Study On Revealing The Genetic Basis Of Parallel Selection Between Pietrain And Duroc Based On Selection Signal Analysis

The long-term goal of breeders is to genetically improve pigs for important economic traits.According to the meat quality,reproduction,growth and carcass traits,pig breeds with different production characteristics have been bred.The ternary hybrid method is applied to the production of modern commercial pigs.Pietrain and Duroc are used as terminal male parents in modern pig hybrid systems due to their fast growth rate and high carcass lean rate.This is the result of long-term artificial selection.Long-term selection will leave relevant selection signal "trace" on the pig genome.The genes related to pig reproductive traits and meat quality traits will be discovered through selection signal research.These genes can analyze the genetic basis for Duroc pigs and Pietrain pigs to be used as terminal male parents.In this study,the author used the 50 K SNP chip data of 376 pietrains and 1290 Duroc and the high-throughput sequencing data of 25 pietrains and 27 Duroc for analysis.The significant candidate regions of parallel selection between Duroc and Pietland can be determined by classical selection signal statistics: intra-group selection signal i HS,inter-group selection signal Fst and △AF.Then candidate genes related to pig economic traits can be obtained through functional annotation.In addition,this study uses the pig whole genome KEGG(Kyoto Encyclopedia of Genes and Genomes)database,the Highest Scoring Subnetwork was detected by constructing a gene network in the whole genome,and then the parallel selection signal related to the important trait between Duroc and Pietland was detected.The main results are as follows:(1)Based on 50 K chip data,parallel selection signals related to spermatogenesis(FAM170A,KLHDC3,MEA1)and fat deposition(SOAT1,ACSL5,PLCB4)were detected between Duroc and Pietrain populations through the classic selection signal detection method.In addition,candidate genes related to the fertilization process(SPACA3)and meat quality(GPD1,CERS5,ADIRF,ITPR1)were detected between different strains of Duroc.In addition,this study used a genetic network screening method.Then 6 significant biological pathways and 29 significant candidate genes were detected between Duroc and Pietrain;1 significant biological pathway and 9 significant candidate genes were screened in different strains of Duroc.These include candidate genes related to pig reproductive traits(ITGB1,CD44)and fat deposition related(VWF).(2)Based on high-throughput sequencing data,this study calculates classical selection signal statistics,22 parallel selection candidate regions and multiple parallel selection cndidate genes related to pig reproductive traits(TJP3,FZR1,CPEB1,NSUN7)and pig fat characteristics(LRP1B,STK39,SC5 D,SORL1)were identified between Pietrain and Duroc.In addition,through genetic network screening methods,this study identified 4biological pathways and 120 candidate genes between Pietrain and Duroc,including candidate genes related to pig sperm production(ITGB1,PLCZ1)and pig fat deposition(TNC,PDE4 B,AMPD1,AK4,AK5,INPP5 K,PIK3C3).In this study,the chip and sequencing data were used to perform parallel selection signal detection between different subgroups of Duroc and Pietrain.And a certain number of parallel selection candidate genes were detected.The research results prove that the sequencing data analysis supplements the shortcomings of the chip data analysis.And gene network analysis supplements the deficiencies of the classic selection signal detection methods.