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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #264627

Title: How SNP chips will advance our knowledge of factors controlling puberty and aid in selecting replacement females

item Snelling, Warren
item Cushman, Robert - Bob
item Bennett, Gary
item Keele, John
item Kuehn, Larry
item McDaneld, Tara
item Thallman, Richard - Mark
item THOMAS, MILTON - New Mexico State University

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: 2/18/2011
Publication Date: 7/1/2011
Citation: Snelling, W.M., Cushman, R.A., Bennett, G.L., Keele, J.W., Kuehn, L.A., Mcdaneld, T.G., Thallman, R.M., Thomas, M.G. 2011. How SNP chips will advance our knowledge of factors controlling puberty and aid in selecting replacement females [abstract]. Journal of Animal Science Supplement. 89(E-Supplement 1):494. Abstract # 534.

Interpretive Summary:

Technical Abstract: The promise of genomic selection is that genetic potential can be accurately predicted from genotypes. Simple deoxyribonucleic acid (DNA) tests might replace low accuracy predictions based on performance and pedigree for expensive or lowly heritable measures of puberty and fertility. The promise is greatest if the DNA variants affecting puberty and other measures of fertility are known with some certainty. Several of the 50,000 single nucleotide polymorphisms (SNP) in a standard assay have tentatively been associated with age at puberty, antral follicle count, pregnancy and related traits measured on different sets of heifers. At best, these SNP may be imperfectly correlated with causal variants and indicate genomic regions affecting puberty, but sample sizes are too small and SNP density too sparse to be definitive. Associations between individual SNP and similar phenotypes are inconsistent across data sets, and genomic predictions do not appear applicable to unrelated cattle. Discrepancies may be a result of different quantitative trait loci (QTL) segregating in the sampled populations, differences in linkage disequilibrium (LD) patterns so the same SNP are not correlated with the same QTL, and spurious correlations with phenotype. Larger samples and denser SNP will increase power to detect real associations with SNP having more consistent LD with underlying QTL. Meta-analysis combining results from different studies will effectively increase sample size. High-density genotyping with heifers pooled by early and late puberty, or extremes for quantitative indicators of puberty, can be a cost-effective means to sample large numbers. Networks of genes, implicated by associations with multiple traits correlated with puberty and fertility, could provide insight into the complex nature of these traits, especially if corroborated by functional annotation, established gene interaction pathways, and transcript expression. Integrating information about gene function and regulation with statistical associations from whole-genome SNP genotyping assays will enhance knowledge of genomic mechanisms affecting puberty, enabling development of more reliable DNA tests to guide heifer selection decisions.