Publication Publication Date Title
AU2010200649B2 (en) Leptin promoter polymorphisms and uses thereof
US20090269741A1 (en) Method for assessing traits selected from longissimus dorsi peak force, intramuscular fat, retail beef yield and net feed intake in bovine animals
WO1992013102A1 (fr) Marqueurs polymorphes d'adn utilises chez les bovins
CA3079473A1 (fr) Polymorphismes mononucleotidiques et efficacite d'alimentation chez le betail
WO2015187564A1 (fr) Marqueurs d'adn pour l'efficacité alimentaire chez le bétail
US20060172329A1 (en) DNA markers for cattle growth
CN113699246B (zh) 一种影响猪饲料转化效率性状的snp分子标记及其用途
US7972790B2 (en) STAT6 effects on livestock animal growth
CA2645861C (fr) Detection du gene de la letalite pour une meilleure fertilite chez les mammaliens
US6849401B1 (en) Methods for determining coat color genotypes in pigs
WO2007065206A1 (fr) Marqueurs de sélection pour la prise alimentaire nette
CA2600677A1 (fr) Association entre des marqueurs dans un gene de leptine et caracteristique de carcasse dans l'engraissement commercial de genisses et de boeufs
KR101796158B1 (ko) 돼지의 산자수 예측용 nat9 유전자의 snp 마커 및 이를 이용한 돼지 다산 개체 선발 방법
JP2013505003A (ja) 家畜のジェノタイピング方法
US20050059021A1 (en) Insulin-like growth factor-1 receptor (IGF-1R) polymorphic alleles and use of the same to identify DNA markers for reproductive longevity
CN116590433A (zh) 大白母猪繁殖性能的分子标记、引物、试剂盒、鉴定方法及应用
JP2007504841A (ja) 第１７染色体の量的形質遺伝子座の詳細マッピングおよびマーカー利用選別のためのその使用
US7074562B2 (en) Ghrelin alleles and use of the same for genetically typing animals
US20120183958A1 (en) Methods for predicting fat and lean phenotypes in chickens
US20150344952A1 (en) Dna markers for beef tenderness in cattle

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application
NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 06827993

Country of ref document: EP

Kind code of ref document: A1