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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 #241928

Title: Genome-Wide Association Study of Growth in Crossbred Beef Cattle

item Snelling, Warren
item Keele, John
item Kuehn, Larry
item McDaneld, Tara
item Smith, Timothy - Tim
item Thallman, Richard - Mark
item Bennett, Gary

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2009
Publication Date: 3/1/2010
Citation: Snelling, W.M., Allan, M.F., Keele, J.W., Kuehn, L.A., Mcdaneld, T.G., Smith, T.P., Sonstegard, T.S., Thallman, R.M., Bennett, G.L. 2010. Genome-Wide Association Study of Growth in Crossbred Beef Cattle. Journal of Animal Science. 88(3):837-848.

Interpretive Summary: Cattle representing two-, three- and four-breed crosses of seven beef breeds (Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental) were genotyped for 44,163 genetic markers. Associations between the genetic markers and growth traits were determined. About 200 markers were strongly associated with one or more measures of weight or gain from birth to yearling. Most of the markers associated with large effects agreed with previously detected chromosome regions associated with growth traits. Over 10,000 additional markers showed weaker associations with relatively small effects. Detecting these markers with small effects agrees with traditional genetic analysis of growth traits, which has assumed many tiny effects add up to meaningful genetic variation. Most of the markers associated with birth weight and gain to weaning or yearling appear to have similar effects on birth weight and gain. Few markers with significant opposite effects on birth weight and gain were identified, although several appear to independently affect either birth weight or gain. Using genetic markers to assist selection for increased gain relative to birth weight (or reduced birth weight relative to gain) might emphasize those with independent effects.

Technical Abstract: Genotypes from the BovineSNP50 BeadChip (50K) were obtained on progeny (F1; 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F12 = F1 x F1; 1306 steers and 707 females) of 150 AI sires representing seven breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Whole-genome association analyses were conducted using birth, weaning and yearling weight records to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning gain (WG), 160-d adjusted postweaning gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT+WG) and 365-d adjusted yearling weight (YW = BWT+WG+PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects, and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P which may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 238 SNP meeting stringent criteria generally coincided with previously described quantitative trait loci affecting growth traits. The 12,780 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although a number of SNP associated with one component but independent of others offer an opportunity for SNP-assisted selection to increase postnatal growth relative to birth weight. Further evaluation of these SNP in other cattle and environments is needed to develop broadly applicable, DNA-based breeding strategies that address profitability of beef production.