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

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.

Marques E ，Nkrumah JD ，Sherman EL ，Moore SS ... -  《-》

Association analysis of adiponectin and somatostatin polymorphisms on BTA1 with growth and carcass traits in Angus cattle.

This study tested positional candidate genes adiponectin (ADIPOQ) and somatostatin (SST) for effects on carcass traits in a commercially relevant cattle population. Both genes are located within a region of BTA1 previously reported to harbour quantitative trait loci (QTL) that affect marbling, quality grade, yield grade, ribeye area and weaning weight in Bos taurus x Bos indicus crosses. Except for the first intron of ADIPOQ, both genes, including over 2 kb upstream of the promoters, were sequenced in five registered Angus sires to identify polymorphisms. A variable copy duplication and three single nucleotide polymorphisms (SNPs) in ADIPOQ and one SNP in SST were genotyped and tested for association with 19 traits in a 14-generation pedigree of 1697 registered Angus artificial insemination sires representing all the major USA lineages of the breed. Linear models that parameterized predicted genetic merits in terms of allele substitution effects were fit by weighted least squares, and goodness-of-fit tests were employed to differentiate causal mutations or polymorphisms in strong linkage disequilibrium (LD) with causal mutations from markers in weak LD with QTL. We confirmed the presence of QTL affecting marbling, ribeye muscle area and fat thickness in the vicinity of SST and ADIPOQ on BTA1 in Angus; excluded SST as underlying the ribeye muscle area QTL; and excluded ADIPOQ as underlying the marbling score QTL. However, association analysis provides very limited information about QTL location and has little intrinsic value when performed in the absence of linkage or LD analysis using flanking marker data to localize the QTL effect relative to positional candidate genes.

Morsci NS ，Schnabel RD ，Taylor JF 《ANIMAL GENETICS》

Bovine quantitative trait loci analysis for growth, carcass, and meat quality traits in an F2 population from a cross between Japanese Black and Limousin.

A genome-wide scan for QTL affecting economically important traits in beef production was performed using an F(2) resource family from a Japanese Black x Limousin cross, where 186 F(2) animals were measured for growth, carcass, and meat-quality traits. All family members were genotyped for 313 informative microsatellite markers that spanned 2,382 cM of bovine autosomes. The centromeric region of BTA2 contained significant QTL (i.e., exceeding the genome-wide 5% threshold) for 5 carcass grading traits [LM area, beef marbling standards (BMS) number, luster, quality grade, and firmness), 8 computer image analysis (CIA) traits [LM lean area, ratio of fat area (RFA) to LM area, LM area, RFA to musculus (M.) trapezius area, M. trapezius lean area, M. semispinalis lean area, RFA to M. semispinalis area, and RFA to M. semispinalis capitis area], and 5 meat quality traits (contents of CP, crude fat, moisture, C16:1, and C18:2 of LM). A significant QTL for withers height was detected at 80.3 cM on BTA5. We detected significant QTL for the C14:0 content in backfat and C14:0 and C14:1 content in intermuscular fat around the 62.3 to 71.0 cM region on BTA19 and for C14:0, C14:1, C18:1, and C16:0 content and ratio of total unsaturated fatty acid content to total SFA content in intramuscular fat at 2 different regions on BTA19 (41.1 cM for C14:1 and 62.3 cM for the other 4 traits). Overall, we identified 9 significant QTL regions controlling 27 traits with genome-wide significance of 5%; of these, 22 traits exceeded the 1% genome-wide threshold. Some of the QTL affecting meat quality traits detected in this study might be the same QTL as previously reported. The QTL we identified need to be validated in commercial Japanese Black cattle populations.

Abe T ，Saburi J ，Hasebe H ，Nakagawa T ，Kawamura T ，Saito K ，Nade T ，Misumi S ，Okumura T ，Kuchida K ，Hayashi T ，Nakane S ，Mitsuhasi T ，Nirasawa K ，Sugimoto Y ，Kobayashi E ... -  《-》

Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Carcass and meat quality traits.

Pigs from the F(2) generation of a Duroc x Pietrain resource population were evaluated to discover QTL affecting carcass composition and meat quality traits. Carcass composition phenotypes included primal cut weights, skeletal characteristics, backfat thickness, and LM area. Meat quality data included LM pH, temperature, objective and subjective color information, marbling and firmness scores, and drip loss. Additionally, chops were analyzed for moisture, protein, and fat composition as well as cook yield and Warner-Bratzler shear force measurements. Palatability of chops was determined by a trained sensory panel. A total of 510 F(2) animals were genotyped for 124 microsatellite markers evenly spaced across the genome. Data were analyzed with line cross, least squares regression interval, mapping methods using sex and litter as fixed effects and carcass weight or slaughter age as covariates. Significance thresholds of the F-statistic for single QTL with additive, dominance, or imprinted effects were determined on chromosome- and genome-wise levels by permutation tests. A total of 94 QTL for 35 of the 38 traits analyzed were found to be significant at the 5% chromosome-wise level. Of these 94 QTL, 44 were significant at the 1% chromosome-wise, 28 of these 44 were also significant at the 5% genome-wise, and 14 of these 28 were also significant at the 1% genome-wise significance thresholds. Putative QTL were discovered for 45-min pH and pH decline from 45 min to 24 h on SSC 3, marbling score and carcass backfat on SSC 6, carcass length and number of ribs on SSC 7, marbling score on SSC 12, and color measurements and tenderness score on SSC 15. These results will facilitate fine mapping efforts to identify genes controlling carcass composition and meat quality traits that can be incorporated into marker-assisted selection programs to accelerate genetic improvement in pig populations.

Edwards DB ，Ernst CW ，Raney NE ，Doumit ME ，Hoge MD ，Bates RO ... -  《-》

Association analyses of a SNP in the promoter of IGF1 with fat deposition and carcass merit traits in hybrid, Angus and Charolais beef cattle.

A SNP in the promoter region of insulin like growth factor-1 (IGF1) (c.-512C>T) was analysed for associations with 10 fat deposition and carcass merit traits in hybrid (n = 455), Angus (n = 204) and Charolais (n = 186) beef cattle populations. Significant associations of the SNP were found for ultrasound backfat thickness (P = 0.030), carcass average backfat (P = 0.015) and carcass lean meat yield (LMY) (P = 0.023) in the Angus beef population, with the 'CC' genotype showing higher fat depth and lower LMY than the 'TT' genotype. Analyses of transcription factor binding sites based on transcription element search system prediction revealed that the 'C' allele introduces a binding site for nuclear factor I, which has an adipose tissue-specific regulatory role and thus may contribute to the SNP effect on fat deposition in the population of pure Angus cattle, a breed with greater fat depth than the hybrid and Charolais breeds.

Islam KK ，Vinsky M ，Crews RE ，Okine E ，Moore SS ，Crews DH Jr ，Li C ... -  《-》