Compositions, methods and systems for inferring bovine breed or trait

• US 7,709,206 B2
• Filed: 02/13/2008
• Issued: 05/04/2010
• 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), Metamorphix Incorporated
• Inventors: Holm, Tom, Rosenfeld, David, Bates, Stephen, DeNise, Sue K., Charteris, Paul
• Primary Examiner(s): Horlick; Kenneth R.
• Assistant Examiner(s): Thomas; David C
• Application Number:
  US12/069,845
• Publication Number:
  US 20080268454A1
• Time in Patent Office: 811 Days
• Field of Search: None
• US Class Current: 435/6.12
• 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 identifying a trait of a bovine subject from a nucleic acid sample of the bovine subject, comprising

identifying in the nucleic acid sample an occurrence of at least three single nucleotide polymorphisms (SNPs)

wherein the at least three SNPs are associated with the trait, and

wherein the at least three SNPs occur in more than one gene.

2. The method of claim 1, wherein occurrences of at least five single nucleotide polymorphisms (SNP) are identified.

3. The method of claim 1, wherein occurrences of at least seven single nucleotide polymorphisms (SNP) are identified.

4. The method of claim 1, wherein occurrences of at least ten single nucleotide polymorphisms (SNP) are identified.

5. The method of claim 1, wherein the nucleic acid sample comprises substantially the entire genome of the bovine subject.

6. The method of claim 1, wherein at least one additional SNP occurs in a non-coding region of the genome.

7. The method of claim 1, wherein the SNPs are identified in a whole genome association study.

8. The method of claim 1, wherein the trait is selected from the group consisting of marbling, tenderness, quality grade, yield 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, hide quality, susceptibility to buller syndrome, stress susceptibility and response, temperament, digestive capacity, production of calpain, production of calpastatin, production of myostatin, pattern of fat deposition, ribeye area, fertility, ovulation rate, conception rate, heat tolerance, environmental adaptability, robustness, susceptibility to infection with pathogens, and shedding of pathogens.

9. The method of claim 1, further comprising analyzing a hypermutable sequence in combination with identifying the occurrences of at least three SNP.

10. The method of claim 9, wherein the hypermutable sequence is a microsatellite nucleic acid sequence.

11. The method of claim 1, wherein at least one additional SNP is located in a target region within 500,000 nucleotides of a trait-associated SNP.

12. The method of claim 1, wherein the association is at a confidence interval of 0.01 or greater.

14. The method of claim 1 wherein the trait is selected from marbling, tenderness, fat thickness, retail yield, or average daily weight gain.

15. The method of claim 1 further comprising inferring if the bovine subject will have a trait value, based on the inferred trait associated with the at least 3 SNPs, that is greater than the 50^th percentile, or less than the 50^th percentile.

16. The method of claim 1 wherein the trait is marbling.

17. The method of claim 1 wherein the trait is tenderness.

18. The method of claim 1 wherein the trait is fat thickness.

19. The method of claim 1 wherein the trait is retail yield.

13. A method of inferring a trait, comprising hybridizing a nucleic acid sample from a bovine subject to a system wherein the hybridizing comprises:

a substrate; and

specific binding pair members corresponding to a series of at least three SNPs,

wherein the at least three SNPs are associated with a trait in the bovine subject, and

wherein the at least three SNPs occur in more than one gene,

where selective hybridization of the nucleic acid sample to the system indicates the presence of a SNP associated with a trait.

21. The method of claim 13 wherein the trait is marbling.

22. The method of claim 13 wherein the trait is tenderness.

23. The method of claim 13 wherein the trait is fat thickness.

24. The method of claim 13 wherein the trait is retail yield.

20. A method of inferring at least one trait in at least two bovine subjects comprising identifying in a nucleic acid sample from each bovine subject an occurrence of at least three single nucleotide polymorphisms (SNPs)

wherein the at least 3 SNPs are associated with the trait,

wherein the at least three SNPs occur in more than one gene and

sorting the at least two bovine subjects based on the inferred trait.