Chinese Journal OF Rice Science >
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
【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
WANG Shilin, WU Ting, ZHOU Shiqi, SONG Siming, HU Biaolin . Identification of QTLs for Seed Storability in Dongxiang Wild Rice by Integrating BSA-Seq and QTL Analysis[J]. Chinese Journal OF Rice Science, 2025 , 39(6) : 789 -800 . DOI: 10.16819/j.1001-7216.2025.240807
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