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

• US 7,972,783 B2
• Filed: 11/17/2006
• Issued: 07/05/2011
• Est. Priority Date: 11/24/2003
• Status: Active Grant

• Current Assignee: Igenity Inc.
• Original Assignee: Branhaven LLC
• Inventors: Ferrie, Bonita, Chevalier, Philip, Hutton, Michelle, Oberg, Emily, DeNise, Sue, Rosenfeld, David, Kerr, Richard
• Primary Examiner(s): KAPUSHOC, STEPHEN THOMAS
• Application Number:
  US11/601,433
• Publication Number:
  US 20070134701A1
• Time in Patent Office: 1,691 Days
• Field of Search: None
• US Class Current: 435/6.11
• 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 determining a polled genotype in a bovine subject comprising:

a) detecting in a nucleic acid sample isolated from the bovine subject, an AAT haplotype indicative of the polled phenotype, wherein the AAT haplotype comprises an A at position 300 of SEQ ID NO;

53 (marker MMBT25287), an A at position 300 of SEQ ID NO;

59 (marker MMBT25303), and a T at position 300 of SEQ ID NO;

52 (marker MMBT25281),

wherein detection of the AAT haplotype is indicative of a polled genotype in the bovine subject.

2. The method of claim 1 wherein step a) further comprises measurement of a nucleotide occurrence of SNPs at position 300 of SEQ ID NO:

63 (marker MMBT25316), SEQ ID NO;

62 (marker MMBT25314), and SEQ ID NO;

61 (marker MMBT25313).

3. The method of claim 1 wherein step a) further comprises measurement of a nucleotide occurrence of SNPs at position 300 of SEQ ID NO:

63 (marker MMBT25316), SEQ ID NO;

62 (marker MMBT25314), SEQ ID NO;

61 (marker MMBT25313), SEQ ID NO;

50 (marker MMBT10493), and SEQ ID NO;

64 (marker MMBT25986).

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

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

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

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

8. The method of claim 2 wherein the haplotype is associated with a polled phenotype and is selected from:

AATGGG, AATGGC, AATCAC, or AATCGC in a nucleic acid sample from the subject

wherein the sequence of letters of the haplotype represent the nucleotide occurrence of a single nucleotide polymorphism corresponding to nucleotide position 300 of SEQ ID NO;

53 (marker MMBT25287), SEQ ID NO;

59 (marker MMBT25303), SEQ ID NO;

52 (marker MMBT25281), SEQ ID NO;

63 (marker MMBT25316), SEQ ID NO;

62 (marker MMBT25314), and SEQ ID NO;

61 (marker MMBT25313) respectively.

9. The method of claim 3 further comprising detecting a polled haplotype selected from:

AATCACGG, AATCACGG, AATGACGG, AATGGGAG, AATCGCGT, AATCGCGG, AATGGCGT, AATGGCGG, AATGGGGG AATGGGGT, AATCACAT, AATCGGGG, AATCGGGT or AATCGCAG in a nucleic acid sample from the subject

wherein the sequence of letters of the haplotype represent the nucleotide occurrence of a single nucleotide polymorphism corresponding to nucleotide position 300 of SEQ ID NO;

53 (marker MMBT25287), SEQ ID NO;

59 (marker MMBT25303), SEQ ID NO;

52 (marker MMBT25281), SEQ ID NO;

63 (marker MMBT25316), SEQ ID NO;

62 (marker MMBT25314), SEQ ID NO;

61 (marker MMBT25313), SEQ ID NO;

50 (marker MMBT10493), and SEQ ID NO;

64 (marker MMBT25986) respectively.

10. The method of claim 8, comprising detecting a diploid pair of haplotype alleles.

11. The method of claim 8, wherein the bovine subject is a member of a breed selected from Angus, Charolais, Gelbvieh, Hereford, Limousin, or Simmental.

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

13. The method of claim 11, wherein the bovine subject is a member of a breed raised for beef and milk production.