Intergrating Genome And Transcriptome Analyses To Identify Selection Signatures In Pigs

Modern pigs have been domesticated from wild boars,so the process of domestication is also the process of human selection to pigs.The performances of pigs have been changed greatly,such as body shapes,yield and lifestyle,etc.The phenotypic changes indicate that the genes related to these traits have been mutated specifically,so the variations could leave information on genome-wide,which were called selection signatures or selection footprints.The research of important traits in domestication animals could help to reveal the genetic mechanisms of phenotypic variations in domestication,and identify the related genes with these traits,and provide the theory basis for molecular breeding.In this study,the population structure and selection signatures of different breeds from China and European pigs were analyzed by high density SNP chip and whole genome re-sequencing data,identified the selected regions/genes which associated with growth,reproduction,immune traits.Especially,using genomic and transcriptomics data,the domesticated genes associated with reproductive and immune traits were identified in commercial lean Large White and obese Tongcheng pigs.Mainly results were listed as follows:(1)With porcine Illumina Porcine 60K SNP Beadchip genotyping data from 207 Chinese indigenous,117 South American village and 408 Large White pigs,the variations of LD were estimated by VarLD on genome-wide between populations.The top 0.1%standardized VarLD scores were selected in all comparisons,and then compared with LD blocks,a total of four selection signatures on Sus scrofa chromosome(SSC)7,9,13 and 14 were identified in all populations.These regions were overlapped with quantitative trait loci(QTL)for linoleic acid content,body length,number of muscle fibers per unit area,hip structure and body weight.Among them,one of the signatures(56.5-56.6 Mb on SSC7)in Large White pigs harbored the ADAMTSL3 gene,which is known to be associated with body length.(2)The relative extended haplotype homozygosity(REHH)and FST methods were used to detect selection signatures in Large White and Tongcheng pigs.We found 34 candidate regions,including 61 known genes,from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs.According to quantitative trait loci(QTL)and Ingenuity Pathway Analysis(IPA),most genes in Large White were associated with growth and reproduction traits,and selected genes were mostly linked to immune responses in Tongcheng pigs.In addition,the average genetic differentiation coefficient FST was 0.254,which meant that there had already been significant differentiation between the breeds.(3)With the DNA sequencing datasets from 6 European wild boars,7 Chinese wild boars,20 Large White pigs and 28 Tongcheng pigs(including a mixed pool of 18 Tongcheng pigs and 10 Tongcheng individuals),the selection signatures of Large White and Tongcheng pig were identified by CLR and nucleotide polymorphism(π)methods.The FST index was calculated to detect the high differentiation regions/genes between Large White and Tongcheng pig.RNA sequencing was performed on the testis,spleen and Inguinaly lymph nodes(ILN)of 3 Large White and 3 Tongcheng pigs.The different genetic mechanisms in reproduction and immunology traits were analysed by integrating domesticated genes and differentially expressed genes(DEG).In the results,758 and 708 selected genes were identified in Large White and Tongcheng pig,respectively.Gene enrichment analyses showed that these selected genes were mainly associated with growth(body size,daily gain)and reproduction(embryonic development,litter size,male reproductive development)and other phenotypes.In the 6430 DEGs of testis tissue,many genes(e.g.,CATSPERD,PCSK4 and INSL6)were related to the biological processes of sperm formation,sperm cell development,sperm motility,meiosis,and so on.A total of 183 highly differentiated genes(e.g.,NFKB1,PIK3R1,IL6 and FADD)selected by the FST method to participate in the immune system,interleukin and Wnt signaling pathways.Multiple DEGs(e.g.,AZU1,CCNF,KIF4A,ELOB and TBCB)in spleen and/or LIN tissues were only highly expressed in Tongcheng pigs.