Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 9, 2005
Publication Date: September 1, 2005
Citation: Stone, R.T., Casas, E., Smith, T.P.L., Keele, J.W., Harhay, G.P., Bennett, G.L., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Snelling, W.M. 2005. Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map. Journal of Animal Science. 83:2280-2288. Interpretive Summary: We targeted a region of cattle chromosome 5 for SNP-based marker development where previous results suggested the presence of QTL affecting carcass and growth traits. These markers were genotyped in 574 steers and their sires representing seven of the most popular Bos taurus breeds in the U.S. Combinations of SNP segregating together, haplotypes, were associated with traits related to carcass fat and tenderness at separate locations on the chromosome. These data demonstrate that with low level marker coverage of a broad chromosomal region, associations between genotype and phenotype can be detected. In that these finding were based on a population consisting of seven breeds, it is plausible to assume that these associations between genotype and carcass traits can be verified in additional populations. Presently, these markers are being further evaluated in additional populations at MARC.
Technical Abstract: As genetic markers, single nucleotide polymorphisms (SNP) are well suited for development of genetic test for production traits in livestock. They are stable through many generations, and can provide direct assessment of individual animal’s genetic merit if they are in linkage disequilibrium and phase with functional genetic variation. Bovine chromosome 5 has been shown to harbor genetic variation affecting production traits in multiple cattle populations, thus, this chromosome was targeted for SNP-based marker development and subsequent association analysis with carcass and growth phenotypes. Discovery of SNP was preformed in a panel of 16 sires representing two sires from each of seven beef breeds and two Holstein sires by PCR amplification and sequencing using primers designed from genomic sequence obtained by low-coverage sequencing of bacterial artificial chromosome (BAC) clones. From 550 SNP, 296 (54%) were tentatively identified as having a minor allele frequency > 10%. Forty-five SNP derived from 15 BACs were chosen based on minor allele frequency and were genotyped in 574 steers and their sires. Production and carcass data were collected on the steers as a part of the Germplasm Evaluation, Cycle VII Project at the U.S. Meat Animal Research Center (Clay Center, NE) which involves the evaluation of sires from seven of the most popular U.S. breeds. Haplotypes based on seven SNP derived from a BAC containing the bovine genes HEM1 and PDE1B were associated with traits related to carcass fat. Steers homozygous for the major haplotype had 0.15 ± 0.04 cm less subcutaneous fat, 0.57 ± 0.18 kg less rib fat, 0.18 ± 0.07 lower yield grade, 1.11 ± 0.35% less predicted fat yield and 0.79 ± 0.3% greater predicted retail product yield compared to heterozygotes. The frequency of the major haplotype was 0.86 in the steers and ranged from 0.44 (Limousin) to 0.98 (Simmental and Gelbvieh) in a panel consisting of an average of 20 purebred sires from each of the seven breeds. A second set of haplotypes based on four SNP derived from a BAC containing the genes NOL1 and CHD4 was associated with Warner-Bratzler shear force. Steers homozygous for the major haplotype had 0.27 ± 0.11 kg greater shear force than those heterozygous for the major haplotype and one of two minor haplotypes. The frequency of the major haplotype was 0.63 in the steers and ranged from 0.27 (Hereford) to about 0.95 (Angus and Red Angus) in the panel of purebred sires. These results demonstrate the feasibility of targeting QTL regions for SNP-based marker development and that a low level of coverage can identify markers associated with phenotypic traits.