Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets.

BACKGROUND: Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics. RESULTS: In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes in healthy and FLHS hens. The study results indicated that H3K27me3 levels were increased in the FLHS hens on a genome-wide scale. Additionally, H3K27me3 was found to occupy the entire gene and the distant intergenic region, which may function as silencer-like regulatory elements. The analysis of transcription factor (TF) motifs in hypermethylated peaks has demonstrated that 23 TFs are involved in the regulation of liver metabolism and development. Transcriptomic analysis indicated that differentially expressed genes (DEGs) were enriched in fatty acid metabolism, amino acid, and carbohydrate metabolism. The hub gene identified from PPI network is fatty acid synthase (FASN). Combined ChIP-seq and transcriptome analysis revealed that the increased H3K27me3 and down-regulated genes have significant enrichment in the ECM-receptor interaction, tight junction, cell adhesion molecules, adherens junction, and TGF-beta signaling pathways. CONCLUSIONS: Overall, the trimethylation modification of H3K27 has been shown to have significant regulatory function in FLHS, mediating the expression of crucial genes associated with the ECM-receptor interaction pathway. This highlights the epigenetic mechanisms of H3K27me3 and provides insights into exploring core regulatory targets and nutritional regulation strategies in FLHS.

Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method.

HIV-1 viruses, which are predominant in the family of HIV viruses, have strong pathogenicity and infectivity. They can evolve into many different variants in a very short time. In this study, we propose a new and effective alignment-free method for the phylogenetic analysis of HIV-1 viruses using complete genome sequences. Our method combines the position distribution information and the counts of the k-mers together. We also propose a metric to determine the optimal k value. We name our method the Position-Weighted k-mers (PWkmer) method. Validation and comparison with the Robinson-Foulds distance method and the modified bootstrap method on a benchmark dataset show that our method is reliable for the phylogenetic analysis of HIV-1 viruses. PWkmer can resolve within-group variations for different known subtypes of Group M of HIV-1 viruses. This method is simple and computationally fast for whole genome phylogenetic analysis.

Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects.

BACKGROUND: Meat production from the commercial crossbred Duroc × (Landrace × Yorkshire) (DLY) pig is predominant in the pork industry, but its meat quality is often impaired by low ultimate pH (pHu). Muscle glycogen level at slaughter is closely associated with pHu and meat technological quality, but its genetic basis remains elusive. The aim of this study was to identify genes and/or causative mutations associated with muscle glycogen level and other meat quality traits by performing a genome-wide association study (GWAS) and additional analyses in a population of 610 DLY pigs. RESULTS: Our initial GWAS identified a genome-wide significant (P = 2.54e-11) quantitative trait locus (QTL) on SSC15 (SSC for Sus scrofa chromosome) for the level of residual glycogen and glucose (RG) in the longissimus muscle at 45 min post-mortem. Then, we demonstrated that a low-frequency (minor allele frequency = 0.014) R200Q missense mutation in the PRKAG3 (RN) gene caused this major QTL effect on RG. Moreover, we showed that the 200Q (RN-) allele was introgressed from the Hampshire breed into more than one of the parental breeds of the DLY pigs. After conditioning on R200Q, re-association analysis revealed three additional QTL for RG on SSC3 and 4, and on an unmapped scaffold (AEMK02000452.1). The SSC3 QTL was most likely caused by a splice mutation (g.8283C>A) in the PHKG1 gene that we had previously identified. Based on functional annotation, the genes TMCO1 on SSC4 and CKB on the scaffold represent promising candidate genes for the other two QTL. There were significant interaction effects of the GWAS tag SNPs at those two loci with PRKAG3 R200Q on RG. In addition, a number of common variants with potentially smaller effects on RG (P < 10-4) were uncovered by a second conditional GWAS after adjusting for the two causal SNPs, R200Q and g.8283C>A. CONCLUSIONS: We found that the RN- allele segregates in the parental lines of our DLY population and strongly influences its meat quality. Our findings also indicate that the genetic basis of RG in DLY can be mainly attributed to two major genes (PRKAG3 and PHKG1), along with many minor genes.

A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle.

Glycolytic potential (GP) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the phenotype QTL (pQTL). We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL) mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK), which functions in the cascade activation of glycogen breakdown. Deep sequencing of PHKG1 revealed a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. The mutation causes an increase of 43% in GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs.

Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations.

BACKGROUND: Fatty acid composition in muscle is an important factor that affects the nutritive value and taste of pork. To investigate the genetic architecture of fatty acid composition of pork, we measured fatty acid contents in longissimus dorsi muscle of 1244 pigs from three divergent populations and conducted genome-wide association studies (GWAS) for fatty acid contents. RESULTS: We detected 26 genome-wide significant quantitative trait loci (QTL) on eight chromosomes (SSC for Sus scrofa) for eight fatty acids. These loci not only replicated previously reported QTL for C18:0 on SSC14 and C20:0 on SSC16, but also included several novel QTL such as those for C20:1 on SSC7, C14:0 on SSC9, and C14:0, C16:0 and C16:1 on SSC12. Furthermore, we performed a meta-analysis of GWAS on five populations, including the three populations that were investigated in this study and two additional populations that we had previously examined. This enhanced the strength of the associations detected between fatty acid composition and several marker loci, especially for those for C18:0 on SSC14 and C20:0 on SSC16. The genes ELOVL5, ELOVL6, ELOVL7, FASN, SCD and THRSP, which have functions that are directly relevant to fatty acid metabolism, are proximal to the top associated markers at six significant QTL. CONCLUSIONS: The findings improve our understanding of the genetic architecture of fatty acid composition in pork and contribute to further fine-map and characterize genes that influence fatty acid composition.

Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs.

Meat quality traits have economically significant impacts on the pig industry, and can be improved using molecular approaches in pig breeding. Since 1994 when the first genome-wide scan for quantitative trait loci (QTLs) in pig was reported, over the past two decades, numerous QTLs have been identified for meat quality traits by family based linkage analyses. However, little is known about the genetic variants for meat quality traits in Chinese purebred or outbred populations. To unveil it, we performed a genome-wide association study for 10 meat quality traits in Chinese purebred Laiwu pigs. In total, 75 significant SNPs (P < 1.01 × 10(-6)) and 33 suggestive SNPs (P < 2.03 × 10(-5)) were identified. On SSC12, a region between 56.22 and 61.49 Mb harbored a cluster of SNPs that were associated with meat color parameters (L*, lightness; a*, redness; b*, yellowness) and moisture content of longissimus muscle (LM) and semimembranosus muscle at the genome-wide significance level. A region on SSC4 also has pleiotropic effects on moisture content and drip loss of LM. In addition, this study revealed at least five novel QTLs and several candidate genes including 4-linked MYH genes (MYH1, MYH2, MYH3, and MYH13), MAL2, LPAR1, and PRKAG3 at four significant loci. Except for the SSC12 QTL, other QTLs are likely tissue-specific. These results provide new insights into the genetic basis of meat quality traits in Chinese Laiwu pigs and some significant SNPs reported here could be incorporated into the selection programs involving this breed.

Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles.

There has been a growing interest in alignment-free methods for whole genome comparison and phylogenomic studies. In this study, we propose an alignment-free method for phylogenetic tree construction using whole-proteome sequences. Based on the inter-amino-acid distances, we first convert the whole-proteome sequences into inter-amino-acid distance vectors, which are called observed inter-amino-acid distance profiles. Then, we propose to use conditional geometric distribution profiles (the distributions of sequences where the amino acids are placed randomly and independently) as the reference distribution profiles. Last the relative deviation between the observed and reference distribution profiles is used to define a simple metric that reflects the phylogenetic relationships between whole-proteome sequences of different organisms. We name our method inter-amino-acid distances and conditional geometric distribution profiles (IAGDP). We evaluate our method on two data sets: the benchmark dataset including 29 genomes used in previous published papers, and another one including 67 mammal genomes. Our results demonstrate that the new method is useful and efficient.

Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations.

BACKGROUND: Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population. RESULTS: We identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits. CONCLUSIONS: We confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.

Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population.

BACKGROUND: Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population. METHODS: Three hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F2 and Sutai pig populations. RESULTS: We detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several relevant candidate genes. CONCLUSIONS: These findings provide valuable insights into the molecular basis of convergent evolution of meat quality traits in Chinese and Western breeds that show divergent phenotypes. They may contribute to genetic improvement of purebreds for crossbred performance.

Population history and genomic signatures for high-altitude adaptation in Tibetan pigs.

BACKGROUND: The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds. RESULTS: Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals. CONCLUSION: Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

Microbial characterization based on multifractal analysis of metagenomes.

Introduction: The species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research. Method and Results: Firstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences. Conclusion and Discussion: There is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants' gut microbiomes are related to the development of the infants.

An in situ-forming polyzwitterion hydrogel: Towards vitreous substitute application.

Development of a biostable and biosafe vitreous substitute is highly desirable, but remains a grand challenge. Herein, we propose a novel strategy for constructing a readily administered vitreous substitute based on a thiol-acrylate clickable polyzwitterion macromonomer. A biocompatible multivinyl polycarboxybetaine (PCB-OAA) macromonomer is designed and synthesized, and mixed with dithiothreitol (DTT) via a Michael addition reaction to form a hydrogel in vitreous cavity. This resultant PCB-OAA hydrogel exhibits controllable gelation time, super anti-fouling ability against proteins and cells, excellent biocompatibility, and approximate key parameters to human vitreous body including equilibrium water content, density, optical properties, modulus. Remarkably, outperforming clinically used silicone oil in biocompatibility, this rapidly formed hydrogel in the vitreous cavity of rabbit eyes remains stable in vitreous cavity, showing an appealing ability to prevent significantly inflammatory response, fibrosis and complications such as raised intraocular pressure (IOP), and cataract formation. This zwitterionic polymer hydrogel holds great potential as a vitreous substitute.

Restoring Cardiac Functions after Myocardial Infarction-Ischemia/Reperfusion via an Exosome Anchoring Conductive Hydrogel.

Both myocardial infarction (MI) and the follow-up reperfusion will lead to an inevitable injury to myocardial tissues, such as cardiac dysfunctions, fibrosis, and reduction of intercellular cell-to-cell interactions. Recently, exosomes (Exo) derived from stem cells have demonstrated a robust capability to promote angiogenesis and tissue repair. However, the short half-life of Exo and rapid clearance lead to insufficient therapeutic doses in the lesion area. Herein, an injectable conductive hydrogel is constructed to bind Exo derived from human umbilical cord mesenchymal stem cells to treat myocardial injuries after myocardial infarction-ischemia/reperfusion (MI-I/R). To this end, a hyperbranched epoxy macromer (EHBPE) grafted by an aniline tetramer (AT) was synthesized to cross-link thiolated hyaluronic acid (HA-SH) and thiolated Exo anchoring a CP05 peptide via an epoxy/thiol "click" reaction. The resulting Gel@Exo composite system possesses multiple features, such as controllable gelation kinetics, shear-thinning injectability, conductivity matching the native myocardium, soft and dynamic stability adapting to heartbeats, and excellent cytocompatibility. After being injected into injured hearts of rats, the hydrogel effectively prolongs the retention of Exo in the ischemic myocardium. The cardiac functions have been considerably improved by Gel@Exo administration, as indicated by the enhancing ejection fraction and fractional shortening, and reducing fibrosis area. Immunofluorescence staining and reverse transcription-polymerase chain reaction (RT-PCR) results demonstrate that the expression of cardiac-related proteins (Cx43, Ki67, CD31, and α-SMA) and genes (VEGF-A, VEGF-B, vWF, TGF-ß1, MMP-9, and Serca2a) are remarkably upregulated. The conductive Gel@Exo system can significantly improve cell-to-cell interactions, promote cell proliferation and angiogenesis, and result in a prominent therapeutic effect on MI-I/R, providing a promising therapeutic method for injured myocardial tissues.

Effects of a high energy and low protein diet on hepatic and plasma characteristics and Cidea and Cidec mRNA expression in liver and adipose tissue of laying hens with fatty liver hemorrhagic syndrome.

Cidea and Cidec are two members of Cell death-inducing DNA fragmentation factor-alpha-like effector family proteins, which could be involved in lipid or fat metabolism. To better understand the roles of Cidea and Cidec in fatty liver hemorrhagic syndrome (FLHS), 150 healthy 155-day-old Hyline Brown laying hens were randomly divided into control group (fed with basic diet) and experimental group (fed with high-energy low-protein [HELP] diet). Analysis of the liver by tissue sectioning and hematoxylin and eosin staining showed that the HELP diet induced micro-vesicular steatosis in laying hens. Subsequently, based on the liver color scores and the range of lipid accumulation observed in histological examination, we classified livers with <50% vacuolization as mild FLHS and >50% as severe FLHS. The results showed that the levels of Cidea and Cidec mRNA expression were markedly elevated in the liver and adipose tissues with FLHS and the levels of Cidea and Cidec mRNA expression in the liver with severe FLHS were significantly higher than that in the liver with mild FLHS. Thus, the present study revealed that the Cidea and Cidec genes may be involved in pathways of FLHS formation.

Fractal and multifractal analyses of bipartite networks.

Bipartite networks have attracted considerable interest in various fields. Fractality and multifractality of unipartite (classical) networks have been studied in recent years, but there is no work to study these properties of bipartite networks. In this paper, we try to unfold the self-similarity structure of bipartite networks by performing the fractal and multifractal analyses for a variety of real-world bipartite network data sets and models. First, we find the fractality in some bipartite networks, including the CiteULike, Netflix, MovieLens (ml-20m), Delicious data sets and (u, v)-flower model. Meanwhile, we observe the shifted power-law or exponential behavior in other several networks. We then focus on the multifractal properties of bipartite networks. Our results indicate that the multifractality exists in those bipartite networks possessing fractality. To capture the inherent attribute of bipartite network with two types different nodes, we give the different weights for the nodes of different classes, and show the existence of multifractality in these node-weighted bipartite networks. In addition, for the data sets with ratings, we modify the two existing algorithms for fractal and multifractal analyses of edge-weighted unipartite networks to study the self-similarity of the corresponding edge-weighted bipartite networks. The results show that our modified algorithms are feasible and can effectively uncover the self-similarity structure of these edge-weighted bipartite networks and their corresponding node-weighted versions.

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.

Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.

Genome-wide association analyses for fatty acid composition in porcine muscle and abdominal fat tissues.

Fatty acid composition is an important phenotypic trait in pigs as it affects nutritional, technical and sensory quality of pork. Here, we reported a genome-wide association study (GWAS) for fatty acid composition in the longissimus muscle and abdominal fat tissues of 591 White Duroc×Erhualian F2 animals and in muscle samples of 282 Chinese Sutai pigs. A total of 46 loci surpassing the suggestive significance level were identified on 15 pig chromosomes (SSC) for 12 fatty acids, revealing the complex genetic architecture of fatty acid composition in pigs. Of the 46 loci, 15 on SSC5, 7, 14 and 16 reached the genome-wide significance level. The two most significant SNPs were ss131535508 (P = 2.48×10(-25)) at 41.39 Mb on SSC16 for C20∶0 in abdominal fat and ss478935891 (P = 3.29×10(-13)) at 121.31 Mb on SSC14 for muscle C18∶0. A meta-analysis of GWAS identified 4 novel loci and enhanced the association strength at 6 loci compared to those evidenced in a single population, suggesting the presence of common underlying variants. The longissimus muscle and abdominal fat showed consistent association profiles at most of the identified loci and distinct association signals at several loci. All loci have specific effects on fatty acid composition, except for two loci on SSC4 and SSC7 affecting multiple fatness traits. Several promising candidate genes were found in the neighboring regions of the lead SNPs at the genome-wide significant loci, such as SCD for C18∶0 and C16∶1 on SSC14 and ELOVL7 for C20∶0 on SSC16. The findings provide insights into the molecular basis of fatty acid composition in pigs, and would benefit the final identification of the underlying mutations.

Genome-wide association study of meat quality traits in a White Duroc×Erhualian F2 intercross and Chinese Sutai pigs.

Thousands of QTLs for meat quality traits have been identified by linkage mapping studies, but most of them lack precise position or replication between populations, which hinder their application in pig breeding programs. To localize QTLs for meat quality traits to precise genomic regions, we performed a genome-wide association (GWA) study using the Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality traits, including pH, color, drip loss, moisture content, protein content and intramuscular fat content (IMF), marbling and firmness scores in the M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on the two populations. In total, 127 chromosome-wide significant SNPs for these traits were identified. Among them, 11 SNPs reached genome-wise significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28 genomic regions of approximately 10 Mb or less. Most of these regions corresponded to previously reported QTL regions and spanned smaller intervals than before. The loci on SSC3 and SSC7 appeared to have pleiotropic effects on several related traits. Besides them, a few QTL signals were replicated between the two populations. Further, we identified thirteen new candidate genes for IMF, marbling and firmness, on the basis of their positions, functional annotations and reported expression patterns. The findings will contribute to further identification of the causal mutation underlying these QTLs and future marker-assisted selection in pigs.