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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVE NUTRIENT MANAGEMENT AND EFFICIENCY IN CATTLE Title: Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

Authors
item Lindholm-Perry, Amanda
item Sexten, Andrea -
item Kuehn, Larry
item Smith, Timothy
item King, David
item Shackelford, Steven
item Wheeler, Tommy
item Ferrell, Calvin -
item Jenkins, Thomas -
item Snelling, Warren
item Freetly, Harvey

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 14, 2011
Publication Date: December 20, 2011
Citation: Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Ferrell, C.L., Jenkins, T.G., Snelling, W.M., Freetly, H.C. 2011. Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BioMed Central (BMC) Genetics. 12:103.

Interpretive Summary: A large region on bovine chromosome 6 was previously identified that contains candidate genes for beef cattle average daily feed intake (ADFI) or average daily gain (ADG). Genetic markers that are informative over many breeds of cattle for these traits will allow producers to genetically select for animals that consume less feed and/or produce animals with optimal production weights and should have a positive economic impact for beef cattle producers. The goal of the present study was to develop and examine additional markers that are optimal for distinguishing variation. Twelve markers located within a narrow region that included two genes known to be involved with cattle growth and human height were significantly associated with feed intake and gain phenotypes. These markers were also significant for hot carcass weight, ribeye area, and adjusted fat thickness suggesting that a gene in this region contributes to lean growth and reduced fat deposition. To validate these markers further, they were genotyped on a separate crossbred population of animals consisting of 14 beef cattle breeds. Two markers within the gene associated with human height were significantly associated with ADG. These two markers may be more robust for the prediction of ADG across multiple breeds and populations of cattle.

Technical Abstract: Background: In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P</=0.003) with average daily gain (ADG) and 3 of these were also associated (P</=0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine LAP3, NCAPG, and LCORL genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, and potentially identify functional variation. Results: Animals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the NCAPG-LCORL locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P</=0.005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the LCORL gene locus remained significant for ADG (P</=0.04). Conclusions: Several markers within the NCAPG-LCORL locus were significantly associated with feed intake and gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle.

Last Modified: 4/19/2014