Whole-genome sequencing association analysis reveals the genetic architecture of meat quality traits in Chinese Qingyu pigs.

The Chinese Qingyu pig breed is an invaluable indigenous genetic resource. However, few studies have investigated the genetic architecture of meat quality traits in Qingyu pigs. Here, 30 purebred Qingyu pigs were subjected to whole-genome sequencing. After quality control, 18 436 759 SNPs were retained. Genome-wide association studies (GWAS) were then performed for meat pH and color at three postmortem time points (45 min, 24 h, and 48 h) using single-marker regression analysis. In total, 11 and 69 SNPs were associated with meat pH and color of the longissimus thoracis muscle (LTM), respectively, while 54 and 29 SNPs were associated with meat pH and color of the semimembranosus muscle (SM), respectively. Seven SNPs associated with pork pH were shared by all three postmortem time points. Several candidate genes for meat traits were identified, including four genes (CXXC5, RYR3, BNIP3, and MYCT1) related to skeletal muscle development, regulation of Ca2+ release in the muscle, and anaerobic respiration, which are promising candidates for selecting superior meat quality traits in Qingyu pigs. To our knowledge, this is the first study investigating the postmortem genetic architecture of pork pH and color in Qingyu pigs. Our findings further the current understanding of the genetic factors influencing meat quality.

Pork muscle profiling: pH and instrumental color of the longissimus thoracis is not representative of pH and instrumental color of shoulder and ham muscles.

From a population of 351 pork carcasses, 3.0-cm thick chops from the 10th rib location of the longissimus thoracis, faced surfaces of the triceps brachii and serratus ventralis muscles from the boneless shoulder, and faced surfaces of the biceps femoris, semitendinosus, semimembranosus, adductor, rectus femoris, and vastus lateralis muscles from the boneless ham were evaluated for pH and instrumental color (Minolta CR-400). Evaluations were conducted for at least three different locations on each of the muscle samples and averaged before data analysis occurred. The longissimus thoracis had the lowest pH and the lightest and least red color compared with the other eight muscles evaluated in this study (mean differences ranged from 0.98 to 8.70 for L*, 3.98 to 12.56 for a*, and 0.026 to 0.409 for pH). Furthermore, regression analysis suggested that pH and color values for the longissimus thoracis were not adequate predictors for pH and color values obtained from other muscles and therefore consideration should be given to the individual muscles that are of interest.