A genome-wide analysis of the ultimate pH in swine

A novel QTL region for pH and meat color in Duroc pigs

One of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional candidate genes in these regions included PRKAG3 and PHKG1. The SSC8 region, at 71.6 Mb, was novel and, although no candidate causative gene could be identified, it may have regulatory effects. Subsequent analysis on 828 pigs from the same population confirmed the impact of the three associated regions on pH and meat color. We detected no interaction between the three regions. Further investigations are necessary to unravel the functional significance of the novel genomic region at SSC8. These variants could be used as markers in marker-assisted selection for improving meat quality.

Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations

Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations: Asian domesticated (AD), European domesticated (ED), Asian wild (AW), European wild (EW), and Near Eastern wild (NEW). In total, 21,673 genes were identified on 154,872 copy number variation region (CNVR). Differences in gene copy numbers between populations were measured by considering the variance-based value [Formula: see text] and the one-way ANOVA test followed by Scheffe test. As a result, 111 genes were suggested as copy number variable genes. Abnormally gained copy number on EEA1 in all populations was suggested the presence of minor CNV in the reference genome assembly, Sscrofa11.1. Copy number variable genes were related to meat quality, immune response, and reproduction traits. Hierarchical clustering of all individuals and mean pairwise [Formula: see text] in breed level were visualized genetic relationship of 328 individuals and 56 populations separately. Our findings have shown how the complex history of pig evolution appears in genome-wide CNV of various populations with different regions and lifestyles.

Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs

Improvement of feed efficiency (FE) is key for Sustainability and cost reduction in pig production. Our aim was to characterize the muscle transcriptomic profiles in Danbred Duroc (Duroc; n = 13) and Danbred Landrace (Landrace; n = 28), in relation to FE for identifying potential biomarkers. RNA-seq data on the 41 pigs was analyzed employing differential gene expression methods, gene-gene interaction and network analysis, including pathway and functional analysis. We also compared the results with genome regulation in human exercise data, hypothesizing that increased FE mimics processes triggered in exercised muscle. In the differential expression analysis, 13 genes were differentially expressed, including: MRPS11, MTRF1, TRIM63, MGAT4A, KLH30. Based on a novel gene selection method, the divergent count, we performed pathway enrichment analysis. We found five significantly enriched pathways related to feed conversion ratio (FCR). These pathways were mainly related to mitochondria, and summarized in the mitochondrial translation elongation (MTR) pathway. In the gene interaction analysis, the most interesting genes included the mitochondrial genes: PPIF, MRPL35, NDUFS4 and the fat metabolism and obesity genes: AACS, SMPDL3B, CTNNBL1, NDUFS4, and LIMD2. In the network analysis, we identified two modules significantly correlated with FCR. Pathway enrichment of module genes identified MTR, electron transport chain and DNA repair as enriched pathways. The network analysis revealed the mitochondrial gene group NDUF as key network hub genes, showing their potential as biomarkers. Results show that genes related to human exercise were enriched in identified FCR related genes. We conclude that mitochondrial activity is a key driver for FCR in muscle tissue, and mitochondrial genes could be potential biomarkers for FCR in pigs.

Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs

BACKGROUND

The pig breeding industry has undergone a large number of mergers in the past decades. Various commercial lines were merged or discontinued, which is expected to reduce the genetic diversity of the pig species. The objective of the current study was to investigate the genetic diversity of different former Dutch Landrace breeding lines and quantify their relationship with the current Dutch Landrace breed that originated from these lines.

RESULTS

Principal component analysis clearly divided the former Landrace lines into two main clusters, which are represented by Norwegian/Finnish Landrace lines and Dutch Landrace lines. Structure analysis revealed that each of the lines that are present in the Dutch Gene bank has a unique genetic identity. The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former lines. The Dumeco N-line, which is conserved in the Dutch Gene bank, is poorly represented in the current Dutch Landrace. All seven lines (the six former and the current line) contribute almost equally to the genetic diversity of the Dutch Landrace breed. As expected, the current Dutch Landrace breed comprises only a small proportion of unique genetic diversity that was not present in the other lines. The genetic diversity level, as measured by Eding's core set method, was equal to 0.89 for the current Dutch Landrace breed, whereas total genetic diversity across the seven lines, measured by the same method, was equal to 0.99.

CONCLUSIONS

The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former Dutch Landrace lines. Merging of commercial Landrace lines has reduced the genetic diversity of the Landrace population in the Netherlands, although a large proportion of the original variation is maintained. Thus, our recommendation is to conserve breeding lines in a gene bank before they are merged.

Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds

The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by F_st within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.

Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

BACKGROUND

Piglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. The current study focused on identifying loci associated with PSL through a genome-wide association study (GWAS) performed with the Illumina Porcine60 SNP Beadchip v2.0. The study was a case/control design with four pig populations (Duroc, Landrace, Yorkshire and one crossbred of Landrace × Yorkshire).

RESULT

After quality control of the genotyping data, 185 animals (73 cases, 112 controls) and 43,495 SNPs were retained for further analysis. Principal components (PCs) identified from the genomic kinship matrix were included in the statistical model for correcting the effect of population structure. Seven chromosome-wide significant SNPs were identified on Sus scrofa chromosome 1 (SSC1), SSC2 (2 SNPs), SSC7, SSC15 (2 SNPs) and SSC16 after strict Bonferroni correction. Four genes (HOMER1 and JMY on SSC2, ITGA1 on SSC16, and RAB32 on SSC1) related to muscle development, glycogen metabolism and mitochondrial dynamics were identified as potential candidate genes for PSL.

CONCLUSIONS

We identified seven chromosome-wide significant SNPs associated with PSL and four potential candidate genes for PSL. To our knowledge, this is the first pilot study aiming to identify the loci associated with PSL using GWAS. Further investigations and validations for those findings are encouraged.

Genetic determinants of pig birth weight variability

Background

Piglet birth weight variability, a trait also known as the within-litter homogeneity of birth weight, reflects the sow’s prolificacy, because it is positively genetically correlated with preweaning mortality but negatively correlated with the mean growth of piglets during sucking. In addition, the maternal additive genetic variance and heritability has been found exist for this trait, thus, reduction in the variability of piglet birth weight to improve the sow prolificacy is possible by selective breeding.

Results

We performed a genome wide association study (GWAS) in 82 sows with extreme standard deviation of birth weights within the first parity to identify significant SNPs, and finally 266 genome-wide significant SNPs (p < 0.01) were identified. These SNPs were mainly enriched on chromosome 7, 1, 13, 14, 15 and 18. We further scanned genes of the top 50 SNPs with the lowest p values and found some genes involved in plasma glucose homeostasis (GLP1R) and lipid metabolism as well as maternal-fetal lipid transport (AACS, APOB, OSBPL10 and LRP1B) which may contribute to the birth weight variability trait.

Conclusions

Birth weight variability trait has a low heritability. It is not easy to get significant signal by GWAS using small sample size. Herein, we identified some candidate chromosome regions especially chromosome 7 and suggested five genes which may provide some information for the further study.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0309-6) contains supplementary material, which is available to authorized users.