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.

Effects of dietary coated cysteamine hydrochloride on pork color in finishing pigs.

BACKGROUND: Coated cysteamine hydrochloride (CC) was applied as a feed additive in animal production. The influence and the mechanisms of CC used as a feed additive in promoting meat quality in finishing pigs were investigated. RESULTS: Dietary CC supplementation increased (P < 0.05) the a* and H* values and reduced (P < 0.05) the L* value in the longissimus dorsi muscles at 48 h postmortem (P < 0.05). The deoxymyoglobin content was enhanced (P < 0.05) and the metmyoglobin and malondialdehyde contents were reduced (P < 0.05) in pigs fed the dietary CC. Pigs fed a dietary CC of 0.035 g kg-1 had a lower cooking loss (P < 0.05) and a higher a* (24 h) value in the longissimus dorsi muscles than pigs on control treatment. The messenger RNA expression of superoxide dismutase 1 was upregulated (P < 0.05) in the longissimus dorsi. CONCLUSION: Dietary supplementation with CC could improve antioxidant status and delay meat discoloration by improving glutathione levels and antioxidase activity after longer chill storage (for 48 h after slaughter). Dietary supplementation with CC at 0.035 g kg-1 may promote the stability of pork color by reducing oxidation. © 2017 Society of Chemical Industry.

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.

Imputation to whole-genome sequence and its use in genome-wide association studies for pork colour traits in crossbred and purebred pigs.

Imputed whole-genome sequence (WGS) has been proposed to improve genome-wide association studies (GWAS), since all causative mutations responsible for phenotypic variation are expected to be present in the data. This approach was applied on a large number of purebred (PB) and crossbred (CB) pigs for 18 pork color traits to evaluate the impact of using imputed WGS relative to medium-density marker panels. The traits included Minolta A*, B*, and L* for fat (FCOL), quadriceps femoris muscle (QFCOL), thawed loin muscle (TMCOL), fresh ham gluteus medius (GMCOL), ham iliopsoas muscle (ICOL), and longissimus dorsi muscle on the fresh loin (FMCOL). Sequence variants were imputed from a medium-density marker panel (61K for CBs and 50K for PBs) in all genotyped pigs using BeagleV5.0. We obtained high imputation accuracy (average of 0.97 for PBs and 0.91 for CBs). GWAS were conducted for three datasets: 954 CBs and 891 PBs, and the combined CBs and PBs. For most traits, no significant associations were detected, regardless of panel density or population type. However, quantitative trait loci (QTL) regions were only found for a few traits including TMCOL Minolta A* and GMCOL Minolta B* (CBs), FMCOL Minolta B*, FMCOL Minolta L*, and ICOL Minolta B* (PBs) and FMCOL Minolta A*, FMCOL Minolta B*, GMCOL Minolta B*, and ICOL Minolta B* (Combined dataset). More QTL regions were identified with WGS (n = 58) relative to medium-density marker panels (n = 22). Most of the QTL were linked to previously reported QTLs or candidate genes that have been previously reported to be associated with meat quality, pH and pork color; e.g., VIL1, PRKAG3, TTLL4, and SLC11A1, USP37. CTDSP1 gene on SSC15 has not been previously associated with meat color traits in pigs. The findings suggest any added value of WGS was only for detecting novel QTL regions when the sample size is sufficiently large as with the Combined dataset in this study. The percentage of phenotypic variance explained by the most significant SNPs also increased with WGS compared with medium-density panels. The results provide additional insights into identification of a number of candidate regions and genes for pork color traits in different pig populations.

Estimation of Genetic Parameters for Pork Quality, Novel Carcass, Primal-Cut and Growth Traits in Duroc Pigs.

More recently, swine breeding programs have aimed to include pork quality and novel carcass (e.g., specific primal cuts such as the Boston butt or belly that are not commonly used in selection indexes) and belly traits together with growth, feed efficiency and carcass leanness in the selection indexes of terminal-sire lines, in order to efficiently produce pork with improved quality at a low cost to consumers. In this context, the success of genetic selection for such traits relies on accurate estimates of heritabilities and genetic correlations between traits. The objective of this study was to estimate genetic parameters for 39 traits in Duroc pigs (three growth, eight conventional carcass (commonly measured production traits; e.g., backfat depth), 10 pork quality and 18 novel carcass traits). Phenotypic measurements were collected on 2583 purebred Duroc gilts, and the variance components were estimated using both univariate and bivariate models and REML procedures. Moderate to high heritability estimates were found for most traits, while genetic correlations tended to be low to moderate overall. Moderate to high genetic correlations were found between growth, primal-cuts and novel carcass traits, while low to moderate correlations were found between pork quality and growth and carcass traits. Some genetic antagonisms were observed, but they are of low to moderate magnitude. This indicates that genetic progress can be achieved for all traits when using an adequate selection index.

Prediction of pork color attributes using computer vision system.

Color image processing and regression methods were utilized to evaluate color score of pork center cut loin samples. One hundred loin samples of subjective color scores 1 to 5 (NPB, 2011; n=20 for each color score) were selected to determine correlation values between Minolta colorimeter measurements and image processing features. Eighteen image color features were extracted from three different RGB (red, green, blue) model, HSI (hue, saturation, intensity) and L*a*b* color spaces. When comparing Minolta colorimeter values with those obtained from image processing, correlations were significant (P<0.0001) for L* (0.91), a* (0.80), and b* (0.66). Two comparable regression models (linear and stepwise) were used to evaluate prediction results of pork color attributes. The proposed linear regression model had a coefficient of determination (R(2)) of 0.83 compared to the stepwise regression results (R(2)=0.70). These results indicate that computer vision methods have potential to be used as a tool in predicting pork color attributes.