Submitted to: Frontiers in Livestock Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/21/2012
Publication Date: 12/14/2012
Citation: Huang, Y., Maltecca, C., MacNeil, M.D., Alexander, L.J., Snelling, W.M., Cassady, J.P. 2012. Using 50 K single nucleotide polymorphisms to elucidate genomic architecture of line 1 Hereford cattle. Frontiers in Livestock Genomics. DOI: 10.3389/fgene.2012.00285. Interpretive Summary: Molecular genetic architecture of Miles City Line 1, a closed sub-population of Hereford cattle selected primarily for yearling weight since 1934, was characterized by comparison to cattle sampled from the general U.S. Hereford population, estimating effects of selection on Line 1 allele frequencies and examining effects of heterozygosity within Line 1. Cattle sampled from Line 1 and the U.S. Hereford population were genotyped for more than 54,000 single-nucleotide polymorphisms (SNP) across the bovine genome. Linkage disequilibrium, the association between SNP genotypes, was stronger in Line 1 than in the general U.S. Hereford population. Higher Line 1 linkage disequilibrium for adjacent SNP diminishing to low, nearly equal linkage disequilibrium in Line 1 and U.S. Herefords for widely separated SNP reflects recent divergence of Line 1 from the general Hereford population. Regression of Line 1 postweaning gain cumulative selection differential on minor allele frequencies revealed quantitative trait loci (QTL) co-located with previously identified growth trait QTL. Inbreeding and genome-wide heterozygosity had significant effects on postweaning gain, but individual SNP showing a significant advantage for heterozygotes were not identified.
Technical Abstract: Hereford is a major beef breed in the USA and has been subjected to selection for a variety of goals. A sub-population, known as Line 1 (L1), was established in 1934 by joining two paternal half-sib bulls with 50 unrelated females. L1 has since been maintained as a closed population and selected primarily for growth to one year of age. Objectives of this research were to characterize the molecular genetic architecture of L1 (n = 240) by: comparing a cross-section of L1 with the general U.S. Hereford population (AHA, n = 311), estimating effects of imposed selection within L1 on allele frequencies at 50K SNP loci, and examining loci-specific effects of heterozygosity on the selection criterion used in L1. All animals were genotyped using the Illumina BovineSNP50 Beadchip. The SNP were mapped to UMD3.0 assembly of the bovine genome sequence. Average LD of adjacent SNPs was 0.36 and 0.16 in L1 and AHA, respectively. Difference in LD between L1 and AHA decreased as SNP spacing increased. Persistence of phase between L1 and AHA decreased from 0.45 to 0.14 as SNP spacing increased from 50 kb to 5,000 kb. Extended haplotype homozygosity was greater in L1 than in AHA for 95.6% of the SNP. Knowledge of selection applied to L1 facilitated a novel approach to QTL discovery. Minor allele frequency was significantly (FDR < 0.01) affected by cumulative selection differential at 191 out of 25,901 SNPs. With the FDR relaxed to 0.05, 14 regions on BTA2, 5, 6, 9, 11, 14, 15, 18, 23, and 26 are co-located with previously identified QTL for growth traits. After adjustment of postweaning gain phenotypes for fixed effects and direct additive genetic effects, regression of residuals on genome-wide heterozygosity was -235.3 ± 91.6 kg. However, no SNP-specific loci where heterozygotes were significantly superior to the average of homozygotes were revealed (FDR = 0.17). In conclusion, genome-wide SNP genotypes clarified relationships between the population segment L1 and AHA.