Polymorphisms and haplotypes in the bovine NPY, GHR, GHRL, IGF2, UCP2, and UCP3 genes and their associations with measures of growth, performance, feed efficiency and carcass merit in beef cattle

¹ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
² Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada; Igenity Livestock Production Business Unit, Merial Ltd.
³ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada; Agriculture and Agri-Food Canada Research Centre, Lacombe, Alberta, T4L 1W1 Canada

^* To whom correspondence should be addressed. E-mail: stephen.moore{at}ualberta.ca.

	Abstract

Genes that regulate metabolism and energy partitioning have the potential to influence economically important traits in farm animals, as do polymorphisms within these genes. In the present study, single nucleotide polymorphisms (SNP) in the bovine neuropeptide Y (NPY), growth hormone receptor (GHR), ghrelin (GHRL), uncoupling proteins 2 and 3 (UCP2 and UCP3), IGF2, corticotrophin-releasing hormone (CRH), cocaine and amphetamine regulated transcript (CART), melanocortin-4 receptor (MC4R), pro-opiomelanocortin (POMC) and GH genes were evaluated for associations with growth, feed efficiency and carcass merit in beef steers. In total, 24 SNP were evaluated for associations with these traits and haplotypes were constructed within each gene when 2 or more SNP showed significant associations. An A/G SNP located in intron 4 of the GHR gene had the largest effects on BW of the animals (dominance effect P < 0.01) and feed efficiency (allele substation effect P < 0.05). Another A/G SNP located in the promoter region of GHR had similar effects but the haplotypes of these two SNP reduced the effects of the SNP located in intron 4. Three SNP in the NPY gene showed the associations to marbling (P < 0.001) as well as with ADG, BW, and feed conversion ratio (FCR) (P < 0.05). The combination of these 3 SNP into haplotypes generally improved the association or had a similar scale of association as each single SNP. Only one SNP in UCP3, an A/G SNP in intron 3, was associated with ADG (P = 0.025), partial efficiency of growth (PEG) and FCR (P < 0.01). Three SNP in UCP2 gene were in almost complete linkage disequilibrium and showed associations with lean meat yield, yield grade, DMI and BW (P < 0.05). Haplotypes between the SNP in UCP3 and UCP2 generally reduced the associations seen individually in each SNP. An A/G SNP in the GHRL gene tended to show effects on residual feed intake, FCR and PEG (P < 0.10). The IGF2 SNP most strongly affected LM area (P < 0.01), back fat, ADG and FCR (P < 0.05). The SNP in the CART, MC4R, POMC, GH and CRH genes did not show associations at P < 0.05 with any of the traits. Although most of the SNP that showed associations do not cause amino acid changes, these SNP could be linked to other yet to be detected causative mutations or nearby QTL. It will be very important to verify these results in other cattle populations.

Key Words: candidate genes, cattle, feed efficiency, carcass merit, haplotype, SNP