Whole Genome ROH Detection and Selection Signal Analysis in Sushan Pigs and Berkshire Pigs
In order to clarify the genetic variation sites and polymorphic information of the Sushan pig population and the Berkshire pig population,the DNA samples from 43 Sushan pigs and 21 Berkshire pigs were extracted and SNP sites were detected by 50K SNP beadchip in this study.Plink software was used for principal component analysis of the SNP sites;The DetectRUNS software package was used for whole-genome ROH detection of the samples;Three methods(ROH,CLR,and iHS)were used to analyze the selection signals.A total of 42 282 SNPs were identified in Sushan pigs and 27 718 SNPs in Berkshire pigs.Both breeds were divided into 3 fam-ilies.There were 2 071 ROH segments were detected in Sushan pigs with an average FROH value of 0.096,and 1 853 ROH segments were detected in Berkshire pigs with an average FROH value of 0.199.Four and 40 high-frequency ROH regions were detected in the Sushan pig and Berkshire pig populations,respectively,which were annotated to 8 and 103 genes.There were 50 signifi-cant candidate genes were identified through enrichment analysis.Additionally,three selection signal analysis methods(ROH,CLR and iHS)were used to identify selection signal regions in Sushan pigs and Berkshire pigs,which illustrated that 42 genes could be under selection.This study preliminarily revealed the genomic SNP pattern of Sushan pigs and Berkshire pigs and excavated some genes that may affect pig growth and development,meat quality,nutrition,and general disease resistance by high-frequency ROH analysis and selection signal detection,which provided a theoretical basis for the breeding and utilization of Sushan pigs and Berkshire pigs.
万方数据
维普
