摘要
【目的】为全面解析大豆重组自交系群体中调控百粒重性状的QTL体系,将限制性两阶段多位点全基因组关联分析方法(RTM-GWAS)和不同定位方法进行比较、优选,为后续候选基因体系探索及分子标记辅助育种设计提供依据。【方法】利用以科丰1号和南农1138-2为亲本衍生的重组自交系群体NJRIKY的427个家系,通过由全基因组39353个SNP构建的3683个SNPLDB标记及3个环境下的百粒重表型数据,选用复合区间作图法(CIM)、基于混合线性模型的全基因组关联分析方法(MLM-GWAS)和RTM-GWAS 3种方法检测百粒重QTL,通过QTL数目和总的表型变异解释率比较检测功效,挑选最佳定位结果进行NJRIKY群体中的百粒重遗传体系解析。通过候选基因体系的功能注释,挖掘调控大豆百粒重的生物学途径。【结果】科丰1号与南农1138-2的百粒重差异较大,多环境平均数分别为9.0和17.9 g,遗传变异系数为12.4%,遗传率为85.4%,适用于百粒重性状的遗传解析。比较3种方法定位结果表明RTM-GWAS方法表现最佳,检测QTL数目最多(57个),解释表型变异最多(70.78%)。而CIM仅检测到14个QTL,解释了56.47%的表型变异,MLM-GWAS仅定位到6个QTL,解释了18.47%的表型变异。RTM-GWAS共检测到57个QTL,分布在19条染色体上,表型变异解释率为0.03%—7.57%,其中41个QTL覆盖了已报道的来自30个双亲群体的81个百粒重QTL,16个QTL为新发现位点,包含一个表型变异解释率大于3%的大效应位点Sw-09-2。此外,检测的57个QTL中有20个位点与环境存在互作效应。这57个QTL构成了影响NJRIKY群体百粒重性状的遗传体系。通过SNPLDB标记与预测基因内的SNP进行χ^2检验,共筛选到36个候选基因,其中4个候选基因来自大效应QTL,剩余32个候选基因来自小效应QTL。通过GO注释发现这些候选基因功能注释丰富,其中13个候选基因与籽粒发育直接相关,剩余的候选基因功能丰富,包含转运、转录调节因子等,表明不同生物学途径的基因共同调控NJRIKY群体中百粒重性状的表达。【结论】3种定位方法中,高效的RTM-GWAS方法检测到较为全面的NJRIKY群体的百粒重QTL,更适用于双亲RIL群体的QTL定位。不同功能的候选基因共同调控了复杂的百粒重性状的表达。
【Objective】To thoroughly dissect the QTL system conferring 100-seed weight in a recombinant inbred lines population,the restricted two-stage multi-locus genome-wide association analysis(RTM-GWAS)method was compared with other mapping methods for method optimization,which will provides basis for further exploration of candidate gene system and molecular marker-assisted design breeding.【Method】A recombinant inbred line population consisting of 427 lines derived from a cross between Kefeng-1 and NN1138-2 was tested for its 100-seed weight under three environments.A total of 3683 SNPLDBs(SNP linkage disequilibrium blocks)composed of 39353 SNPs were applied to QTL mapping using three different mapping procedures,including the composite interval mapping(CIM)method,the mixed linear model(MLM-GWAS)method and the RTM-GWAS method,and the best mapping procedure was selected for the analysis of the 100-seed weight genetic system in NJRIKY population through comparing their detection power,including the detected number of QTLs and total phenotypic variation explained.【Result】The 100-seed weight of Kefeng-1 and NN1138-2 were 9.0 g and 17.9 g,respectively,showing significant difference.The genotypic coefficient of variation and heritability of the trait were 12.4% and 85.4%,respectively.These results indicated that the population was suitable for genetic analysis of 100-seed weight trait.The RTM-GWAS procedure performed the best with the largest number of QTLs(57)explaining the most phenotypic variation(PVE=70.78%),while a total of 14 and 6 QTLs contributing 56.47% and 18.47% phenotypic variation were detected using CIM and MLM-GWAS,respectively.The 57 QTLs detected from the RTM-GWAS distributed on 19 chromosomes,of which 41 QTLs overlapped with 81 QTLs identified from 30 bi-parental populations in the literature.Furthermore,the PVE of 57 QTLs ranged from 0.03% to 7.57%,of which 16 QTLs were novel ones,including one large contribution major QTL Sw-09-2(PVE>3%).Furthermore,20 QTLs had significant interaction effect with environment.A total of 36 candidate genes were annotated from 37 QTLs through χ^2 test between SNPLDB markers and SNPs harboring in the predicted genes,of which 4 candidate genes were from the large contribution QTLs and other 32 candidate genes were from the small contribution QTLs.These candidate genes were included in different biological processes,of which 13 candidate genes were grouped in seed development directly,and the remaining candidate genes were grouped into different functions,such as transport,transcriptional regulators,etc.,indicating that these genes from different biological pathways regulate the expression of 100-seed weight trait in NJRIKY together.【Conclusion】Among the three different mapping procedures,RTM-GWAS procedure is the most powerful one which can provide a relatively thorough detection of 100-seed weight QTLs in NJRIKY population,therefore,it is more suitable for QTL mapping in bi-parental population such as RIL population.The candidate genes with various functions jointly regulated the complex expression of 100-seed weight trait.
作者
潘丽媛
贺建波
赵晋铭
王吴彬
邢光南
喻德跃
张小燕
李春燕
陈受宜
盖钧镒
PAN LiYuan;HE JianBo;ZHAO JinMing;WANG WuBin;XING GuangNan;YU DeYue;ZHANG XiaoYan;LI ChunYan;CHEN ShouYi;GAI JunYi(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;Institute of Genetics and Developmental Biology,Chinese Academy of Sciences/State Key Laboratory of Plant Genomics,Beijing 100101;Shandong Shofine Seed Technology Co.Ltd.,Jiaxiang 272400,Shandong)
出处
《中国农业科学》
CAS
CSCD
北大核心
2020年第9期1730-1742,共13页
Scientia Agricultura Sinica
基金
国家自然科学基金(31701447)
国家作物育种重点研发计划(2017YFD0101500,2017YFD0102002)
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。
关键词
大豆
百粒重
QTL
重组自交家系
限制性两阶段多位点全基因组关联分析
soybean[Glycine max(L.)Merr.]
100-seed weight
QTL(quantitative trait locus)
recombinant inbred lines population
restricted two-stage multi-locus genome-wide association analysis
