北京黑猪全基因组ROH检测和选择信号分析  

Analysis of the Whole Genome Run of Homozygosity(ROH)and Selection Signal in Beijing Black Pigs

作　　者：田晶晶 王晓庆 李棉燕 王海玲 吴启钿 王立贤[1] 张龙超 赵福平[1] TIAN Jingjing;WANG Xiaoqing;LI Mianyan;WANG Hailing;WU Qitian;WANG Lixian;ZHANG Longchao;ZHAO Fuping(Institute of Animal Science,Chinese Academy of Agricultural Sciences,Beijing 100193,China)

机构地区：[1]中国农业科学院北京畜牧兽医研究所,北京100193

出　　处：《畜牧兽医学报》2024年第9期3833-3842,共10页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：国家重点研发计划(2021YFD1301101);中国农业科学院科技创新工程(ASTIP-IAS02);国家生猪产业技术体系(CARS-35)。

摘　　要：旨在基于长纯合片段(ROH)和选择信号iHS分析北京黑猪群体的遗传结构,挖掘与经济性状相关的候选基因。本研究的对象为北京黑猪群体,平均日龄为210 d。对729头北京黑猪的illumina Porcine 50K芯片数据进行质控和填充后,进行ROH和iHS的分析。本研究选择参与组成ROHs的前1%的SNPs作为ROH岛的阈值,将超过此阈值的区域称为ROH岛。保留标准化的iHS值中排在前1%的所有SNPs位点,将位点上下游各延伸200 kb作为选择信号iHS得到的强受选择区域。将选择信号的强受选择区域与ROH岛重叠的区段定为本研究的候选区域。本研究最终保留724个体和45585个SNPs,通过ROH分析共识别到10个ROH岛,这些岛内包含449个SNPs。iHS分析的结果显示,保留得分排在前1%的位点后,共有376个强受选择位点。最终,在iHS的强受选择区域与ROH岛的5个重叠区域内注释到18个基因,其中包括一些已知的影响猪肉质和生长发育过程的基因。本研究分析了北京黑猪群体ROH的分布,并结合选择信号,揭示了北京黑猪受选择的位点和候选基因,该研究结果为深入探讨北京黑猪的群体特性及经济性状的遗传机制提供重要参考。This study aimed to investigate the genetic structure of the Beijing black pigs based on runs of homozygosity(ROH)and selection signals iHS analysis and to identify candidate genes related to economic traits.The subjects of this study were Beijing black pigs,with an average age of 210 days.After quality control and imputation of the illumina Porcine 50K chip data from 729 Beijing black pigs,the ROH and iHS were analyzed.In this study,the threshold for ROH islands was set at the SNPs that constituted the top 1%of ROHs,and regions exceeding this threshold were termed ROH islands.All SNPs in the top 1%of standardized iHS values were retained,and the areas extending 200 kb upstream and downstream of these SNPs were considered as the strong selection regions obtained by the iHS.The overlapping areas between the strong selection regions of the selection signals and the ROH islands were defined as the candidate regions for this study.In this study,724 individuals and 45585 SNPs were retained,and a total of 10 ROH islands containing 449 SNPs were identified by ROH analysis,and the results of iHS analysis showed that a total of 376 strongly selected SNPs were retained after the top 1%SNPs with the highest score were retained.In the end,a total of 18 genes in the overlapping regions of the 5 strongly selected regions of iHS and ROH islands were annotated,including some genes known to affect pork quality and growth and development.This study analyzed the distribution of ROH in the Beijing black pigs and revealed potential selected SNPs and candidate genes combined with selection signals.The results provide an important reference for further exploring the population characteristics and genetic mechanisms of economic traits of Beijing black pigs.

关 键 词：北京黑猪 芯片数据 ROH IHS 

分 类 号：S828.2[农业科学—畜牧学]