文章摘要
孙雪,李胜杰,姜鹏,杜金星,周家辉,白俊杰.利用RNA-Seq技术分析草鱼生长性状相关基因和SNP标记[J].水产学报,2021,45(3):333~344
利用RNA-Seq技术分析草鱼生长性状相关基因和SNP标记
RNA sequencing to identify genes and SNP markers associated with growth traits in Ctenopharyngodon idella
投稿时间:2019-09-25  修订日期:2020-05-16
DOI:10.11964/jfc.20190911988
中文关键词: 草鱼  转录组测序  差异表达基因  单核苷酸多态性  生长性状
英文关键词: Ctenopharyngodon idella  transcriptome sequencing  differentially expressed genes  single nucleotide polymorphism  growth traits
基金项目:现代农业产业技术体系专项(CARS-45-04);中国水产科学研究院中央级公益性科研院所基本科研业务费专项(2020TD34, 2019ZX-001);广州市科技计划项目(201906010004)
作者单位E-mail
孙雪 中国水产科学研究院珠江水产研究所农业农村部热带亚热带水产资源利用与养殖重点实验室广东 广州 510380
上海海洋大学水产科学国家级实验教学示范中心上海 201306 
 
李胜杰 中国水产科学研究院珠江水产研究所农业农村部热带亚热带水产资源利用与养殖重点实验室广东 广州 510380 ssjjli@163.com 
姜鹏 中国水产科学研究院珠江水产研究所农业农村部热带亚热带水产资源利用与养殖重点实验室广东 广州 510380  
杜金星 中国水产科学研究院珠江水产研究所农业农村部热带亚热带水产资源利用与养殖重点实验室广东 广州 510380  
周家辉 中国水产科学研究院珠江水产研究所农业农村部热带亚热带水产资源利用与养殖重点实验室广东 广州 510380
上海海洋大学水产科学国家级实验教学示范中心上海 201306 
 
白俊杰 中国水产科学研究院珠江水产研究所农业农村部热带亚热带水产资源利用与养殖重点实验室广东 广州 510380  
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中文摘要:
      为开发与草鱼生长性状相关基因及单核苷酸多态性(single nucleotide polymorphism,SNP)标记,实验采用转录组测序技术(RNA sequencing,RNA-Seq)对草鱼快长组和慢长组的肝脏、肌肉和脑组织分别进行分析,共获得31 465万条高质量短读序(clean reads),经组装得到34 147条拼接基因(unigene),平均长度为1 060 bp,其中有30 751条unigene获得注释。在肝脏、肌肉和脑组织中分别筛选到1 013、552和372个差异表达基因,并从中检测到4 580个SNP标记。采用SNaPshot技术对其中34个SNP标记在300尾草鱼生长性状极端群体中进行多态性检测和验证,30个SNP标记分型成功,准确率为88.24%。进一步采用一般线性模型分析30个SNP标记与生长性状的相关性,结果显示,unigene00810126-8014标记CC基因型的体质量、体长、体高、头长和尾柄长性状均值显著高于TT基因型。unigene00810126-2903标记AA基因型的体质量显著高于GG基因型。unigene00870394-525标记AA基因型的体质量和体长性状均值显著高于GG基因型。unigene02938762-011628标记的TT基因型与CC基因型在体质量、体长和头长性状上的差异均达到显著水平。这4个标记位于生长催乳素α基因 (slα)、早期生长反应蛋白-1基因 (egr-1)和肌球蛋白重链基因 (myh) 上。其他标记不同基因型个体间的生长性状均不存在显著差异。其中8个SNP标记在草鱼群体中的平均多态信息含量(PIC)、平均期望杂合度(He)和平均观测杂合度(Ho)分别为0.300、0.377和0.363,表明草鱼选育群体遗传多样性较高。本研究获得与生长性状相关的1 937个差异表达基因和4个SNP标记,为草鱼分子辅助育种研究提供基础资料。
英文摘要:
      In order to identify genes associated with growth traits and SNP (Single nucleotide polymorphism) markers in Ctenopharyngodon idella, RNA-Seq (RNA Sequencing technology) was used to analyze the transcriptomes of liver, muscle and brain tissues of fast-growing and slow-growing C. idella groups. A total of 314.65 million clean reads were gained for the fast-growing and slow-growing groups, and 34 147 unigenes were assembled, with an average length of 1 060 bp, of which 30 751 genes were annotated. 1 013, 552, and 372 significant differentially expressed genes were screened in liver, muscle, and brain tissues, respectively, of which 4 580 SNP markers were detected. Then, the polymorphisms of 34 SNP markers was detected and validated with SNaPshot technique in the extreme populations of growth traits of C. idella (n=300), and among which, 30 SNPs (83.24%) were successfully genotyped. A general linear model was used to analyze the correlation between 30 SNPs and growth traits. The results showed that at the position of Unigene00810126-8014, the body weight, body length, body height, head length and caudal peduncle length in individuals with CC genotype had significantly higher values than TT genotype. At the position of Unigene00810126-2903, the body weight of AA genotype was significantly higher than those with GG genotype. At the position of Unigene00870394-525, individuals with the AA genotype had significantly higher values in body weight and body height than those with GG genotype. At the position of Unigene02938762-011628, TT and CC genotypes had significant differences in body mass, body length and head length traits. Besides, other SNPs loci were not significantly correlated with growth traits. The four selected markers were located at Somatolactin alpha (slα), Early growth response protein-1 (egr-1) and Myosin heavy chain (myh) genes. The average polymorphism information content (PIC), average expected heterozygosity (He) and average observed heterozygosity(Ho) of 8 EST-SNP markers in C. idella population were 0.300, 0.377 and 0.363, respectively, indicating that genetic diversity of C. idella breeding population had relatively high level. In conclusion, 1 937 differentially expressed genes and four SNP markers related to growth traits were obtained, which can be used as candidate genes and for molecular marker-assisted selection of C. idella, and can also be used in subsequent breeding work.
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