畜禽全基因组长纯合片段检测的研究进展  

Advance in Genome-Wide Scan of Runs of Homozygosity in Domestic Animals

作　　者：张鹏飞 史良玉 刘家鑫 李洋 吴成斌 王立贤[1] 赵福平[1] ZHANG PengFei;SHI LiangYu;LIU JiaXin;LI Yang;WU ChengBin;WANG LiXian;ZHAO FuPing(Key laborary of Animal Genetics Breeding and Reproduction(poultry),Ministry of Agriculture,Institute of Animal Science,Chinese Academy of Agricultural Sciences,Beijing 100193;Quarantine Station of Animal Health Supervision and Administration Bureau in Maochikou Town,Changping District,Beijing 102202)

机构地区：[1]中国农业科学院北京畜牧兽医研究所/农业部动物遗传育种与繁殖(家禽)重点实验室,北京100193 [2]北京市昌平区动物卫生监督管理局马池口防疫站,北京102202

出　　处：《中国农业科学》2021年第24期5316-5326,共11页Scientia Agricultura Sinica

基　　金：国家自然科学基金(31572357);国家生猪产业技术体系(CARS-35);中国农业科学院创新工程(ASTIP-IAS02)。

摘　　要：长纯合片段(runs of homozygosity,ROH)是在个体和群体中常见的连续性纯合片段,是亲代将同源相同的单倍型遗传给同一个后代而形成的。ROH蕴藏着种群丰富的遗传信息,这使ROH成为一种有用的工具,可以提供关于种群是如何随着时间的演变而变化的信息。ROH也可以用于估计个体间遗传关系,有助于将近亲交配率降至最低,还可以暴露基因组中有害的变异。ROH在基因组中的大小、分布和频率受到自然选择和人工选择、重组、连锁不平衡、群体历史、突变率和近交水平等诸多因素的影响。近年来,随着高通量基因分型技术的使用以及二代测序成本的降低,畜禽育种已经进入基因组时代。对优秀种畜禽的选择强度大大提高,这在改善畜禽生产性能的同时不可避免地会造成动物的近交,从而导致近交衰退。根据ROH的分子信息能更准确地估计纯合性并可以检测过去和最近的近亲交配情况。基于ROH计算近交系数(FROH)反映的是个体的真实近交系数,即为实现的近交系数,而系谱近交系数FPED得到的是期望值。FROH在缺乏系谱信息的情况下,也可以用来推断一个群体的历史和近亲交配水平的信息。选择会改变优良畜禽的表型,并重塑了基因组不同区域的ROH模式。此外,选择增加了目标位点周围的纯合性,有害的变异被认为更频繁地出现在ROH区域,可以通过ROH检测,降低复杂疾病发生的风险。经过长期选择,品种内同群个体相同ROH在基因组中高频出现,产生ROH岛。研究证实了ROH和正在选择的基因组区域之间具有相关性。在实际应用中,可以通过生物信息的方法在ROH岛注释到ROH区域与经济性状相关的基因。此外,ROH也为评估畜禽遗传多样性提供了新的视角,对群体进行全基因组ROH检测,剖析每个群体的遗传结构,并利用FROH对当前育种计划中近交的影响进行评估,来调整育种方案,保护品种的�Runs of homozygosity(ROH)is a long tract of homozygous genotypes commonly found in individuals and populations,which generates on the offspring’s genome inherited identical haplotypes from each parent.ROH contains a wealth of genetic information about populations,which makes it a useful tool for providing information to study how populations change over time.Moreover,ROH can estimate the genetic relationships between individuals to minimize the inbreeding mating rates.In addition,ROH can expose harmful mutations in the genome.The frequencies,sizes and distributions of ROHs in the genome are influenced by natural and artificial selection,recombination,linkage disequilibrium,population history,mutation rate and inbreeding level.Recently,with the use of high-throughput genotype technology and the reduction of second-generation sequencing costs,livestock and poultry breeding have entered into the genomic era.The selection intensity of the elites in livestock and poultry significantly increase to improve their performances,but it will increase inbreeding and cause inbreeding depression as well.Based on ROH molecular information,it is more accurately to detect past and nearest in close relative mating.The ROH-based inbreeding coefficient(FROH)can obtain an individual's true inbreeding coefficient,i.e.the realized inbreeding coefficient,and the pedigree-based FPED is the expectation value of inbreeding coefficient.In the absence of genealogical information,FROH can be used to infer information about a group's history and the inbreeding levels.Meanwhile,the selection reshapes ROH patterns in different regions of the genome.In addition,the selection can increase the homozygosities around the target point,and harmful mutations are thought to occur more frequently in the ROH region,which can be detected by ROH to reduce the risk of complex diseases.After long-term selection,one ROH appeared in multiple individuals’genomes in the same population,resulting in ROH islands.It has confirmed the correlation between ROH and th

关 键 词：长纯合片段 畜禽育种 单核苷酸多态性 近交评估 候选基因鉴定 

分 类 号：S813[农业科学—畜牧学]