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Title: A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle

Author
item Lindholm-Perry, Amanda
item Kuehn, Larry
item Smith, Timothy - Tim
item FERRELL, CALVIN - Retired ARS Employee
item JENKINS, THOMAS - Retired ARS Employee
item Freetly, Harvey
item Snelling, Warren

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2011
Publication Date: 4/20/2012
Citation: Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C., Snelling, W.M. 2012. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle. Animal Genetics. 43(2):216-219.

Interpretive Summary: The largest expense incurred during production of most beef cattle in the U.S. lies in purchase of feed, which has raised interest in the potential of selecting for improved feed efficiency within and among cattle breeds to increase profitability and reduce waste and environmental impact. A broad region on bovine chromosome 14 was identified that appears to have an impact on the feed intake, average daily gain and a measure of feed efficiency in steers. Two genes in this region that are involved in appetite control and fat metabolism appeared to be logical positional and functional candidate genes. Genetic markers within and surrounding these genes were evaluated for association with the feed intake and gain. Five markers near one of these genes were predictive for feed intake and gain in this population of cattle. These markers may be useful for the identification and selection of animals that consume less feed, although further evaluation of these markers in unrelated cattle populations and for their effects on other production traits will be necessary.

Technical Abstract: The cost of feed for beef cattle is the largest expense incurred by cattle producers. Development of genetic markers to enhance selection of more efficient animals that require less feed while still achieving acceptable levels of production has the potential to substantially reduce production costs. A genome-wide marker association approach based on the Illumina BovineSNP50 BeadChip™ was used to identify genomic regions harboring variation affecting average daily feed intake (ADFI), average daily gain (ADG), and residual feed intake (RFI) traits in a population of 1195 crossbred steers. This approach identified a region on BTA14 from 22.02 - 23.92Mb containing several single nucleotide polymorphisms (SNP) having significant association with at least one of the traits. Two genes in this region, lysophospolipase1 (LYPLA1) and transmembrane protein 68 (TMEM68), appeared to be logical positional and functional candidate genes. LYPLA1 deacylates ghrelin, a hormone involved in regulation of appetite, in the rat stomach, while TMEM68 is expressed in bovine rumen and abomassum and is predicted to function in lipid biosynthetic processes. A total of 55 additional SNP lying in or near these two genes were identified by sequencing a subset of animals with extreme phenotypes, and tested for association in the same population. After correction for multiple testing, 5 markers within 22.79-22.84Mb, located downstream of TMEM68, and between TMEM68 and the neighboring gene XKR4, were significant for both ADFI and ADG (P-values < 0.05). Genetic markers predictive for feed intake and weight gain phenotypes in this population of cattle may be useful for the identification and selection of animals that consume less feed, although further evaluation of these markers in additional populations and their potential for effects on additional production traits will be required.