Analysis Of Selection Signatures In Baoshan Pigs Based On Whole Sequencing Data

Baoshan pig is a local pig breed in Yunnan province,China,with excellent characteristics such as good meat quality,higher large litter size,good maternal performance,strong adaptability,tolerance to rough feeding,and strong disease resistance;However,there are shortcomings such as slow growth speed and low lean meat rate due to the continuous decrease in the distribution range and number of Baoshan pigs,and the intraspecific genetic diversity has decreased.In this study,the whole genome of 12 Baoshan pigs was resequenced to detect the genetic variation in genome.The Asian wild boar and Duroc pigs were used as reference groups,and the selection signal analysis was conducted by combining Fst and π ratio analysis to identify the selected regions.GO and KEGG enrichment analysis and QTL mapping were used to perform biological function.Then screen candidate genes related to germplasm characteristics of Baoshan pig.The results were as followed.(1)Resequencing results of the whole genome: A total of 339.12 G of original data were obtained,and 23 386,277 SNP loci were obtained after quality control.Most of the genetic variation was in the intergene region,followed by the intron region,and the number of variation in the exon region was the least.Most of the genetic variation was more conversions than transversions and more synonymous mutations than missense mutations.(2)Used Asian wild pigs as reference group,the selection signature analysis of Baoshan pig was conducted.A total of 779 selected regions were identified,including377 genes.The potential selected regions overlapped with the QTLs of antibody level,immunity,daily gain,PH,etc.NCOA7,NLRC3 and ZC3H10 genes related to immunity and disease.LIPE,ECI1 and HMGA1 genes related to carcass and meat quality.CSN1S1 and AKT2 genes related to reproduction.And MC1 R genes related to coat color of Baoshan pigs were annotated.(3)Used Duroc pigs as reference group,the selection signature analysis of Baoshan pigs was conducted.A total of 212 selected regions were identified,containing 159 genes.The potential selected regions mostly overlapped with the QTLs of antibody level,immunity,backfat thickness,ketone body length,etc.NCOA7,NLRC3 and ABCA3 genes related to immunity and disease.MEF2 A,CKM and CKMT2 genes related to growth and development.RSPO3,MARK4,LIPE and AURKC genes related to reproduction.PFKM genes related to glucose metabolism of Baoshan pigs were annotated.In this study,genome data and genetic variation information of Baoshan pig population were obtained by whole genome resequencing technology,and some candidate genes were screened which were related to reproduction,immunity,metabolism,hair color,we initially revealed the genetic basis of germplasm characteristics of Baoshan pig,and provided reference for breeding preservation,breeding,and discovered characteristic molecular markers of Baoshan pig.