Methods and systems for inferring bovine traits

• US 7,468,248 B2
• Filed: 12/31/2003
• Issued: 12/23/2008
• Est. Priority Date: 12/31/2002
• Status: Active Grant

• Current Assignee: Branhaven LLC, Cargill, Inc. (Agricultural Services Division)
• Original Assignee: Cargill, Inc. (Agricultural Services Division), MMI Genomics Incorporated (Neogen Corporation)
• Inventors: Fantin, Dennis, Holm, Tom, Rosenfeld, David, Bates, Stephen, DeNise, Sue K., Kerr, Richard
• Primary Examiner(s): Horlick; Kenneth R.
• Assistant Examiner(s): Thomas; David C
• Application Number:
  US10/750,623
• Publication Number:
  US 20050287531A1
• Time in Patent Office: 1,819 Days
• Field of Search: None
• US Class Current: 435/6.17
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 2600/124 Animal traits, i.e. production traits, including athletic performance or the like
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/172 Haplotypes
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Methods, compositions, and systems are provided for managing bovine subjects in order to maximize their individual potential performance and edible meat value, and to maximize profits obtained in marketing the bovine subjects. The methods and systems draw an inference of a trait of a bovine subject by determining the nucleotide occurrence of at least one bovine SNP that is identified herein as being associated with the trait. The inference is used in methods of the present invention to establish the economic value of a bovine subject, to improve profits related to selling beef from a bovine subject; to manage bovine subjects, to sort bovine subjects; to improve the genetics of a bovine population by selecting and breeding of bovine subjects, to clone a bovine subject with a specific trait, to track meat or another commercial product of a bovine subject; and to diagnose a health condition of a bovine subject. Methods are also disclosed for identifying additional SNPs associated with a trait, by using the associated SNPs identified herein.

Claims

1. A method for inferring a trait of a bovine subject from a nucleic acid sample of the bovine subject, comprising identifying in the nucleic acid sample, a nucleotide occurrence of a single nucleotide polymorphism (SNP) at position 300 of SEQ ID NO:

21645, thereby inferring the trait, wherein the trait is marbling, tenderness, fat thickness, red meat yield, or average daily weight gain.

2. The method of claim 1, wherein the nucleotide occurrence of at least 2 SNPs is determined to infer the trait, wherein one of the SNPs is at position 300 of SEQ ID NO:

21645 and the remaining SNP or SNPs are at position 300 of any of SEQ ID NO;

19473 to SEQ ID NO;

21644, or SEQ ID NO;

21646 to SEQ ID NO;

21982.

3. The method of claim 2, wherein the nucleotide occurrences of at least 2 SNPs comprise a haplotype allele, and wherein the method infers the trait using the identified haplotype allele.

4. The method of claim 2, wherein at least 2 SNPs are related by dominance and/or epistasis.

5. The method of claim 4, further comprising identifying a diploid pair of haplotype alleles and inferring the trait using the diploid pair of haplotype alleles.

6. The method of claim 2, wherein the remaining SNP or SNPs is associated with a trait selected from the group consisting of marbling, tenderness, quality grade, muscle content, fat thickness, feed efficiency, red meat yield, average daily weight gain, disease resistance, disease susceptibility, feed intake, protein content, bone content, maintenance energy requirement, mature size, amino acid profile, fatty acid profile, milk production, a milk quality susceptibility to the buller syndrome, stress susceptibility and response, temperament, digestive capacity, production of calpain, caplastatin and myostatin, pattern of fat deposition, ribeye area, fertility, ovulation rate, conception rate, and susceptibility to infection with and shedding of pathogens.

7. The method of claim 2, wherein the trait is fat thickness.

8. The method of claim 7, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with high fat thickness.

9. The method of claim 7, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low fat thickness.

10. The method of claim 2, wherein the trait is retail yield.

11. The method of claim 10, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with high retail yield.

12. The method of claim 10, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low retail yield.

13. The method of claim 2, wherein the trait is tenderness.

14. The method of claim 13, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with high tenderness.

15. The method of claim 13, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low tenderness.

16. The method of claim 2, wherein the trait is marbling.

17. The method of claim 16, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with more abundant marbling.

18. The method of claim 16, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with less abundant marbling.

19. The method of claim 2, wherein the trait is average daily gain.

20. The method of claim 19, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with a high daily gain.

21. The method of claim 19, wherein at least one SNP and at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low daily gain.

22. A method for determining a nucleotide occurrence of a polymorphism in a bovine sample, comprising:

a) contacting a bovine polynucleotide in the sample with an oligonucleotide that binds to a target region, wherein the target region comprises a position at position 300 of SEQ ID NO;

21645 or wherein the target region is within 3000 nucleotides of a nucleotide at position 300 of SEQ ID NO;

21645, and

b) determining the nucleotide occurrence of a single nucleotide polymorphism (SNP) at position 300 of SEQ ID NO;

21645, wherein the determination comprises analyzing binding of the oligonucleotide or detecting an amplification product generated using the oligonucleotide, thereby determining the nucleotide occurrence of the polymorphism.

23. The method of claim 22, wherein the oligonucleotide binds to a target sequence that comprises a single nucleotide polymorphism (SNP) at position 300 of SEQ ID NO:

21645 and the nucleotide occurrence is determined based on the binding of the oligonucleotide to the target sequence.

24. The method of claim 22, wherein the bovine polynucleotide is contacted with a pair of oligonucleotides that comprise a primer pair, and the nucleotide occurrence is determined using an amplification product generated using the primer pair.

25. The method of claim 22, wherein the terminal nucleotide of the oligonucleotide binds to the SNP.

26. The method of claim 24, wherein the polynucleotide is contacted with a pair of oligonucleotides each comprising a different detectable label.

27. The method of claim 26, wherein the terminal nucleotide of each oligonucleotide pair is complementary to a different nucleotide at position 300 of SEQ ID NO:

21645, or a complement thereof.

28. A method for identifying a bovine single nucleotide polymorphism (SNP) associated with a trait, comprising identifying a test SNP that is in disequilibrium with a SNP position at position 300 of SEQ ID NO:

21645.

29. The method of claim 28, wherein the test SNP is in a target region of a bovine genome, wherein the target region is within about 500,000 nucleotides from a SNP position at position 300 of SEQ ID NO:

21645.

30. The method of claim 29, wherein the target region consists of at least 20 contiguous nucleotides of SEQ ID NOS:

24493 to 64886.

31. The method of claim 29, wherein the target region consists of at least 20 contiguous nucleotides of SEQ ID NOS:

19473 to 21982.

32. The method of claim 28, wherein the trait is marbling, tenderness, quality grade, muscle content, fat thickness, feed efficiency, red meat yield, average daily weight gain, disease resistance, disease susceptibility, feed intake, protein content, bone content, maintenance energy requirement, mature size, amino acid profile, fatty acid profile, milk production, a milk quality susceptibility to the buller syndrome, stress susceptibility and response, temperament, digestive capacity, production of calpain, caplastatin and myostatin, pattern of fat deposition, ribeye area, fertility, ovulation rate, conception rate, or susceptibility to infection with and shedding of pathogens.

33. The method of claim 32, wherein the trait is fat thickness, retail yield, tenderness, marbling, or average daily gain.