结合BSA-seq和QTL分析鉴定东乡野生稻耐储性QTL
收稿日期: 2024-08-07
修回日期: 2024-10-14
网络出版日期: 2025-11-19
基金资助
江西省农业科学院基础研究与人才培养专项(JXSNKYJCRC202218);江西省自然科学基金重点项目(20224ACB205001)
Identification of QTLs for Seed Storability in Dongxiang Wild Rice by Integrating BSA-Seq and QTL Analysis
Received date: 2024-08-07
Revised date: 2024-10-14
Online published: 2025-11-19
【目的】水稻种子储藏对保障粮食安全生产具有重要意义，挖掘水稻耐储性基因资源，为培育耐储藏水稻新品种奠定遗传基础。【方法】以东乡野生稻东野80为供体、栽培稻R974为轮回亲本，分别构建了364份回交重组自交系和84份BC3F7单片段代换系。统计人工老化处理种子发芽率，并结合QTL和BSA-seq分析联合检测水稻耐储性QTL，进一步通过基因注释信息、GO富集分析和基因测序预测候选基因。【结果】利用单片段代换系共检测到9个耐储性QTL，分别为qSS1.1、qSS1.2、qSS2.1、qSS2.2、qSS3、qSS6、qSS7、qSS9.1和qSS11，贡献率为1.60%~17.82%，其中7个QTL的增效等位基因来自东野80，且qSS7和qSS11为新的QTL。而利用回交重组自交系进行BSA-seq分析，共关联到37个位点，分布于2、4、5、6、7、8、9和11号染色体上。其中，qSS7在2种方法中均被检测，将其进一步缩小至480.1 kb区间内。此外，qSS4和qSS9.2分别被缩小至199.7 kb和177.8 kb的交叠区间内。结合基因注释信息查询、GO富集分析和基因测序结果，推测LOC_Os04g31040和LOC_Os04g31070为qSS4的候选基因，LOC_Os07g07930为qSS7的候选基因，LOC_Os09g15800和LOC_Os09g15835为qSS9.2的候选基因。【结论】本研究通过QTL和BSA-Seq分析分别鉴定到9个和37个耐储性QTL，并推测了qSS4、qSS7和qSS9.2的候选基因。其中，qSS4和qSS9.2的东野80增效等位基因显著提高水稻种子耐储性，可为东乡野生稻耐储性QTL克隆及其在栽培稻耐储性遗传育种利用提供新的有利位点。
王世林, 吴婷, 周诗琪, 宋思铭, 胡标林 . 结合BSA-seq和QTL分析鉴定东乡野生稻耐储性QTL[J]. 中国水稻科学, 2025 , 39(6) : 789 -800 . DOI: 10.16819/j.1001-7216.2025.240807
【Objective】 The storage of rice seeds is crucial for ensuring food security and supporting sustainable agricultural production. Mining more genetic resources associated with seed storability is conducive to laying a genetic foundation for developing new storage-tolerant varieties.【Method】 Using Dongxiang wild rice accession Dongye 80 as the donor and cultivated rice R974 as the recurrent parent, two sets of BC₃F₇ populations—backcross recombinant inbred lines (BILs) consisting of 364 lines and single-segment substitution lines (SSSLs) consisting of 84 lines—were constructed. Germination rates were recorded after artificial aging treatment. QTL mapping and BSA-seq analysis were integrated to identify QTLs for seed storability from Dongxiang wild rice. Candidate genes were further predicted using gene annotation, GO enrichment analysis, and gene sequencing.【Result】 A total of nine QTLs for seed storability were detected on chromosomes 1, 2, 3, 6, 7, 9, and 11 using SSSLs, designated qSS1.1, qSS1.2, qSS2.1, qSS2.2, qSS3, qSS6, qSS7, qSS9.1, and qSS11, with phenotypic variation explained (PVE) ranging from 1.60% to 17.82%. Seven of these QTLs carried favorable alleles from Dongye 80, among which qSS7 and qSS11 were novel. Meanwhile, BSA-seq analysis using BILs identified 37 genomic regions associated with seed storability on chromosomes 2, 4, 5, 6, 7, 8, 9, and 11. The qSS7 interval was consistently detected by both methods and was narrowed down to a 480.1 kb overlapping region. In addition, qSS4 and qSS9.2 were delimited to overlapping regions of 199.7 kb and 177.8 kb, respectively. By integrating annotation information, GO enrichment, and gene sequencing, LOC_Os04g31040 and LOC_Os04g31070, LOC_Os07g07930, and LOC_Os09g15800 and LOC_Os09g15835 were proposed as candidate genes for qSS4, qSS7, and qSS9.2, respectively.【Conclusion】 In this study, nine and 37 QTLs for seed storability were identified by QTL mapping and BSA-seq analysis, respectively. Candidate genes for qSS4, qSS7, and qSS9.2 were further inferred. Notably, the favorable alleles of qSS4 and qSS9.2 from Dongye 80 significantly enhanced seed storability. Analysis of the candidate genes for qSS4 and qSS9.2 provides a foundation for cloning seed storability genes from Dongxiang wild rice and utilizing them in genetic improvement of cultivated rice.
Key words： Dongxiang wild rice; seed storability; QTL mapping; BSA-seq
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