Multiple Omics Analysis Revealed Economic Characters Related Genomic Signatures And Molecular Pathways In Enshi Black Pig

The overwhelming reports showed that genes or genomic regions under selection in domesticated organisms can be directly implicated in genetic breeding programs and greatly increases the efficiency of producing novel and desirable phenotypes,and gene methylation level and expression level is significant correlated to selection signature.Enshi black pig is one of typical meat-lard pig breed and could be characterized by several better traits,such as good meat texture,better adaptability,fat storage ability and high fecundity.To explore the genetic regulation mechanism of several traits underlying their domestication,we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations,and sampled liver tissues from Enshi black pig,Large White pig,and Chinese wild boar with 90-days-old and different traits of commercial interest for whole-genome bisulfite sequencing,mRNA sequencing,and microRNA sequencing.Integrated outcomes of four omics are provided and the main points are indicated as follows:(1)We obtained the complete mtDNA sequence for each of the five individuals from three sub-populations of Enshi black pigs in different area of Enshi Tujia and Miao Autonomous Prefecture.The complete mtDNA sequence was about 16.7kb,and genetic divergence among the three kinds of Enshi pig was subtle.(2)A total of 266.30 GB sequencing data were generated from three Enshi black pig populations and a Chinese wild boar population.About 14 M SNPs were found in each group,and 60.92% SNPs were shared between the Enshi black pigs and Chinese wild boar,75.56% SNPs were shared among three Enshi black pig populations.The phylogeny analysis indicated that Enshi black pigs had subtle genetic divergence,especially between large size group(Shizitou)and medium size group(Ermei).(3)A total of 417 genes embedded in selected regions,and they belong predominantly to categories that are related to metabolic processes,response to stimulus,and developmental processes.We also find that RPS10,GSK3 A,INSL6,TBX19,and VASN showed strong signaling of positive selection.These genes are involved in crucial biological processes such as body size,immunity,obesity,male fertility,and early development.(4)We constructed the genome-wide methylome at a single-base resolution for liver tissue of Enshi black pigs,Large White,and Chinese wild boar for the first time,and found the methylation occurred more frequently in the CpG dinucleotide than CHG and CHH contexts.(5)Differentially methylated genes between Enshi black pig and other above two pig breeds were significantly enriched in transport,cell differentiation,and immune-related categories.Differentially expressed genes between Enshi black pig and other above two pig breeds were significantly enriched in energy metabolic and immune-related categories.Differentially expressed miRNAs between Enshi black pig and other above two pig breeds were significantly enriched in metabolic processes and developmental processes.Each omics data can partially reveal the molecular mechanisms of regulating economic traits of Enshi black pig,and the regulation may not be a single behavior but a joint action of all omics via a complicated way in the swine liver tissue.(6)The promoters of highly expressed genes tended to exhibit low methylation levels,while the promoters of genes with low expression were usually highly methylated.Only 50% DEGs are regulated by this pattern,it indicate that the promoter methylation is just one of the many important factors that influence gene expression.The promoters of highly expressed miRNAs tended to exhibit low methylation levels,while the promoters of mi RNAs with low expression were usually highly methylated.But few miRNAs are regulated by promoter methylation and mi RNAs may have a different regulation mechanism from the protein-coding genes.Besides,the selected genes were up-expressed and hypomethylated in all pig breeds,it may indicated that those genes play an important role in basic biological process of pigs.Collectively,these findings could help us uncover the underlying molecular basis of the origin and the development of important economic traits of pigs that will further be used to improve artificial selection efficiency and contribute to the genetic improvements of pig.