利用转录组测序挖掘奶牛基因多态位点的准确性研究  

Accuracy of Single Nucleotide Polymorphism Detection from Transcriptome Sequencing Data in Dairy Cattle

作　　者：姜志国 司敬方 李凯扬 崔恒源 刘林[3] 肖炜 张毅[1] JIANG Zhi-guo;SI Jing-fang;LI Kai-yang;CUI Heng-yuan;LIU Lin;XIAO Wei;ZHANG Yi(College of Animal Science and Technology,China Agricultural University,Beijing 100193;Beijing Animal Husbandry Station,Beijing 100107;Beijing Dairy Cattle Center,Beijing 100192)

机构地区：[1]中国农业大学动物科技学院,北京100193 [2]北京市畜牧总站,北京100107 [3]北京奶牛中心,北京100192

出　　处：《中国奶牛》2024年第10期19-23,共5页China Dairy Cattle

基　　金：国家现代农业产业技术体系(CARS-36);“十四五”国家重点研发计划项目(2022YFD1302204);宁夏回族自治区重点研发项目(2023BCF01004);宁夏回族自治区农业育种专项(2019NYYZ05)。

摘　　要：转录组测序(RNA-Seq)不仅用于揭示基因表达谱,同时还可以检测基因多态位点,是挖掘奶牛蛋白编码基因功能突变的有效策略。本研究对20头中国荷斯坦牛进行全基因组测序(DNA-Seq)与转录组测序(RNA-Seq),以DNA-Seq检出的单核苷酸多态位点(SNP)为参考基准,评估RNA-Seq检出SNP的准确性及其影响因素。结果显示,同一个体DNA-Seq和RNA-Seq的SNP位点一致性为0.65~0.75,而不同个体间的一致性仅为0.28~0.42。通过优化RNA-Seq检测SNP的筛选标准,包括针对连续SNP(SnpCluster)、单一连续碱基(Homopolymer)、测序深度(DP<5)、位点基因型频率(P<0.13)等4个过滤参数的优化,检出的高准确性SNP占比由71.07%提升至95.27%。最后,经功能注释筛选出10号染色体上E1BHN1基因一个起始密码子突变(BTA10:25435325 T/A),该突变导致免疫球蛋白结构域类似物蛋白从异四聚体变成异二聚体,推测该位点可能为奶牛隐性致死突变位点。Transcriptome sequencing(RNA-Seq)can not only reveal gene expression profiles but also detect nucleotide polymorphisms in genes,making it an effective strategy for exploring functional mutations in proteincoding genes of dairy cows.In this study,we performed whole-genome sequencing(DNA-Seq)and transcriptome sequencing(RNA-Seq)on 20 Chinese Holstein cows.Using the SNPs detected by DNA-Seq as reference,we evaluated the accuracy of gene polymorphism detection based on RNA-Seq and its influencing factors.Results showed that the SNP consistency between DNA-Seq and RNA-Seq in the same individual ranged from 0.65 to 0.75,while the consistency between different individuals varied from 0.28 to 0.42.By optimizing the filtering parameters criteria for SNP detection in RNA-Seq,including SnpCluster,homopolymer,sequencing depth(DP<5),and allele frequency(P<0.13),the proportion of high-accuracy SNPs detected increased from 71.07%to 95.27%.Finally,through functional annotation,we identified a start codon mutation(BTA10:25435325 T/A)in the E1BHN1 gene on chromosome 10,which led to a change in the immunoglobulin domain-like protein from a heterotetramer to a heterodimer.This mutation might be a recessive lethal mutation.

关 键 词：全基因组测序 转录组测序 单核苷酸多态 测序深度 功能注释 

分 类 号：S823.3[农业科学—畜牧学]