Using phenotypic and genotypic big data to investigate the effect of muscle fiber characteristics on meat quality and eating quality traits in pigs.

Determining genetic correlations (GCs) between phenotypes that can be replicated across breeds or generations is important for animal breeding. A comprehensive and objective evaluation of this is dependent on enough variations in the studied phenotypes. To this end, we constructed a worldwide distributed eight-breeds crossbreed mosaic pig population and estimated the genetic and phenotypic correlations of muscle fiber characteristics (MFCs) with meat quality and eating quality traits using F6 and F7 generations (∼590 samples/generation) of this population. The GCs of the density of type IIA fibers and type IIB fibers with the loin-eye area, a*, color score, firmness score, and those of the proportions of the two fiber types with pH24h and b* were moderate to high (|rg| ≥ 0.3) in both populations. We also obtained moderate to high GCs of mean fiber density with five sensory quality traits. Our results provide an important reference for improving meat quality through the genetic regulation of MFCs.

The effect of miR-93 on GH secretion in pituitary cells of Yanbian yellow cattle.

Yanbian yellow cattle breeding is limited by slow growth. We previously found that the miRNA miR-93 was differentially expressed between the blood exosomes of Yanbian yellow cattle and Han Yan cattle, which differ in growth characteristics. In this experiment, we evaluated the effects of miR-93 on growth hormone (GH) secretion by pituitary cells of Yanbian yellow cattle using qPCR, Western blot, Targetscan and RNA hybrid analysis software and Dual-Luciferase reporter gene system. The results showed that miR-93 targeted 3' UTR of GHRHR(growth hormone releasing hormone receptor); GH mRNA and protein levels in pituitary cells of Yanbian yellow cattle were significantly lower in the miR-93-mi group than in the NC control group (p < 0.01), while GH mRNA and protein levels were higher in the miR-93-in group than in the iNC control group, but the difference was not significant (p > 0.05); GHRHR mRNA and protein levels were significantly lower in the miR-93-mi group than in the NC control group (p < 0.01), while GHRHR protein levels were significantly higher in the miR-93-in group than in the iNC control group (p < 0.05), but there was no significant difference about GHRHR mRNA level between two groups (p > 0.05). These results prove that miR-93 regulates GH secretion in pituitary cells via GHRHR.

The effect of purine content on sensory quality of pork.

Although high level of purine in foods is considered a risk factor for hyperuricemia and gout, purine-rich foods continue to be popular for their delicious taste. The main objective of this study was to investigate the effects of purine bases on the sensory quality of pork. A total of 406 longissimus thoracis et lumborum samples were collected from a heterogeneous F6 pig population to determine purine composition and its correlation to sensory quality of pork. The contents of total purine and two major uricogenic bases (adenine and hypoxanthine) were negatively correlated with tenderness, juiciness, oiliness and overall liking (r < -0.2, P < 0.05), but they were not significantly correlated with umami. In contrast, guanine content, which accounts for only about 10% of the total purine content, was positively correlated with umami (r = 0.15, P < 0.05), and had no significant relationships with other sensory indicators. These results imply that purine bases with different uricogenic effects also influence different sensory quality indices of pork.

The effect of miR-10b on growth hormone in pituitary cells of Yanbian yellow cattle by somatostatin receptor 2.

This study aimed to evaluate the effect of miR-10b on growth hormone (GH) in pituitary cells of Yanbian yellow cattle. According to analysis of GH and somatostatin receptor 2 (SSTR2) mRNA and protein expression levels, we found that miR-10b targeted 3'UTR of SSTR2. Compared with the negative control (NC) group, GH mRNA transcription and protein expression in pituitary cells of Yanbian yellow cattle were significantly increased by adding miR-10b mimics (p < .01), while these were significantly decreased by adding miR-10b inhibitor (p < .05); compared with the NC group, SSTR2 mRNA transcription and protein expression were significantly inhibited by the addition of miR-10b mimics (p < .01), while these were significantly increased by the addition of miR-10b inhibitor compared with the iNC group (p < .05). This study suggested that miR-10b could regulate GH level by regulating SSTR2 gene expression in pituitary cells of Yanbian yellow cattle.

A large-scale comparison of meat quality and intramuscular fatty acid composition among three Chinese indigenous pig breeds.

Derived from the long historical natural and artificial selection, Chinese indigenous pigs have formed their own special meat characteristics. We herein systematically evaluated 14 meat characteristics and 15 fatty acid composition traits on three Chinese local pig breeds. The experimental pigs were produced by crossing design covering all sire genealogy and most of dam genealogy in each of the three breeds' seed conservation farms. All animals were reared in the same standardized housing and feeding conditions. A Comparison study showed that most of the investigated meat quality traits present significant differences among Bamaxiang, Erhualian and Laiwu breeds. While Erhualian pigs outperformed pH traits, the Laiwu pigs showed extremely high intramuscular fat content, better meat color and lower drip loss (P < .05). The highest contents of total saturated fatty acids and total polyunsaturated fatty acids were found in Laiwu and Erhualian, respectively. These results will benefit the future breeding utilization of these genetic resources for worldwide swine meat quality improvement.

An association study using imputed whole-genome sequence data identifies novel significant loci for growth-related traits in a Duroc × Erhualian F2 population.

The average daily gain (ADG) and body weight (BW) are very important traits for breeding programs and for the meat production industry, which have attracted many researchers to delineate the genetic architecture behind these traits. In the present study, single- and multi-trait genome-wide association studies (GWAS) were performed between imputed whole-genome sequence data and the traits of the ADG and BW at different stages in a large-scale White Duroc × Erhualian F2 population. A bioinformatics annotation analysis was used to assist in the identification of candidate genes that are associated with these traits. Five and seven genome-wide significant quantitative trait loci (QTLs) were identified by single- and multi-trait GWAS, respectively. Furthermore, more than 40 genome-wide suggestive loci were detected. On the basis of the whole-genome sequence association study and the bioinformatics analysis, NDUFAF6, TNS1 and HMGA1 stood out as the strongest candidate genes. The presented single- and multi-trait GWAS analysis using imputed whole-genome sequence data identified several novel QTLs for pig growth-related traits. Integrating the GWAS with bioinformatics analysis can facilitate the more accurate identification of candidate genes. Higher imputation accuracy, time-saving algorithms, improved models and comprehensive databases will accelerate the identification of causal genes or mutations, which will contribute to genomic selection and pig breeding in the future.

A whole-genome sequence based association study on pork eating quality traits and cooking loss in a specially designed heterogeneous F6 pig population.

To determine the genetic basis of pork eating quality traits and cooking loss, we herein performed a genome-wide association study (GWAS) for tenderness, juiciness, oiliness, umami, overall liking and cooking loss by using whole genome sequences of heterogeneous stock F6 pigs which were generated by crossing 4 typical western pig breeds (Duroc, Landrace, Large White and Pietrain) and 4 typical Asian pig breeds (Erhualian, Laiwu, Bamaxiang and Tibetan). We identified 50 associated loci (QTLs) and most of them are novel. Seven loci also showed pleiotropic associations with different traits. In addition, we identified multiple promising candidate genes for these traits, including PAK1 and AQP11 for cooking loss, EP300 for tenderness, SDK1 for juiciness, FITM2 and 5-linked MYH genes for oiliness, and TNNI2 and TNNT3 for overall liking. Our results provide not only a better understanding of the genetic basis for meat quality, but also a potential application in future breeding for these complex traits.

Effects of breeds, tissues and genders on purine contents in pork and the relationships between purine content and other meat quality traits.

The purine contents of animal foods are becoming widely concerned because excess intake of purine increases the risk of hyperuricemia and gout. In this study, we investigated the impacts of breed, tissue and sex on pork purine content and its correlations with multiple meat quality traits. Among six pig breeds, the average value of total purine contents (TP) in longissimus lumborum muscle was lowest in Chinese Laiwu pigs (114.2 mg/100 g) while highest in Chinese Bamaxiang mini pigs (139.3 mg/100 g). Considerable variations in TP were observed within most breeds, as well as among twelve pork organs with the range from 7 to 245 mg/100 g. However, no significant differences in TP were found between barrows and gilts. Intriguingly, lower purine content in meat was significantly associated with higher ultimate pH, better meat color and more abundant intramuscular fat content and marbling. The results thus suggest that the selection of low-purine pig species is available, which may simultaneously improve other meat quality traits.

Genome-wide association study identifies 22 new loci for body dimension and body weight traits in a White Duroc×Erhualian F2 intercross population.

OBJECTIVE: Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study was to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs. METHODS: A genome-wide association study (GWAS) on body dimension and body weight traits was performed in a White Duroc×Erhualian F2 intercross by the illumina PorcineSNP60K Beadchip. A mixed linear model was used to assess the association between single nucleotide polymorphisms (SNPs) and the phenotypes. RESULTS: In total, 611 and 79 SNPs were identified significantly associated with body dimension traits and body weight respectively. All SNPs but 62 were located into 23 genomic regions (quantitative trait loci, QTLs) on 14 autosomal and X chromosomes in Sus scrofa Build 10.2 assembly. Out of the 23 QTLs with the suggestive significance level (5×10-4), three QTLs exceeded the genome-wide significance threshold (1.15×10-6). Except the one on Sus scrofa chromosome (SSC) 7 which was reported previously all the QTLs are novel. In addition, we identified 5 promising candidate genes, including cell division cycle 7 for abdominal circumference, pleiomorphic adenoma gene 1 and neuropeptides B/W receptor 1 for both body weight and cannon bone circumference on SSC4, phosphoenolpyruvate carboxykinase 1, and bone morphogenetic protein 7 for hip circumference on SSC17. CONCLUSION: The results have not only demonstrated a number of potential genes/loci associated with the growth-related traits in pigs, but also laid a foundation for studying the genes' role and further identifying causative variants underlying these loci.

A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI.

Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10-5) and 88 SNPs had suggestive (P < 10-4) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.

Population structure and genome characterization of local pig breeds in Russia, Belorussia, Kazakhstan and Ukraine.

BACKGROUND: It is generally accepted that domestication of pigs took place in multiple locations across Eurasia; the breeds that originated in Europe and Asia have been well studied. However, the genetic structure of pig breeds from Russia, Belorussia, Kazakhstan and Ukraine, which represent large geographical areas and diverse climatic zones in Eurasia, remains largely unknown. RESULTS: This study provides the first genomic survey of 170 pigs representing 13 breeds from Russia, Belorussia, Kazakhstan and Ukraine; 288 pigs from six Chinese and seven European breeds were also included for comparison. Our findings show that the 13 novel breeds tested derived mainly from European pigs through the complex admixture of Large White, Landrace, Duroc, Hampshire and other breeds, and that they display no geographic structure based on genetic distance. We also found a considerable Asian contribution to the miniature Siberian pigs (Minisib breed) from Russia. Apart from the Minisib, Urzhum, Ukrainian Spotted Steppe and Ukrainian White Steppe breeds, which may have undergone intensive inbreeding, the breeds included in this study showed relatively high genetic diversity and low levels of homozygosity compared to the Chinese indigenous pig breeds. CONCLUSIONS: This study provides the first genomic overview of the population structure and genetic diversity of 13 representative pig breeds from Russia, Belorussia, Kazakhstan and Ukraine; this information will be useful for the preservation and management of these breeds.