Erhualian(E),Meishan(MS)and Mi(MI)pigs are excellent indigenous pig breeds in Chinese Taihu Basin,which have made great contributions to the genetic improvement of commercial pigs.Investigation of the genetic structur...Erhualian(E),Meishan(MS)and Mi(MI)pigs are excellent indigenous pig breeds in Chinese Taihu Basin,which have made great contributions to the genetic improvement of commercial pigs.Investigation of the genetic structure and inbreeding level of the 3 pig breeds is of great significance for the sustainable breeding of commercial pigs.The length and number of runs of homozygosity(ROH)as well as the frequency of genomes covered by ROH can be used as indicators to evaluate the level of inbreeding and the origin of the population.In this study,the ROH characteristics of E,MS,MI and Landrace(L)pigs were analyzed by SLAF-seq data,and the inbreeding coefficient based on ROH(F_(ROH))was calculated.In addition,we have identified candidate genes in the genomic regions associated with ROH.A total of10568 ROH were detected in 116 individuals of 4 pig breeds.The analysis showed that there were significant differences in genetic structure between 3 Taihu Basin pig breeds and L,and the genetic structure of E and MI was similar.The results of F_(ROH)showed that the inbreeding level of MS was the highest(0.25±0.07),while E and MI were lower than L.Compared with the other 3 pig populations,MS showed a higher frequency of long ROH(>5 Mb),indicating higher inbreeding in MS in recent generations.A large number of candidate genes related to reproductive traits are located in the genomic regions with a high frequency of ROH,and these genes are expected to be used as candidate genes in marker-assisted selection(MAS)breeding programs.Our findings can provide theoretical support for genetic conservation and genetic improvement of 3 pig breeds in Chinese Taihu Basin.展开更多
基金supported by the Jiangsu Agricultural Science and Technology Innovation Found,China(SCX(20)3290)the Open Foundation of Key Laboratory of Urban Agriculture,Ministry of Agriculture and Rural Affairs of China(201906)the Joint Research Project on Pig Breeding in Anhui Province,China(340000211260001000431)。
文摘Erhualian(E),Meishan(MS)and Mi(MI)pigs are excellent indigenous pig breeds in Chinese Taihu Basin,which have made great contributions to the genetic improvement of commercial pigs.Investigation of the genetic structure and inbreeding level of the 3 pig breeds is of great significance for the sustainable breeding of commercial pigs.The length and number of runs of homozygosity(ROH)as well as the frequency of genomes covered by ROH can be used as indicators to evaluate the level of inbreeding and the origin of the population.In this study,the ROH characteristics of E,MS,MI and Landrace(L)pigs were analyzed by SLAF-seq data,and the inbreeding coefficient based on ROH(F_(ROH))was calculated.In addition,we have identified candidate genes in the genomic regions associated with ROH.A total of10568 ROH were detected in 116 individuals of 4 pig breeds.The analysis showed that there were significant differences in genetic structure between 3 Taihu Basin pig breeds and L,and the genetic structure of E and MI was similar.The results of F_(ROH)showed that the inbreeding level of MS was the highest(0.25±0.07),while E and MI were lower than L.Compared with the other 3 pig populations,MS showed a higher frequency of long ROH(>5 Mb),indicating higher inbreeding in MS in recent generations.A large number of candidate genes related to reproductive traits are located in the genomic regions with a high frequency of ROH,and these genes are expected to be used as candidate genes in marker-assisted selection(MAS)breeding programs.Our findings can provide theoretical support for genetic conservation and genetic improvement of 3 pig breeds in Chinese Taihu Basin.