Polymorphisms in positional candidate genes on BTA14 and BTA26 affect carcass quality in beef cattle

Abstract

Several studies have reported the presence of carcass quality QTL on BTA14 and BTA26, with no specific genes being conclusively linked as their cause. The aim of this study was to identify polymorphisms in genes known to affect lipid metabolism in other species and to assess their association with carcass quality traits. Two genes located on BTA14, 2,4 dienoyl CoA reductase 1 (DECR1) and core binding factor, runt domain, alpha subunit 2, translocated to 1 gene (CBFA2T1), have been previously evaluated in other species and found to contain polymorphisms influencing lipid metabolism. A gene on BTA26, fibroblast growth factor 8 (FGF8), has in recent studies been linked to several QTL affecting obesity in mice, indicating its potential for regulating adiposity in other species. Sequencing analysis identified 9 polymorphisms in DECR1, 4 in CBFA2T1, and 4 in FGF8. Multiple sequence alignment of DECR1 among cattle, humans, and mice showed that 4 of these mutations lie in conserved regions across these species. Using 464 Angus, Charolais, and crossbred animals produced associations with ultrasound marbling score (CBFA2T1, P = 0.019), ultrasound backfat (DECR1, P = 0.012), carcass backfat (FGF8, P = 0.004), and lean meat yield (FGF8, P = 0.005). Quantitative trait loci analysis including a set of previously genotyped markers on BTA14, and 1 DECR1 polymorphism resulted in several significant QTL peaks: ultrasound backfat (UBF) at 91 cM, lean meat yield at 86 cM, carcass gradefat at 15 cM, and yield grade at 87 cM, all at the P < 0.05 level. Using DECR1 as a genetic covariate removed the UBF QTL, indicating that this SNP was contributing to the variation observed in UBF. A similar analysis was performed on BTA26 using 1 of the FGF8 polymorphisms. Results showed significant peaks for lean meat yield at 2 cM and for yield grade at 25 cM, both at P < 0.01, and for carcass backfat at 25 cM (P < 0.05). Removal of FGF8 SNP in further analysis resulted in the disappearance of the carcass backfat QTL. These results suggest that polymorphisms discovered in DECR1, CBFA2T1, and FGF8 may play a role in the lipid metabolism pathway affecting carcass quality traits in beef cattle. However, further studies are needed to confirm that these polymorphisms are responsible for the differences observed in carcass quality in beef cattle.

Haplotype Analysis Improved Evidence for Candidate Genes for Intramuscular Fat Percentage from a Genome Wide Association Study of Cattle

“…SNPs in genes that had previously been associated with intramuscular fat in some way, whether as MS, PSF, or IMF, were tested to see whether any were significantly ( P <0.05) associated to IMF in the GWAS study. Previous studies had found associations between MS, PSF, or IMF, and SNPs in the alphabetically listed candidate and positional candidate genes adiponectin, C1Q and collagen domain containing ( ADIPOQ ) [83], calpain 1 ( CAPN1 ) [84], carboxypeptidase E ( CPE ) [56], [85], CCAAT/enhancer binding protein (C/EBP) alpha ( CEBPA ) [86], the region containing the chemokine (C-X-C) motif receptor 4 ( CXCR4 ) gene near to the genes R3H domain containing 1 ( R3HDM1 ) and zinc finger, RAN domain containing 3 ( ZRANB3 ) [65], 2,4 dienoyl CoA reductase 1 ( DECR1 ) [87], fatty acid binding protein 4 ( FABP4 ) [88], fatty acid synthase ( FASN ) [59], fibroblast growth factor 8 ( FGF8 ) [87], growth hormone 1 ( GH1 ) [89], [90], growth hormone receptor ( GHR ) [91], insulin growth factor 2 ( IGF2 ) [92], leptin ( LEP ) [93], retinoic acid receptor-related orphan receptor C ( RORC ) [94], sterol regulatory element binding transcription factor 1 ( SREBF1 ) [95], steroyl-CoA desaturase ( SCD ) [96], thyroglobulin ( TG ) [97], and titin-cap (telethonin) ( TCAP ) [98]. For the trait LLPF, SNPs in the candidate genes CAST , CAPN1 and calpain 3 ( CAPN3 ) have been reported in cattle [46], [47], [48], [49], [50].…”

Relationships between fed cattle traits and Igenity panel scores1

“…When coupled with economic analysis, the improvement in these traits can be weighed against potential deleterious effects in other traits. Numerous previous studies have identified SNP associated with economically important beef carcass characteristics (Kononoff et al, 2005;Nkrumah et al, 2005Nkrumah et al, , 2007Marques et al, 2009). Such knowledge has led to the commercialization of genetic testing technologies.…”

Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks

“…Core binding factor, runt domain, alpha subunit 2, translocated to 1 (CBFA2T1) is a protein that is encoded by the RUNX1T1 gene and is known to affect lipid metabolism in other species 54. Its polymorphism was found to have significant association with ultrasound marbling score in beef cattle 55. Calcium/calmodulin-dependent protein kinase II alpha (CAMK2A) contributes to myogenesis 56 and can be a candidate gene for activity-dependent skeletal muscle adaptation 57.…”