基于NCⅡ遗传交配设计的籼稻抽穗期全基因组关联分析  

Genome-wide association analysis of indica-rice heading date based on NCⅡ genetic mating design

作　　者：徐凯 郑兴飞 张红燕 胡中立 宁子岚 李兰芝[1] XU Kai;ZHENG Xing-Fei;ZHANG Hong-Yan;HU Zhong-Li;NING Zi-Lan;LI Lan-Zhi(Hunan Engineering&Technology Research Center for Agricultural Big Data Analysis&Decision-making,College of Plant Protection,Hunan Agricultural University,Changsha 410128,Hunan,China;Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement,Food Crop Institute,Hubei Academy of Agricultural Sciences,Wuhan 430064,Hubei,China;Key Laboratory of Hybrid Rice,College of Life Science,Wuhan University,Wuhan 430072,Hubei,China)

机构地区：[1]湖南农业大学植物保护学院/湖南省农业大数据分析与决策工程技术研究中心,湖南长沙410128 [2]湖北省农业科学院粮食作物研究所,湖北武汉430064 [3]武汉大学生命科学学院/杂交水稻国家重点实验室,湖北武汉430072

出　　处：《作物学报》2023年第1期86-96,共11页Acta Agronomica Sinica

基　　金：杂交水稻国家重点实验室(湖南杂交水稻研究中心)开放课题项目(2019KF05);杂交水稻国家重点实验室(武汉大学)开放课题项目(KF201912);湖南省教育厅资助科研项目(19A244);湖南省自然科学基金项目(2020JJ4039,2021JJ30351);湖南省创新型省份建设专项项目(2021NK1011)资助。

摘　　要：抽穗期受光温资源和基因网络的共同调控,影响作物产量和品种的地域适应性,通过关联分析鉴定与抽穗期性状相关的显著位点和基因,对解析抽穗期的遗传基础具有重要意义。本研究按照双因素交叉式遗传设计(North Carolina design Ⅱ,NCⅡ)将115份籼稻品种作为父本,5份不育系作为母本,进行测交,得到了575个F_(1)代的测交群体。对亲本和F_(1)代抽穗期的表型值、亲本品种群体的一般配合力、F_(1)代群体的特殊配合力和超亲优势值进行全基因组关联分析,(1)共定位到104个关联位点,分布在12条染色体上。其中,第4条染色体上检测到的显著位点最多,为16个。在亲本的抽穗期表型、一般配合力、F_(1)代的抽穗期表型、特殊配合力、超亲优势值5个数据集中分别检测到6、5、15、57和21个。对这5个数据集中的显著关联位点进行表型变异分析,发现在亲本抽穗期表型、一般配合力、F_(1)代抽穗期表型、特殊配合力和超亲优势值这5个数据集中的显著关联位点对表型变异的总贡献率(phenotypic variation explained,PVE)分别为79.57%、10.51%、33.35%、56.42%和54.86%。其中,25个位点在多个数据集中被检测到,可能为抽穗期相关的热点区域。(2)通过关联分析得到的显著位点与日本晴参考基因组注释信息比对,共检测到5个已克隆抽穗期基因,其中3个基因与显著关联位点的基因组距离小于200 kb,对这3个基因中的单倍型组合与单个基因的优异单倍型进行比较发现,亲本品种群体中单倍型组合SDG724(Hap.A)_Hd17(Hap.E)_Ghd7(Hap.A)的对应的水稻单株籽粒产量较高,抽穗期较长,该组合中各基因的单倍型对应于单个克隆基因的优异单倍型,表明优异单倍型的聚合的常规稻,具有更高的产量和更长的抽穗期。测交子代未见此情形,测交子代群体中SDG724(Hap.I)_Hd17(Hap.K)_Ghd7(Hap.I)的单倍型组合形式的水稻有适中的抽穗期和较高Heading date is jointly regulated by light and temperature resources and gene network, affecting crop yield and regional adaptability of varieties. Identification of significant loci and genes associated with trait variation by genome-wide association analysis(GWAS) is of great significance to analyze the genetic basis of the heading date in rice. In this study, according to the North Carolina design Ⅱ(NCⅡ), 115 indica rice varieties as the male parents and 5 sterile lines as the female parents had been made test cross, and 575 F1 test-cross lines were obtained. GWAS was performed on the phenotypic value of the heading date of the male parental varieties(V) and testcross lines(TC), the general combining ability(GCA) of the male parent lines, the special combining ability(SCA), and better parent heterosis(BPH) of testcross lines.(1) A total of 104 significantly associated locus were located and distributed on 12 chromosomes. Of these, 16 significantly associated locus were detected on chromosome 4. There were six, five, fifteen, fifty-seven, and twenty-one significantly associated locus detected in V, GCA, TC, SCA, BPH data sets,respectively. Phenotypic variation analysis of significantly associated sites in these five data sets revealed that the total contribution rate(phenotypic variation explained, PVE) of significantly associated loci to phenotypic variation in V, GCA, TC, SCA, and BPH data sets was 79.57%, 10.51%, 33.35%, 56.42%, and 54.86%, respectively. Twenty-five significantly associated locus were simultaneously detected in two or more than two datasets, that probably was hotspot genomic region of heading date in rice.(2)By comparing all significantly associated locus with the annotation information of the Nipponbare reference genome, five cloned genes related to heading date were found. Among them, three of the five genes within 200 kb from the significantly associated locus detected in this study. Compared with the haplotype combinations in the three genes with the superior haplotype of individual

关 键 词：水稻 抽穗期 全基因组关联分析 单倍型 NCⅡ遗传设计 

分 类 号：S511.21[农业科学—作物学]