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Using 50?k single nucleotide polymorphisms to elucidate genomic architecture of line 1 hereford cattle.


ABSTRACT: Hereford is a major beef breed in the USA, and a sub-population, known as Line 1 (L1), was established in 1934 using two paternal half-sib bulls and 50 unrelated females. L1 has since been maintained as a closed population and selected for growth to 1?year of age. Objectives were to characterize the molecular genetic architecture of L1 (n?=?240) by comparing a cross-section of L1 with the general US. Hereford population (AHA, n?=?311), estimating effects of imposed selection within L1 based on allele frequencies at 50?K SNP loci, and examining loci-specific effects of heterozygosity on the selection criterion. Animals were genotyped using the Illumina BovineSNP50 Beadchip, and SNP were mapped to UMD3.0 assembly of the bovine genome sequence. Average linkage disequilibrium (LD), measured by square of Pearson correlation, of adjacent SNP 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 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 (FDR?

SUBMITTER: Huang Y 

PROVIDER: S-EPMC3571696 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Using 50 k single nucleotide polymorphisms to elucidate genomic architecture of line 1 hereford cattle.

Huang Y Y   Maltecca C C   Macneil M D MD   Alexander L J LJ   Snelling W M WM   Cassady J P JP  

Frontiers in genetics 20121214


Hereford is a major beef breed in the USA, and a sub-population, known as Line 1 (L1), was established in 1934 using two paternal half-sib bulls and 50 unrelated females. L1 has since been maintained as a closed population and selected for growth to 1 year of age. Objectives were to characterize the molecular genetic architecture of L1 (n = 240) by comparing a cross-section of L1 with the general US. Hereford population (AHA, n = 311), estimating effects of imposed selection within L1 based on a  ...[more]

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