Exploring The Genetic Diversity And Selection Signatures Of The Conservation Population Of Meishan Pigs

Chinese Meishan pig,which is one of the famous indigenous pig breed in the Taihu Lake region of China,has been renowned for its high prolificacy and superior meat quality.This breed can be divided into two types based on the body size:Middle Meishan(MMS)pigs and Small Meishan(SMS)pigs.Late last century,with the importion of European and American pigs,farmers have started to ignore purebred breeding and pay much attention to the hybridization.This resulted in the mixed ancestry and the serious decrease of purebred Meishan pigs.Thus,in order to protect this valuable genetic resource,some conservation farms were established in Jiangsu and Shanghai in the 1970s.In order to avoid the influence of inbreeding,differentiation,mutation and selection,the conservation method of each farm was:reserve the same descendants in each pedigree.Thus,how does the effect(genetic diversity and genetic structure)of breeds conservation after recent several decades conservation.And what happened to the genome of Meishan pigs(selection signatures).Thus,using the genome sequencing data of the four farms of Meishan pigs,the main work and results of this research were as follows:(1)Genome variants detection.Using the genome sequencing data of the four farms of Meishan pigs,a total of 111,398 SNPs were detected.It was found that the distribution of these SNPS were covered the scope of whole genome.The density of these SNPS was relatively uniform in the whole genome.The minor allele frequence of these SNPs was mainly ranged from 0.05 to 0.2.Compared with the pig SNP database,a total of16,640(14.94%)SNPs were the newfound.A total of 35%of SNPs in the X chromosome were newfound SNPs.These results provide the genetic variants information for the subsequent analysis.These SNPs were also partly reflects the unique characters of Meishan pigs and enriched the pig genome SNP markers.(2)The genetic diversity and genetic structure analysis.Using the111,398 SNPs,the genetic diversity and genetic structure of the Meishan pigs were detected.It was found that every farm of Mishan pigs has a low effective population sizes.The Small Meishan population have a higher H_O and H_E,and the Middle Meishan population has a higher P_N.There is an apparent differentiation and genetic distance between the Middle and Small population with the Fst value is 0.111 and the genetic distance is0.287.There is a moderate differentiation between the two conservation farms of the Middle Meishan pigs(Fst=0.127,D=0.273),and a weak differentiation between the two conservation farms of Small Meishan pigs(Fst=0.055,D=0.239).These analysis results show that the conservation working of Meishan pigs still need to continue.It may be reasonable that the Middle Meishan pigs and Small Meishan pigs were conserved in the different farms.But,in order to avoid the differentiation,the pigs from the same type in different farms may need increase the gene exchange.(3)The annotation of genome variants.The all SNPs,the newfound SNPs,the homozygosity SNPs of the Middle Meishan pigs compared with the Small Meishan pigs,the homozygosity SNPs of the Small Meishan pigs compared with the Middle Meishan pigs.the homozygosity SNPs of the Kunshan population compared with the Jiading population in Middle Meishan pigs,the homozygosity SNPs of the Kunshan population compared with the Jiading population in Middle Meishan pigs were used to analysis.Mapping these SNPs to the genome,a total of 96.40%to97.75%SNPs were located in the intergenic region and a total of 2.17%to 3.14%SNPs were located in the exon.Enrichment analysis showed that these genes related to the all SNPs were mainly associated with immune and fat metabolism.There is unique polymorphism related to reproduction and meat quality in Meishan pigs.Those homozygosity SNPs were mainly associated with immue.Mapping these SNPs to the QTL,the SNPs were mianly located in the QTL of meat and carcasss,reproduction and exterior.In this part,these results may explain the function of variants of Meishan pigs from the genome level.And it also provide to give insight into the differentiation of the different farms of the Meishan pig.(4)The detection of selection signatures.In order to detect the selected signatures of all the Meishan pigs,a total of 52 signatures(p<0.01)were detected based on the REHH test.And these signatures were mainly associated with the reproduction and fat metabolism.In order to detect the selected signatures between the genome of Middle Meishan and Small Meishan populations,XP-EHH and Fst test was used to detect the signals.The results showed that most of the selection signals occurred in the Small meishan population,and they are mainly related to reproduction and growth traits.In order to detect the signals between Jiading population and Kunshan population,XP-EHH and Fst test was used to detect the signals.We found that the signals were mainly related to immune traits,especially respiratory diseases.The results showed that the Meishan population was mainly affected by reproduction and fat-related selection during the past conservation.The population differentiation of Middle Meishan and Small meishan mainly focused on the difference of reproduction and body size.The population differentiation among different conservation sites in Middle meishan population was mainly related to immune traits.