Epistatic analysis of carcass characteristics in pigs reveals genomic interactions between quantitative trait loci attributable to additive and dominance genetic effects.

The present study focused on the identification of epistatic QTL pairs for body composition traits (carcass cut, lean tissue, and fat tissue weights) measured at slaughter weight (140 kg of BW) in a 3-generation full-sib population developed by crossing Pietrain sires with a crossbred dam line. Depending on the trait, phenotypic observations were available for 306 to 315 F(2) animals. For the QTL analysis, 386 animals were genotyped for 88 molecular markers covering chromosomes SSC1, SSC2, SSC4, SSC6, SSC7, SSC8, SSC9, SSC10, SSC13, and SSC14. In total, 23 significant epistatic QTL pairs were identified, with the additive x additive genetic interaction being the most prevalent. Epistatic QTL were identified across all chromosomes except for SSC13, and epistatic QTL pairs accounted for between 5.8 and 10.2% of the phenotypic variance. Seven epistatic QTL pairs were between QTL that resided on the same chromosome, and 16 were between QTL that resided on different chromosomes. Sus scrofa chromosome 1, SSC2, SSC4, SSC6, SSC8, and SSC9 harbored the greatest number of epistatic QTL. The epistatic QTL pair with the greatest effect was for the entire loin weight between 2 locations on SSC7, explaining 10.2% of the phenotypic variance. Epistatic associations were identified between regions of the genome that contain the IGF-2 or melanocortin-4 receptor genes, with QTL residing in other genomic locations. Quantitative trait loci in the region of the melanocortin-4 receptor gene and on SSC7 showed significant positive dominance effects for entire belly weight, which were offset by negative dominance x dominance interactions between these QTL. In contrast, the QTL in the region of the IGF-2 gene showed significant negative dominance effects for entire ham weight, which were largely overcompensated for by positive additive x dominance genetic effects with a QTL on SSC9. The study shows that epistasis is of great importance for the genomic regulation of body composition in pigs and contributes substantially to the variation in complex traits.

Duthie C ，Simm G ，Doeschl-Wilson A ，Kalm E ，Knap PW ，Roehe R ... -  《-》

Quantitative trait loci associated with AutoFOM grading characteristics, carcass cuts and chemical body composition during growth of Sus scrofa.

A three-generation full-sib resource family was constructed by crossing two commercial pig lines. Genotypes for 37 molecular markers covering chromosomes SSC1, SSC6, SSC7 and SSC13 were obtained for 315 F2 animals of 49 families and their parents and grandparents. Phenotypic records of traits including carcass characteristics measured by the AutoFOM grading system, dissected carcass cuts and meat quality characteristics were recorded at 140 kg slaughter weight. Furthermore, phenotypic records on live animals were obtained for chemical composition of the empty body, protein and lipid accretion (determined by the deuterium dilution technique), daily gain and feed intake during the course of growth from 30 to 140 kg body weight. Quantitative trait loci (QTL) detection was conducted using least-squares regression interval mapping. Highest significance at the 0.1% chromosome-wise level was obtained for five QTL: AutoFOM belly weight on SSC1; ham lean-meat weight, percentage of fat of primal cuts and daily feed intake between 60 and 90 kg live weight on SSC6; and loin lean-meat weight on SSC13. QTL affecting daily gain and protein accretion were found on SSC1 in the same region. QTL for protein and lipid content of empty body at 60 kg liveweight were located close to the ryanodine receptor 1 (RYR1) locus on SSC6. On SSC13, significant QTL for protein accretion and feed conversion ratio were detected during growth from 60 to 90 kg. In general, additive genetic effects of alleles originating from the Piétrain line were associated with lower fatness and larger muscularity as well as lower daily gain and lower protein accretion rates. Most of the QTL for carcass characteristics were found on SSC6 and were estimated after adjustment for the RYR1 gene. QTL for carcass traits, fatness and growth on SSC7 reported in the literature, mainly detected in crosses of commercial lines x obese breeds, were not obtained in the present study using crosses of only commercial lines, suggesting that these QTL are not segregating in the analysed commercial lines.

Mohrmann M ，Roehe R ，Knap PW ，Looft H ，Plastow GS ，Kalm E ... -  《ANIMAL GENETICS》

Quantitative trait loci for meat quality traits in pigs considering imprinting and epistatic effects.

The aim of the research was to gain a better understanding of the genomic regulation of meat quality by investigating individual and epistatic QTL in a three-generation full-sib population (Pietrain x crossbred dam line). In total, 386 animals were genotyped for 96 markers. Analysed traits included pH, reflectance value, conductivity, and meat colour. Thirteen significant individual QTL were identified. The most significant QTL were detected on SSC1 and SSC9 for pH, on SSC4 for meat colour, and on SSC8 for conductivity, accounting for 3.4% to 4.7% of the phenotypic variance. Nine significant epistatic QTL pairs were detected accounting for between 5.7% and 10.9% of the phenotypic variance. Epistatic QTL pairs showing the largest effects were for reflectance value between two locations of SSC4, and for pH between SSC10 and SSC13, explaining 9.5% and 10.9% of the phenotypic variance, respectively. This study indicates that meat quality traits are influenced by numerous QTL as well as a complex network of interactions.

Duthie CA ，Simm G ，Doeschl-Wilson A ，Kalm E ，Knap PW ，Roehe R ... -  《-》

The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan x Duroc crossbred population.

Uemoto Y ，Sato S ，Ohnishi C ，Terai S ，Komatsuda A ，Kobayashi E ... -  《-》

Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc x Chinese Erhualian resource population.

Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F(2) animals from a White Duroc x Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.

Ma J ，Ren J ，Guo Y ，Duan Y ，Ding N ，Zhou L ，Li L ，Yan X ，Yang K ，Huang L ，Song Y ，Xie J ，Milan D ，Huang L ... -  《-》