CNV analysis of Meishan pig by nextgeneration sequencing and effects of AHR gene CNV on pig reproductive traits  

作　　者：Xianrui Zheng Pengju Zhao Kaijie Yang Chao Ning Haifei Wang Lei Zhou Jianfeng Liu 

机构地区：[1]National Engineering Laboratory for Animal Breeding,Key Laboratory of Animal Genetics,Breeding and Reproduction,Ministry of Agriculture,College of Animal Science and Technology,China Agricultural University,Beijing 100193,China [2]Department of Animal Genetics,Breeding and Reproduction and Molecular Design,College of Animal Science and Technology,Yangzhou University,Yangzhou 225009,China.

出　　处：《Journal of Animal Science and Biotechnology》2020年第3期667-677,共11页畜牧与生物技术杂志（英文版）

基　　金：This work was financially supported by National Natural Science Foundations of China(31661143013);National Natural Science Foundation of China(No.31790414);National Key R&D Program of China(2018YFD0501200);and Jinxinnong Animal Science Development Foundation.

摘　　要：Background:Reproductive performance of livestock is an economically important aspect of global food production.The Chinese Meishan pig is a prolific breed,with an average of three to five more piglets per litter than European breeds;however,the genetic basis for this difference is not well understood.Results:In this study,we investigated copy number variations(CNVs)of 32 Meishan pigs and 29 Duroc pigs by nextgeneration sequencing.A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions(CNVRs)that were further divided into three categories based on copy number(CN)of the whole population,i.e.,gain(n=7,638),and loss(n=5,030)CNVRs.We then compared Meishan and Duroc pigs and identified 17.17Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor(AHR)gene.We found that normal AHR CN was more frequent than CN loss in four different pig breeds.An association analysis showed that AHR CN had a positive effect on litter size(P<0.05)and that a higher CN was associated with higher total number born(P<0.05),number born alive(P<0.05),number of weaned piglets,and birth weight.Conclusions:The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing.Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig.In addition,the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.

关 键 词：AHR Copy number variation MEISHAN Next-generation sequencing PIG REPRODUCTION 

分 类 号：S828.3[农业科学—畜牧学]