首页|全基因组重测序探究晋南牛优势性状的分子基础

全基因组重测序探究晋南牛优势性状的分子基础

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原文链接
  • 国家科技期刊平台
  • NETL
  • NSTL
  • 万方数据
  • 维普
[目的]探究晋南牛优势性状所基于的遗传基础,为后续晋南牛种质资源利用以及分子育种提供参考.[方法]采集12头健康的纯种晋南牛耳缘组织,提取基因组DNA进行全基因组重测序,将测序数据以及NCBI数据库12头红安格斯牛基因组数据比对到牛参考基因组(ARS-UCD1.2),检测群体SNPs位点,采用ANNOVAR软件对变异位点进行注释;对晋南牛与红安格斯牛变异基因进行韦恩分析,筛选晋南牛特异性变异基因并进行GO功能和KEGG通路富集分析,采用Cytoscape软件将显著富集的变异基因进行功能互作分析.[结果]晋南牛基因组DNA测序共获取clean reads 2 621 153 222条,Q30平均值达93.5％,碱基分布均匀且无明显偏向性,平均测序深度11.19×,覆盖率(≥4×)平均值为92.64％;检测到SNPs位点117 773 201个,注释外显子区域获得nonsynonymous、stopgain/stoploss SNPs共405 506个,覆盖于16 690个基因,筛选出晋南牛特异性变异基因5 289个.GO功能和KEGG通路分析表明,基因广泛富集于线粒体、核糖体、细胞器膜相关生物过程以及氧化磷酸化、细胞色素P450(CYP)代谢通路中;线粒体呼吸链蛋白(NDU)、细胞色素C氧化酶(COX)、葡萄糖醛酸基转移酶(UGT)广泛富集于氧化磷酸化途径;CYP1A1、CYP2E1、UGT1A6、UGT1A1基因富集于细胞色素P450相关的多条代谢通路;GSTM2、GSTT1、GSTT2、GSTK1基因富集于谷胱甘肽(GST)代谢途径与细胞色素P450相关路径;线粒体核糖体蛋白(MRP)、核糖体蛋白(RP)基因家族子网络富集于核糖体蛋白形成过程.[结论]晋南牛特异性变异基因与细胞能量代谢显著相关,推断其对晋南牛饲料高效转化率具有潜在遗传效应.本研究结果为筛选显著影响育肥性状的SNPs标记,繁育高饲料转化率的晋南牛提供方向.
Whole-Genome Resequencing Reveals Genetic Potential for Phenotypic Merit in Jinnan Cattle
[Objective]The aim of this study was to investigate the genetic basis on which the phenotypic advantage of Jinnan cattle were based and provide a reference for the subsequent utilization of germplasm resources and molecular breeding in Jinan cattle.[Method]12 healthy purebred Jinnan cattle ear margin tissues were collected,and genomic DNA was extracted for whole genome resequencing.Compare the sequencing data and the genome data of 12 Red Angus cattle in NCBI database to the bovine reference genome(ARS-UCD1.2),and detect the SNPs loci in the population,and annotate the mutation sites using ANNOVAR software.The variant genes of Jinnan cattle and Red Angus cattle were analyzed by Venn method to screen for specific variant genes of Jinnan cattle,and conduct GO function and KEGG pathway enrichment analysis.The functional interaction of significantly enriched variant genes were analyzed by Cytoscape software.[Result]A total of 2 621 153 222 clean reads were sequenced from the Jinnan cattle genome,with an average Q30 value of 93.5％.The base distribution was uniform and without significant bias,and the average sequencing depth of 11.19×and an average coverage rate(≥4×)of 92.64％were obtained.A total of 117 773 201 SNPs loci were detected.A total of 405 506 non-synonymous,stopgain/stoploss SNPs were obtained by annotating the exon region,covering 16 690 genes,and 5 289 specific variant genes were screened out in Jinnan cattle.GO and KEGG analysis showed that genes were widely enriched in mitochondrial,ribosome,organelle membrane related biological processes,as well as oxidative phosphorylation and cytochrome P450(CYP)metabolic pathways.Mitochondrial respiratory chain protein(NDU),cytochrome C oxidase(COX),and glucuronic acid transferase(UGT)were widely enriched in the oxidative phosphorylation pathway.The CYP1A1,CYP2E1,UGT1A6,and UGT1A1 genes were enriched in multiple metabolic pathways related to cytochrome P450.The GSTM2,GSTT1,GSTT2,and GSTK1 genes were enriched in the glutathione(GST)metabolic pathway and cytochrome P450 related pathways.The sub network of mitochondrial ribosomal protein(MRP)and ribosomal protein(RP)gene families were enriched in the process of ribosomal protein formation.[Conclusion]The cattle-specific variant genes were significantly associated with cellular energy metabolism.It was inferred that they had a potential genetic effect on the feed efficiency of Jinan cattle.The results provided direction for screening SNPs markers that significantly affect fattening traits and breeding Jinnan cattle with high feed conversion.

Jinnan cattleresequencingSNPmitochondriacellular energy metabolismfeed efficiency

贾雪纯、戎艳花、朱芷葳、李鹏飞

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山西农业大学生命科学学院,太谷 030801

晋南牛 重测序 SNP 线粒体 细胞能量代谢 饲料转化率

国家自然科学基金面上项目山西省应用基础研究计划面上项目山西农业大学横向科技项目山西农业大学横向科技项目山西农业大学横向科技项目山西农业大学横向科技项目山西省现代农业产业技术体系建设专项

31873002202103021233802022HX0102021HX232020HX062019HX03

2024

10.16431/j.cnki.1671-7236.2024.01.001

中国畜牧兽医
中国农业科学院北京畜牧兽医研究所

中国畜牧兽医

CSTPCD北大核心
影响因子：0.72
ISSN：1671-7236
年,卷(期)：2024.51(1)
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