基于家系基因组测序对骡基因组结构多样性分析  

Structural diversity analysis of mule genome based on family genome sequencing

作　　者：任秀娟[1] 苏少锋 李雅静 蔺雅楠 贾紫洁 丁文淇 白东义[1] 李蓓[1] 杜明 芒来[1] 赵一萍[1] REN Xiujuan;SU Shaofeng;LI Yajing;LIN Yanan;JIA Zijie;DING Wenqi;BAI Dongyi;LI Bei;DU Ming;DUGARJAVIIN Manglai;ZHAO Yiping(Equine Research Center/College of Animal Science,Inner Mongolia Agricultural University,Hohhot 010018,China;Inner Mongolia Academy of Agricultural and Animal Husbandry Sceinces,Hohhot 010031,China)

机构地区：[1]内蒙古农业大学动物科学学院/马属动物研究中心,呼和浩特010018 [2]内蒙古自治区农牧业科学院,呼和浩特010031

出　　处：《中国农业大学学报》2023年第11期151-164,共14页Journal of China Agricultural University

基　　金：国家自然科学基金项目(31960657);内蒙古自治区重大专项(2021ZD0018,2020ZD004);内蒙古农业大学动物科学学院项目(QN202103)。

摘　　要：为分析马(Equus caballus)和驴(Equus asinus)杂交后两套结构和功能完善的独立基因组在骡基因组中整合后的结构多样性,本研究以马属动物三成员家系的全基因组序列为研究对象,分别以纯血马基因组和驴基因组为参考,识别驴、马和骡的InDel、SNP和CNV;通过生物信息分析,分析骡的de novo SNP及其突变频率、识别骡特异性CNV,并进行功能分析。结果显示:1)驴、马和骡分别获得100.01、103.78和114.36 Gb的高质量Illumina基因组测序数据。2)以纯血马基因组为参考,识别的InDels、SNPs和CNVs分别为402533~2110786、5012403~23819055和2126~3761;以驴基因组为参考,识别的InDels、SNPs和CNVs分别为527351~2279875、3212499~23549224和3572~7812。3)骡de novo SNPs分别为555和419,其突变频率为1.72×10^(-7)~2.21×10^(-7)。4)获得骡特异性CNVs分别为396和859,总长度分别为2.15和3.77 Mb。5)变异相关基因主要和机体的免疫及癌症过程相关。综上,骡基因组发生了高频率的de novo SNPs和特异性CNVs,这些结构变异可能对马和驴异种杂交不相容以及骡的遗传适应性具有重要意义,为进一步开展马和驴异种杂交的遗传基础及其分子机制的研究提供候选遗传位点。In order to analyze the structural diversity of the mule genome combining the two sets of perfectly functional and structurally well-characterized genetic programs after hybridization between horses(Equus caballus)and donkeys(Equus asinus),the study identified InDel,SNP,and CNV for the donkeys,horses,and mules,basing on the wholegenome sequences from an Equus parent-offspring trio and using the Thoroughbred genome and donkey genome as reference.Through bioinformatics analysis,the de novo SNP and its mutation frequency of mule were analyzed,the mule specific CNV was identified,and functional analysis was carried out.The results showed that:1)for the donkey,horse and mule,100.01,103.78and 114.36Gb high-quality Illumina genome sequencing data were generated,respectively.2)Using the Thoroughbred genome as reference,the identified InDels,SNPs and CNVs were 402533-2110786,5012403-23819055and 2126-3761,respectively.Using the donkey genome as reference,the identified InDels,SNPs and CNVs were 527351-2279875,3212499-23549224and 3572-7812.3)De novo SNPs of mule were 555and 419,respectively,with a mutation frequency of 1.72×10^(-7)-2.21×10^(-7).4)A total of 396and 859mule-specific CNVs were also identified,with a total length of 2.15and 3.77Mb,respectively.5)The genes associated with the structural variation were mainly involved in immune processes and cancer processes.In summary,the genome of the mule exhibits high frequency of de novo SNPs and specific CNVs,which may be of great significance for the incompatibility of interspecific hybridization?3 between horses and donkeys and the genetic adaptability of mules.These structural variations provides candidate genetic sites for further research on the genetic basis and molecular mechanisms of the crossing of horses and donkeys.

关 键 词：骡 异种杂交 De novo单核苷酸多态性 拷贝数变异 

分 类 号：S821.2[农业科学—畜牧学]