Detection Of Selection Signatures Among Different Pig Breeds

Selection signatures are the selection footprints across the genome due to long term natural or artificial selection in a specie.It could not only reflect the effect of selection on the cultivation of a new breed,but also help to understand the mechanism of selection.Hainan pigs,Wuzhishan pigs and Liangguangxiaohua pigs are the excellent breeds of South China indigenous pigs.These pigs are reputed not only for resistance to rough feeding,but also for early sexual maturity,and superior meat quality.Duroc pig is famous for fast growth rate,high feeding efficiency and high lean meat percentage after a long time of positive selection.After genotyping by Gene Seek Genomic Profiler(GGP)Porcine SNP80 Bead Chip,Illumina 60 K SNP Bead Chip and GGP Procine SNP50 Bead Chip,the relative extended haplotype homozygosity test was used to detect selection signatures in the Duroc pig population,meanwhile,both cross population extended haplotype test and FST statistic were used to detect selection signatures in six breeds(subpopulations)of South China indigenous pigs and Duroc pigs.The aim of this study was to explore the differentiation of the selection footprints across the genome among different pig breeds due to selection,meanwhile,some bioinformatics databases was used to analyze the biological information reflected by the selection signatures.The results of this study were as follows:1)154 potential selection regions were detected in the Duroc pigs’ genome,a total of 551 candidate genes were annotated,nine GO biological processes and five KEGG pathways were enriched in this study.The Quantitative trait loci(QTLs)overlapped with potential selection regions were associated with average daily gain and so on.2)The Hainan indigenous pig breeds(Wuzhishan pigs and Hainan pigs)were used as the test group,and Duroc pigs as the reference group: no potential selection regions was detected in the test group.Six potential selection regions were detected in the reference group,a total of six candidate genes were annotated.Moreover,the QTLs overlapped with these potential selection regions were associated with days to 100 kg.3)The Liangguangxiaohua pigs were used as the test group and the Duroc pigs as the reference group: no potential selection regions were detected in the test group.Two significant potential selection regions were detected in the reference group,only one candidate gene was annotated.The QTLs overlapped with these potential selection regions were associated with aspartate aminotransferase activity.4)The Hainan indigenous pig breeds(Wuzhishan pigs and Hainan pigs)were used as the test group,and Liangguangxiaohua pigs as the reference group: two potential selection regions were detected in the test group,a total of seven candidate genes were annotated.The QTLs overlapped with these potential selection regions were associated with age at puberty and Actinobacillus pleuropneumoniae susceptibility.Meanwhile,thirteen potential selection regions were detected in the reference group,and a total of 28 candidate genes were annotated.The QTLs overlapped with potential selection regions were associated with meat quality traits(meat color,drip loss,shear force).In conclusion,the selection direction of Duroc pig mainly was growth traits,while the selection direction of Hainan indigenous pigs mainly was age at puberty,and the selection direction of Liangguangxiaohua pig mainly was meat quality traits.