Method and markers for determining the genotype of horned/polled cattle

• US 20070134701A1
• Filed: 11/17/2006
• Published: 06/14/2007
• Est. Priority Date: 11/24/2003
• Status: Active Grant

• Current Assignee: Igenity Inc.
• Original Assignee: Branhaven LLC
• Inventors: Rosenfeld, David, Ferrie, Bonita, Chevalier, Philip, Hutton, Michelle, Kerr, Richard, Oberg, Emily, DeNise, Sue
• Granted Patent: US 7,972,783 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 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 2600/172 Haplotypes
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

Provided herein are methods to discover and use single nucleotide polymorphisms (SNP) for determining the genotype of a horned/polled ruminant subject. The present invention further provides specific nucleic acid sequences, SNPs, and SNP patterns that can be used for determining the genotype of a horned/polled ruminant subject.

Claims

1. A method for identifying the polled phenotype in a bovine subject, comprising detecting a dominant polled haplotype allele in a nucleic acid sample from the subject selected from:

2. The method of claim 1, comprising detecting a diploid pair of haplotype alleles.

3. The method of claim 1, wherein the bovine subject is a member of a breed selected from Angus, Charolais, Gelbvieh, Hereford, Limousin, or Simmental.

4. The method of claim 1, wherein the bovine subject is a member of a breed raised for beef production.

5. The method of claim 4, wherein the bovine subject is a member of a breed raised for beef and milk production.

13. The method of claim 1, 6, or 10, wherein the nucleic acid sample is isolated from a tissue or bodily fluid.

14. The method of claim 1, 6, or 10, wherein the nucleic acid sample comprises DNA.

15. The method of claim 14, wherein the DNA is genomic DNA.

6. A method for identifying the horned phenotype in a bovine subject, comprising:

detecting a pair of recessive horned haplotype alleles in a nucleic acid sample from the subject, wherein each haplotype allele is independently selected from;

7. The method of claim 6, wherein the bovine subject is a member of a breed selected from Charolais, Gelbvieh, Hereford, Limousin, or Simmental.

8. The method of claim 6, wherein the bovine subject is a member of a breed raised for beef production.

9. The method of claim 8, wherein the bovine subject is a member of a breed raised for beef and milk production.

10. A method for identifying the polled phenotype in a bovine subject:

a. detecting a GATCGG haplotype allele in a nucleic acid sample from the subject, wherein the sequence of letters of the haplotype allele represent the nucleotide occurrence of a single nucleotide polymorphism corresponding to nucleotide position 300 of SEQ ID NOs;

53 (marker MMBT25287), 59 (marker MMBT25303), 52 (marker MMBT25281), 63 (marker MMBT25316), 62 (marker MMBT25314), and 61 (marker MMBT25313) respectively; and

b. detecting the GATCGG haplotype in a nucleic acid sample from at least one polled parent of the subject.

11. The method of claim 10, wherein the bovine subject is a dairy animal.

12. The method of claim 10, where the bovine subject is a member of a breed selected from Limousin, Jersey, or Holstein.

16. A method for identifying a haplotype allele associated with a horned phenotype in a bovine subject comprising

a. determining a haplotype in at least one allele of at least one horned bovine subject, wherein the haplotype allele comprises the nucleotide occurrence of a nucleotide polymorphism corresponding to nucleotide position 300 of each of SEQ ID NOs:

53, 59, 52, 63, 62, and 61,

b. thereby, identifying a haplotype allele associated the horned phenotype in a bovine subject.

17. The method of claim 16, wherein the haplotype of both alleles is detected.

18. The method of claim 17, wherein the haplotypes of each allele of the bovine subject is different, and thereby two haplotype alleles associated with the horned phenotype are detected

19. A method for identifying a haplotype allele associated with a polled phenotype in a bovine subject comprising:

a. detecting the nucleotide occurrence of single nucleotide polymorphisms corresponding to nucleotide position 300 of each of SEQ ID NOs;

53, 59, 52, 63, 62, and 61, in both first and second alleles of a first bovine subject, wherein the first subject displays the polled phenotype;

b. identifying the horned or polled phenotype of a second bovine subject, wherein the second subject is homozygous for the first haplotype allele identified in step a, wherein a polled phenotype of the second subject identifies the first haplotype allele as a haplotype allele associated with the polled phenotype, and wherein a horned phenotype of the second subject identifies the second haplotype allele as a haplotype allele associated with the polled phenotype,

thereby, identifying a haplotype allele associated the polled phenotype in a bovine subject.

20. The method of claim 19, wherein the first and second alleles of the first bovine subject are the same.