Single nucleotide polymorphisms and feeding efficiency in cattle

2:

• The method of claim 1, wherein said SNPs comprise a panel of less than 250 SNPs.

3:

• The method of claim 1, wherein detecting comprises extracting and/or amplifying DNA from the sample and contacting the DNA with an array comprising at least one probe suitable for determining the identity of said allele at each of said one or more SNPs.

4:

• The method of claim 3, wherein the array is a DNA array, a DNA microarray or a bead array.

5:

• The method of claim 1, wherein said nucleic acid molecule is detected by amplifying a region of the nucleic acid sample using an oligonucleotide primer pair, to form nucleic acid amplification products comprising said one or more SNPs.

6:

• The method of claim 5, wherein at least one primer of said oligonucleotide primer pair comprises at least 10 contiguous sequences flanking said one or more SNPs.

7:

• A method of feeding Bos sp., the method comprising, obtaining a nucleic acid sample from at least one Bos sp. animal, detecting in the sample whether one or more single nucleotide polymorphisms (SNPs) identified in Table 8 in the first column labeled “NCBI_dpSNP_rs_ID” are present in said sample, and providing less feed to said bovine if there is present at least one of the first favorable alleles as identified in Table 8 in the column labelled “Alleles”.

8:

• A method of selection of one or more Bos sp. animals, the method comprising, obtaining a nucleic acid sample from a population of Bos sp. animal, detecting in the sample whether one or more single nucleotide polymorphism (SNP) identified in Table 2, 3, 4, 5, 11, 12 and/or in linkage disequilibrium with said one or more of SNPs, or a combination thereof are present in the sample, determining the breeding value of said population of Bos sp. animal and selecting at least one Bos sp. animal from said population if the breeding value exceeds the lowest 15% breeding value of the population of Bos sp. animals.

9:

• The method of claim 8, wherein said one or more animal is selected for breeding.

10:

• The method of claim 8, wherein said one or more animal is selected for meat production.

11:

• The method of claim 8, wherein said breeding value is determined by combining the estimate of allele substitution, or genotype, or additive and dominance effects, reported in any of Table 2, 3, 4, 5, 11 and/or 12 for any of said SNPs present in said animal.

12:

• The method of claim 1, wherein said SNPs are selected from one or a combination of the SNPs of Table 2.

13:

• The method of claim 1, wherein said SNPs comprise all of the SNPs of Table 2.

14:

• The method of claim 1, wherein said SNPs are selected from one or a combination of the SNPs of Table 11.

15:

• The method of claim 1, wherein said SNPs comprise all of the SNPs of Table 11.

16:

• The method of claim 1, wherein said SNPS are selected from one or a combination of the SNPs of Table 2 wherein both RFI and RFIf is reduced.

17:

• The method of claim 1, wherein said SNPs are selected from one or a combination of the SNPs of Table 8 associated with Average Daily Gain (ADG), Dry Matter Intake (DMI) or Midpoint Metabolic Weight (MMWT) or Residual Feed Intake (RFT) or Residual Feed Intake adjusted for backfat (RFIf) or backfat (BFat) a combination of ADG, DMI, MMWT, RFI, RFIf or Bfat.

18:

• The method of claim 17, wherein said SNPs are selected from one or a combination of the SNPs of Table 2, 11 or 12.

19:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 3.

20:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 3 associated with Residual Feed Intake adjusted for backfat RFI or Residual Feed Intake adjusted for backfat RFIf or both.

21:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 4.

22:

• The method of claim 1, wherein said one or more SNPs are selected from one or more of the SNPs of Table 4 associated with dry matter intake.

23:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 4 associated with average daily gain.

24:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 5.

25:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 5 associated with Backfat.

26:

• The method of claim 1, wherein said SNPs are selected from one or more of the SNPs of Table 8 and one or more of the SNPs identified in Table 13 under the heading “F-250 SNPs”.

27:

• The method of claim 1, wherein said SNPs comprise all of the SNPs of Table 13.

28:

• A kit comprising one or more of the SNPs of Table 8 or in linkage disequilibrium with said one or more SNPs.

29:

• The kit of claim 28, wherein said kit comprises less than 250 SNPs.

30:

• The kit of claim 28 wherein said kit comprises one or more of the SNPs of Table 2, 3, 4, 5, 8, 11 or 12.

31:

• The kit of claim 28, wherein said kit comprises one or more of the SNPs of Table 2.

32:

• The kit of claim 28 wherein said kit comprises all the SNPs of Table 2.

33:

• The kit of claim 28, wherein said kit comprises one or more of the SNPs of Table 11.

34:

• The kit of claim 28, wherein said kit comprises all of the SNPs of Table 11.

35:

• The kit of claim 28, wherein said kit comprises one of more of the SNPs of Table 12.

36:

• The kit of claim 28, wherein said kit comprises all of the SNPs of Table 12.

37:

• The kit of claim 28, wherein said SNPs are selected from one or more of the SNPs of Table 8 and one or more of the SNPs identified in Table 13 under the heading “F-250 SNPs”.

38:

• A method for determining feed efficiency in Bos sp., the method comprising producing a single nucleotide polymorphism (SNP) panel comprising 250 or less of said SNPs and genotyping a sample from at least one Bos sp. animal with said panel.

39:

• The method of claim 38, wherein said panel comprises 200 or less SNPs.

40:

• The method of claim 38, wherein said panel comprises 100 or less SNPs.

41:

• The method of claim 38, wherein said panel comprises 70 or less SNPs.

42:

• The method of claim 38, wherein said panel comprises 60 or less SNPs.

43:

• The method of claim 38, wherein said panel comprises 50 or less SNPs.

44:

• The method of claim 38, wherein said panel comprises 40 or less SNPs.

45:

• The method of claim 38, wherein said panel comprises one or more of the SNPs of Table 2, 3, 4, 5, 8, 11 or 12 or in linkage disequilibrium with said one or more SNPs.

46:

• The method of claim 45, wherein said panel comprises one or more of the SNPs of Table 8.

47:

• The method of claim 45, wherein said panel comprises one or more of the SNPs of Table 2.

48:

• The method of claim 45, wherein said panel comprises all of the SNPs of Table 2.

49:

• The method of claim 45, wherein said panel comprises one or more of the SNPs of Table 11.

50:

• The method of claim 45, wherein said panel comprises all of the SNPs of Table 11.

51:

• The method of claim 45, wherein said panel comprises one or more of the SNPs of Table 12.

52:

• The method of claim 45, wherein said SNPs are selected from one or more of the SNPs of Table 8 and one or more of the SNPs identified in Table 13 under the heading “F-250 SNPs”.

53:

• A method for determining feed efficiency in Bos sp., the method comprising identifying SNPs associated with feed efficiency traits in a population of Bos sp. animals and producing a single nucleotide polymorphism (SNP) panel comprising 250 or less of said SNPs and genotyping a sample from at least one Bos sp. animal with said panel.