Identification of QTLs for Seed Storability in Dongxiang Wild Rice by Integrating BSA-Seq and QTL Analysis

doi:10.16819/j.1001-7216.2025.240807

Abstract

Abstract:

【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

摘要：

【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。

关键词: 东乡野生稻, 耐储性, QTL定位, 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.

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.

Figures/Tables 10

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名称 Name	正向引物 Forward primer (5'-3')	反向引物 Reverse primer (5'-3')	候选基因 Candidate gene
Fou31040	CAGGTCAGAGGAACTCAG	GGATGCATTAGCAGATTC	LOC_Os04g31040
Fou31070	GATCTCGATGAGGAGGTG	GCAGATGGACAGGTAATTG	LOC_Os04g31070
Fou31240	GCGATATCCTATAGCCAA	CAGTCTAGCAATTCATGC	LOC_Os04g31240
Sev07420	GTGCTCGATGTGGCTTAG	CATGCATGTTGCAATGC	LOC_Os07g07420
Sev07790	CAATCACCTCATCACACAC	CATGGCACACTCAACAC	LOC_Os07g07790
Sev07860	TGAGACCAATGGAAATGG	GATTCCATCACTTCACAC	LOC_Os07g07860
Sev07870	CTGAGAGACATACATCAATC	GATACTCATCAGAAGGCATAC	LOC_Os07g07870
Sev07880	CTTTACCGAATGGAGACCAG	GGATTTACACTAGCAAGT	LOC_Os07g07880
Sev07930	CAGACACCAAGAGCATC	CGAATTCCTACACGCAC	LOC_Os07g07930
Nin15800	GACCGAGTGAGTCATCAAG	GTGAGTACTCTACATGATAC	LOC_Os09g15800
Nin15810	CACAGTATCTTCCTGCTAC	CAAGCATGGACATGCTAATC	LOC_Os09g15810
Nin15835	CTCTGGTTAGATCTTGCAC	CAATATGAATACCCTGCA	LOC_Os09g15835

名称 Name	正向引物 Forward primer (5'-3')	反向引物 Reverse primer (5'-3')	候选基因 Candidate gene
Fou31040	CAGGTCAGAGGAACTCAG	GGATGCATTAGCAGATTC	LOC_Os04g31040
Fou31070	GATCTCGATGAGGAGGTG	GCAGATGGACAGGTAATTG	LOC_Os04g31070
Fou31240	GCGATATCCTATAGCCAA	CAGTCTAGCAATTCATGC	LOC_Os04g31240
Sev07420	GTGCTCGATGTGGCTTAG	CATGCATGTTGCAATGC	LOC_Os07g07420
Sev07790	CAATCACCTCATCACACAC	CATGGCACACTCAACAC	LOC_Os07g07790
Sev07860	TGAGACCAATGGAAATGG	GATTCCATCACTTCACAC	LOC_Os07g07860
Sev07870	CTGAGAGACATACATCAATC	GATACTCATCAGAAGGCATAC	LOC_Os07g07870
Sev07880	CTTTACCGAATGGAGACCAG	GGATTTACACTAGCAAGT	LOC_Os07g07880
Sev07930	CAGACACCAAGAGCATC	CGAATTCCTACACGCAC	LOC_Os07g07930
Nin15800	GACCGAGTGAGTCATCAAG	GTGAGTACTCTACATGATAC	LOC_Os09g15800
Nin15810	CACAGTATCTTCCTGCTAC	CAAGCATGGACATGCTAATC	LOC_Os09g15810
Nin15835	CTCTGGTTAGATCTTGCAC	CAATATGAATACCCTGCA	LOC_Os09g15835

染色体 Chromosome	QTL	区间 Interval	位置 Position	LOD值 LOD	加性效应 A	贡献率 R²(%)	已克隆基因 Cloned genes
1	qSS1.1	chr1-204.9-chr1-216.3	36,735,178-40,016,503	2.55	13.77	1.64
1	qSS1.2	chr1-216.3-chr1-230.0	40,016,503-41,198,359	3.07	9.19	2.23
2	qSS2.1	chr2-84.6-chr2-101.9	27,538,266-28,417,539	6.77	13.54	4.78
2	qSS2.2	chr2-101.9-chr2-123.4	28,417,539-33,682,808	7.97	13.40	4.79	OsbZIP23
3	qSS3	chr3-111.7-chr3-121.4	30,677,202-33,003,423	2.56	14.09	1.60	OsLOX2
6	qSS6	chr6-34.7-chr6-50.0	17,953,681-24,234,137	10.29	−24.17	7.70
7	qSS7	chr7-21.1-chr7-25.2	3,146,214-5,200,751	8.82	−30.51	6.24
9	qSS9.1	chr9-69.2-chr9-78.9	13,164,222-14,567,027	3.33	10.01	2.09
11	qSS11	chr11-37.6-chr11-48.2	8,990,534-9,368,443	17.36	23.81	17.82

染色体 Chromosome	QTL	区间 Interval	位置 Position	LOD值 LOD	加性效应 A	贡献率 R²(%)	已克隆基因 Cloned genes
1	qSS1.1	chr1-204.9-chr1-216.3	36,735,178-40,016,503	2.55	13.77	1.64
1	qSS1.2	chr1-216.3-chr1-230.0	40,016,503-41,198,359	3.07	9.19	2.23
2	qSS2.1	chr2-84.6-chr2-101.9	27,538,266-28,417,539	6.77	13.54	4.78
2	qSS2.2	chr2-101.9-chr2-123.4	28,417,539-33,682,808	7.97	13.40	4.79	OsbZIP23
3	qSS3	chr3-111.7-chr3-121.4	30,677,202-33,003,423	2.56	14.09	1.60	OsLOX2
6	qSS6	chr6-34.7-chr6-50.0	17,953,681-24,234,137	10.29	−24.17	7.70
7	qSS7	chr7-21.1-chr7-25.2	3,146,214-5,200,751	8.82	−30.51	6.24
9	qSS9.1	chr9-69.2-chr9-78.9	13,164,222-14,567,027	3.33	10.01	2.09
11	qSS11	chr11-37.6-chr11-48.2	8,990,534-9,368,443	17.36	23.81	17.82

样品 Sample	原始数据 Raw base (bp)	过滤后的有效数据 Clean base (bp)	比对率 Mapping ratio (%)	平均测序深度 Average depth (×)	大于或等于30的碱基所占百分比 Clean Q30 (%)
R974	11,531,262,900	10,612,006,654	99.04	30.41	88.59
东野80 Dongye 80	12,730,838,700	12,019,467,219	98.55	32.58	94.20
S池S-bulk	11,921,866,200	11,435,986,027	97.44	31.16	92.52
W池W-bulk	11,710,934,400	11,116,889,747	97.73	30.00	93.70