基于全基因组重测序的山羊产羔数性状关键调控基因的筛选  

Screening of Key Regulatory Genes for Litter Size Trait Based on Whole Genome Re-Sequencing in Goats(Capra hircus)

作　　者：李恒[1] 字向东[1] 王会 熊燕[1] 吕明杰 刘宇 蒋旭东 LI Heng;ZI XiangDong;WANG Hui;XIONG Yan;LÜ MingJie;LIU Yu;JIANG XuDong(Key Laboratory of Animal Science of National Ethnic Affairs Commission,Southwest Minzu University,Chengdu 610041;Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education,Southwest Minzu University,Chengdu 610041)

机构地区：[1]西南民族大学动物科学国家民委重点实验室,成都610041 [2]西南民族大学青藏高原动物遗传资源保护与利用教育部重点实验室,成都610041

出　　处：《中国农业科学》2022年第23期4753-4768,共16页Scientia Agricultura Sinica

基　　金：国家自然科学基金(31902154);西南民族大学中央高校基本科研业务专项(2021PTJS26)。

摘　　要：【目的】对产羔数不同的山羊进行全基因组重测序分析,挖掘参与调控川中黑山羊产羔数性状关键调控基因,为解析山羊产羔数性状遗传机制及分子遗传改良提供理论依据。【方法】选择6只产4—6羔的川中黑山羊为高繁组(high fecundity,HF)和6只产单羔的川中黑山羊为低繁组(low fecundity,LF),采集颈静脉血液样本提取基因组DNA,构建350 bp双末端测序文库,利用Illumina HiSeq PE150平台对12个文库进行全基因组重测序。测序产出的净数据经BWA软件比对至山羊参考基因组ARS1,所获得的高质量SNPs通过两种全基因组扫描分析方法(Fst、Hp)的综合分析确定候选区域,候选区域的注释基因分别利用g:Profiler和KOBAS在线数据库进行GO分析与KEGG通路分析,以筛选调节川中黑山羊产羔数性状候选基因。为了进一步鉴定调节山羊产羔数目的关键遗传标记,根据基因组重测序变异分析,对繁殖候选基因的同义与非同义SNPs进行定位筛选,后续将12个山羊样本的扩增产物进行Sanger测序以验证重测序结果。【结果】12只山羊共获得431.50 Gb净数据,经变异检测与注释发现,HF组山羊共发现7771417个单核苷酸多态性(single nucleotide polymorphism,SNPs),LF组山羊检测到8935907个SNPs,且LF组各类SNPs均多于HF组。设置同时达到top 5%最大ZFst值和top 5%最小ZHp值的窗口为候选区域,在低杂合性、高遗传分化的区域共注释130个强选择信号,其中HF组、LF组以及共享窗口的注释基因分别为84、59和13个,经GO富集与KEGG通路分析发现,19个候选基因参与川中黑山羊的繁殖、繁殖过程和胚胎发育等调控,包括11个HF组特异性候选基因(ADCY10、DRD1、HS6ST1、IGFBP7、MSX2、NOG、NPHP4、PAPPA、PRLHR、TDRP和XYLT1),5个LF组特异性候选基因(ANXA5、IGF1、EDNRA、FANCL和TAC1)和3个HF组与LF组共享窗口基因(AKR1B3、HDAC4和OPRM1)。同时,大多数GO分析,如G蛋白偶联受体活性、激素反【Objective】The purpose of this study was to analyze the genome of different fecundity populations of goats(Capra hircus)and to explore the key regulatory genes involved in the regulation of litter size traits of Chuanzhong black goats(CBGs),and to provide the theoretical reference for analyzing the genetic mechanism of litter size traits and molecular genetic improvement of fecundity in goats.【Method】The high fecundity(HF)CBG does(n=6)that produced 4-6 kids per doe kidding and low fecundity(LF)does(n=6)that produced only one kid per doe kidding were chosen in this study.The jugular blood samples were collected to extract genomic DNA.The 350 bp double-terminal sequencing library was constructed,and then 12 whole genome libraries were resequenced by IlluminaHiSeqPE150 platform.The clean data from sequencing were mapped to goat reference genome ARS1 by using BWA software,and two whole-genome scanning analysis methods(Fst and Hp)were used to comprehensively analyze the high-quality SNPs obtained to identify candidate regions.GO analysis and KEGG pathway analysis were performed on the G:Profiler and KOBAS online databases,respectively,to screen candidate genes for regulating the number of kids in CBGs.To further identify the key genetic markers that regulate the number of kids,the synonymous and non-synonymous single nucleotide polymorphisms(SNPs)of reproductive candidate genes were mapped and screened according to the variation analysis report of genome resequencing.The amplified products of 12 goat samples were sequenced by Sanger sequencing to verify the resequencing results.【Result】A total of 431.50 Gb clean data were obtained from the genome resequencing study of 12 CBGs.Through mutation detection and annotation,7771417 SNPs were detected in HF group and 8935907 SNPs were detected in LF group,and all types of the LF group SNPs were more than those in HF group.The windows that reach the maximum ZFst value of top 5%and the minimum ZHp value of top 5%were set as candidate regions.A total of 130 strong se

关 键 词：川中黑山羊 基因组重测序 多羔性状 候选基因 

分 类 号：S827.2[农业科学—畜牧学]