利用高密度SNP检测不同猪品种间X染色体选择信号

doi:10.3724/SP.J.1005.2012.01251

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HEREDITAS ›› 2012, Vol. 34 ›› Issue (10): 1251-1260.doi: 10.3724/SP.J.1005.2012.01251

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Detecting selection signatures on X chromosome in pig through high density SNPs

MA Yun-Long, ZHANG Qin, DING Xiang-Dong

College of Animal Science and Technology, China Agricultural University, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory For Animal Breeding, Beijing 100193, China

Received:2012-03-29 Revised:2012-05-08 Online:2012-10-20 Published:2012-10-25

Abstract

Abstract: In the process of domestic pig breeding, many important economic traits were subject to strong artificial selection pressure. With the availability of high density single nucleotide polymorphism (SNP) markers in farm animals, selection occurring in those traits could be traced by detecting selection signatures on genome, and the genes experiencing selection can also be further mined based on selection signatures. Due to the special characteristic of X chromosome, many approaches of genetic analysis fitted for autosome are not plausible for X chromosome. Fortunately, detecting selection signature provides an effective tool to settle such situation. In this study, the Cross Population Extend Haplotype Homozygosity Test (XP-EHH) was implemented to identify selection signatures on chromosome X in three pig breeds (Landrace, Songliao, and Yorkshire) using high density SNPs, and the genes located within selection signature regions were revealed through bioinformatic analysis. In total, 29, 13, and 15 selection signature regions, with 3.59, 4.92, and 4.07 SNPs on average in each region, were identified in Landrace, Songliao, and Yorkshire, respectively. Some overlaps of selection signature regions were observed between Songliao and Landrace, and between Landrace and Yorkshire, while no overlaps between Yorkshire and Songliao were found. Bioinformatic analysis revealed that many genes in the selection signature regions were related to reproduction and immune traits, and some of them have not been reported in pigs, which might serve as important candidate genes in future study.

Key words: X chromosome, selection signatures, pig

MA Yun-Long, ZHANG Qin, DING Xiang-Dong. Detecting selection signatures on X chromosome in pig through high density SNPs[J]. HEREDITAS, 2012, 34(10): 1251-1260.

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Detecting selection signatures on X chromosome in pig through high density SNPs

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