限制性两阶段多位点全基因组关联分析法（RTM-GWAS）的特点、常见提问与应用前景

doi:10.3864/j.issn.0578-1752.2020.09.001

中国农业科学 ›› 2020, Vol. 53 ›› Issue (9): 1699-1703.doi: 10.3864/j.issn.0578-1752.2020.09.001

• 专题：限制性两阶段多位点全基因组关联分析法的应用 • 上一篇下一篇

限制性两阶段多位点全基因组关联分析法（RTM-GWAS）的特点、常见提问与应用前景

盖钧镒,贺建波

南京农业大学大豆研究所/国家大豆改良中心/农业部大豆生物学与遗传育种重点实验室/作物遗传与种质创新国家重点实验室/江苏省现代作物生产协同创新中心,南京 210095

收稿日期:2020-01-02 接受日期:2020-02-15 出版日期:2020-05-01 发布日期:2020-05-13
作者简介:盖钧镒,E-mail：sri@njau.edu.cn。
基金资助:
国家自然科学基金(31701447);国家作物育种重点研发计划(2017YFD0101500);国家作物育种重点研发计划(2017YFD0102002);长江学者和创新团队发展计划(PCSIRT_17R55);教育部111项目(B08025);中央高校基本科研业务费项目(KYT201801);农业部国家大豆产业技术体系CARS-04;江苏省优势学科建设工程专项;江苏省JCIC-MCP项目

Major Characteristics, Often-Raised Queries and Potential Usefulness of the Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis

JunYi GAI,JianBo HE

Soybean Research Institute, Nanjing Agricultural University/National Center for Soybean Improvement/Key Laboratory of Biology and Genetic Improvement of Soybean (General), Ministry of Agriculture/State Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095

Received:2020-01-02 Accepted:2020-02-15 Online:2020-05-01 Published:2020-05-13

摘要/Abstract

摘要：

限制性两阶段多位点全基因组关联分析方法（RTM-GWAS）是新建立的一种可以全面检测自然群体和双（多）亲衍生群体中具有不同复等位变异QTL体系的关联分析方法。本文介绍了提出RTM-GWAS的出发点及其两大主要特点,包括建立适合自然群体和和双（多）亲衍生群体特点的复等位变异标记和控制总体贡献率的多位点关联分析模型。一般读者和编者对RTM-GWAS的方法、原理,对复等位标记和多位点模型并无异议,提问与质疑主要分为两方面：一是RTM-GWAS检测到的QTL数量较多,大大多于单位点MLM模型所检出的QTL数目,怀疑增加的QTL是假阳性所致;另一是采用常规显著水准要求太低,不适于关联分析。本文对此做了严密释疑。最后介绍了关于RTM-GWAS的应用前景,包括遗传体系解析与重要基因克隆,双（多）亲杂交衍生群体遗传解析,群体遗传分化与进化和设计育种等方面。

关键词: 限制性两阶段多位点全基因关联分析, SNP连锁不平衡区段, 复等位变异, 多位点模型, QTL-allele矩阵, 假阳性, 模型显著性

Abstract:

Restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS) is a novel GWAS procedure which provides a way to identify the QTL system with various multiple alleles in natural and bi- or multi-parental derived populations. The major purposes and its two major characteristics of the RTM-GWAS procedure were presented, including the establishment of the SNPLDB markers with multiple alleles fitting the property of the natural and bi- or multi-parental derived populations and the establishment of multi-locus model GWAS procedure with the total genetic contribution controlled within heritability value. Generally, the readers and editors do not doubt about the methods and principles, the multiple allele markers and the multi-locus model, but have questions and queries on the large amount of detected QTLs many more than those from single locus MLM-GWAS procedure and on the general significance level without correction used in RTM-GWAS. These doubts were carefully and seriously explained and relieved. Furthermore, the potential usefulness of the RTM-GWAS procedure in genetic and evolutionary studies were summarized, including usefulness in relatively thorough identification of the QTL-allele system in populations and major gene finding and cloning, usefulness in relatively thorough identification of the QTL-allele system in bi-and multi-parental derived populations, usefulness in studies on population genetic differentiation and evolution and usefulness in breeding by genetic design.

Key words: restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS), SNP linkage disequilibrium block (SNPLDB), multiple alleles, multi-locus model, QTL-allele matrix, false positive, model significance

盖钧镒,贺建波. 限制性两阶段多位点全基因组关联分析法（RTM-GWAS）的特点、常见提问与应用前景[J]. 中国农业科学, 2020, 53(9): 1699-1703.

JunYi GAI,JianBo HE. Major Characteristics, Often-Raised Queries and Potential Usefulness of the Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis[J]. Scientia Agricultura Sinica, 2020, 53(9): 1699-1703.

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限制性两阶段多位点全基因组关联分析法（RTM-GWAS）的特点、常见提问与应用前景

Major Characteristics, Often-Raised Queries and Potential Usefulness of the Restricted Two-Stage Multi-Locus Genome-Wide Association Analysis

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