| 东北大豆种质群体百粒重QTL-等位变异的全基因组解析 |
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| 引用本文： | 郝晓帅,傅蒙蒙,刘再东,贺建波,王燕平,任海祥,王德亮,杨兴勇,程延喜,杜维广,盖钧镒.东北大豆种质群体百粒重QTL-等位变异的全基因组解析[J].中国农业科学,2020,53(9):1717-1729. |
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| 作者姓名： | 郝晓帅 傅蒙蒙 刘再东 贺建波 王燕平 任海祥 王德亮 杨兴勇 程延喜 杜维广 盖钧镒 |
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| 作者单位： | 1 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;2 黑龙江省农业科学院牡丹江分院/国家大豆改良中心牡丹江试验站,黑龙江牡丹江 157041;3 黑龙江省农垦科学院,黑龙江佳木斯 154007;4 黑龙江省农业科学院克山分院,黑龙江克山 161606;5 长春市农业科学院,长春 130111 |
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| 基金项目： | 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 |
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| 摘 要： | 【目的】对东北大豆种质群体百粒重性状进行全基因组关联分析,全面解析中国大豆主产区百粒重QTL-等位变异遗传构成,为东北地区大豆籽粒大小遗传改良提供理论基础。【方法】以东北地区育种和生产上常用的290份大豆材料作为试验群体,于2013和2014年在东北第二生态亚区的克山、牡丹江、佳木斯和长春4个地点进行百粒重表型鉴定试验。利用RAD-seq方法对试验群体进行基因组测序分析,对原始SNP数据进行过滤及填补缺失数据后,最终获得了82 966个高质量的SNP标记。根据限制性两阶段多位点全基因组关联分析（restricted two-stage multi-locus genome-wide association analysis,RTM-GWAS）方法,首先构建获得15 546个具有复等位变异的SNPLDB标记,然后使用两阶段多位点模型对百粒重性状进行全基因组关联分析。对检测到的百粒重关联SNPLDB标记位点附近（50 kb范围内）的基因进行分析,根据基因内SNP与SNPLDB标记位点之间关联性的卡方测验,筛选可能与百粒重性状相关的候选基因并进行功能注释。最后基于检测的百粒重QTL-等位变异体系分析了不同熟期组材料间的遗传分化。【结果】试验群体百粒重变异范围为18.3—20.7 g,性状遗传率为92.3%。RTM-GWAS方法共检测到76个与大豆百粒重性状关联的SNPLDB标记位点,其中15个位点主效不显著,另外61个主效显著位点解释了65.40%的表型变异;68个与环境互作效应显著的位点解释了17.46%的表型变异,另外8个位点与环境互作效应不显著。在检测到的76个位点中有34个位点与已报道的30个百粒重QTL重叠,另外42个位点为本研究新检测百粒重位点。基于检测的SNPLDB标记位点,共筛选到137个百粒重相关候选基因,功能注释显示这些候选基因不仅参与大豆百粒重的调节,还参与了初级新陈代谢、蛋白质修饰、物质运输、胁迫响应和信号转导等。对各熟期组间QTL-等位变异的遗传分化分析显示,尽管熟期组间百粒重差异不明显,但其QTL-等位变异遗传结构却发生了新生和汰除的变化。【结论】RTM-GWAS方法能相对全面地解析东北大豆种质群体百粒重QTL-等位变异遗传构成。东北大豆种质群体百粒重由大量QTL调控,且QTL与环境互作效应大,QTL存在丰富的复等位变异。由RTM-GWAS方法建立的QTL-等位变异矩阵为群体遗传及演化研究提供了新工具。
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| 关 键 词： | 大豆 百粒重 限制性两阶段多位点全基因组关联分析 QTL-allele矩阵 候选基因 |
| 收稿时间： | 2019-09-09 |
Genome-Wide QTL-Allele Dissection of 100-Seed Weight in the Northeast China Soybean Germplasm Population |
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| XiaoShuai HAO,MengMeng FU,ZaiDong LIU,JianBo HE,YanPing WANG,HaiXiang REN,DeLiang WANG,XingYong YANG,YanXi CHENG,WeiGuang DU,JunYi GAI.Genome-Wide QTL-Allele Dissection of 100-Seed Weight in the Northeast China Soybean Germplasm Population[J].Scientia Agricultura Sinica,2020,53(9):1717-1729. |
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| Authors: | XiaoShuai HAO MengMeng FU ZaiDong LIU JianBo HE YanPing WANG HaiXiang REN DeLiang WANG XingYong YANG YanXi CHENG WeiGuang DU JunYi GAI |
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| Abstract: | 【Objective】A genome-wide association study in the Northeast China soybean germplasm population was conducted for a relatively thorough detection of the QTL-allele constitution of 100-seed weight, which may provide a theoretical basis for soybean breeding for seed size improvement. 【Method】In the present study, a total of 290 soybean accessions that were frequently used for soybean breeding and production in the Northeast China were tested in 2013 and 2014 for 100-seed weight at four locations, including Keshan, Mudanjiang, Jiamusi and Changchun, which are all in the second sub-ecoregion of the Northeast China. RAD-seq (restriction site-associated DNA sequencing) was used for SNP genotyping, and 82 966 high-quality SNPs were obtained after filtering and imputation. According to the RTM-GWAS (restricted two-stage multi-locus genome-wide association analysis) method, firstly a total of 15 546 multi-allelic SNPLDBs were constructed, and then a multi-locus model was used for genome-wide association study of 100-seed weight. The genes near (within 50kb) the detected SNPLDBs were analyzed, and candidate genes for 100-seed weight were identified and annotated according to Chi-square test of independence between the SNPs within genes and the detected SNPLDBs. Finally, genetic differentiation among maturity groups were investigated based on the detected QTL-allele system of 100-seed weight. 【Result】The 100-seed weight of the present population ranged from 18.3 to 20.7 g, and the trait heritability was 92.3%. A total of 76 SNPLDBs were detected to be associated with 100-seed weight, among which there were 15 SNPLDBs with non-significant main effect and the 61 SNPLDBs with significant main effect explained 65.40% phenotypic variation. There were 68 SNPLDBs that had significant interaction effect with environment and explained 17.46% phenotypic variation. In addition, 34 out of 76 detected SNPLDBs overlapped 30 previously reported QTLs and 42 SNPLDBs were novel loci. A total of 137 candidate genes for 100-seed weight were annotated in the detected SNPLDB regions, and functional annotation showed that these genes were not only involved in regulation of 100-seed weight, but also involved in primary metabolism, translation, protein modification, material transport, stress response and signal transduction, etc. Although there was no obvious difference in the 100-seed weight among different maturity groups, genetic differentiation analysis showed varying changes of allele emergence and exclusion in QTL-allele structure of 100-seed weight among maturity groups. 【Conclusion】The RTM-GWAS method used in the present study provided a relatively thorough detection of genome-wide QTLs and their multiple alleles for 100-seed weight in the Northeast China soybean germplasm population. The 100-seed weight of the Northeast China soybean germplasm population was controlled by a large number of QTLs with large significant interaction effect with environment, and there was also abundant multiple allelic variation in these QTLs. The QTL-allele matrix established from RTM-GWAS provided an efficient tool for population genetics and evolution study. |
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| Keywords: | soybean [Glycine max (L ) Merr ] 100-seed weight RTM-GWAS QTL-allele matrix candidate gene |
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