Identification of Genes for Rice Seed Storability and Transcriptome Analysis Under Different Aging Conditions

doi:10.16819/j.1001-7216.2026.241110

Abstract

Abstract:

【Objective】Seed storability is crucial for germplasm conservation, food security, and sustainable development. This study aims to identify QTLs associated with rice seed storability and explore the genetic basis of seed storability under different aging conditions.【Method】A set of 131 Oryza nivara introgression lines in the genetic background of the indica variety 93-11 was used. Seeds were subjected to natural aging and artificial aging treatments, and germination rates were measured for QTL mapping. RNA sequencing was performed to analyze genome-wide gene expression patterns in embryos from the storage-tolerant line Ra32 (carrying the O. nivara-derived allele of qASS1.1/qNSS1.1) and the storage-sensitive line Ra146 (without the allele). GO and KEGG enrichment analyses were conducted to explore enriched pathways and to identify genes related to seed storability.【Result】Six QTLs for seed storability were identified on chromosomes 1, 3, 6, 7, and 9, with individual QTLs explaining 3.3% to 21.0% of phenotypic variance. Among them, qASS1.1/qNSS1.1 was consistently detected under both natural and artificial aging treatments, and the O. nivara-derived allele at this QTL enhanced seed storability. Transcriptome analysis revealed 2077 differentially expressed genes (DEGs) under artificial aging and 1468 DEGs under natural aging, with 733 shared DEGs between the two treatments. GO and KEGG analyses showed that DEGs under artificial aging were enriched in 1428 GO terms and 97 metabolic pathways, while DEGs under natural aging were enriched in 1199 GO terms and 85 pathways. Two biological processes (circadian regulation of translation and hydrogen peroxide catabolic process) and 12 metabolic pathways (including MAPK signaling pathway, zeatin biosynthesis, histidine metabolism, and ascorbate and aldarate metabolism) were commonly enriched in both treatments, suggesting that seed storability may be regulated by antioxidant systems, energy metabolism, and accumulation of seed storage substances. Based on functional annotation of DEGs near the qASS1.1/qNSS1.1 locus, five candidate genes for qASS1.1/qNSS1.1 were further identified.【Conclusion】This study identified QTLs related to seed storability and screened multiple candidate genes, revealing that rice seeds enhance storability under different aging treatments mainly by regulating antioxidant defense, maintaining cellular stability, and modulating metabolic processes. These findings provide new genetic resources for improving seed storability in rice.

Key words: wild rice, introgression line, QTL, seed storability, transcriptome, differentially expressed gene

摘要：

【目的】水稻种子耐储性对种质资源保护、粮食安全和可持续发展具有重要意义。本研究旨在挖掘控制水稻种子耐储性的QTL，并探索不同老化方式下耐储性的遗传基础。【方法】以籼稻93-11为背景的131个尼瓦拉野生稻渗入系为材料，分别采用自然老化和人工老化处理，测定发芽率进行QTL定位。通过转录组测序比较携带qASS1.1/qNSS1.1野生稻等位基因的耐储材料Ra32与不携带增效等位基因的不耐储材料Ra146，筛选差异表达基因(Differentially expressed genes, DEGs)，并通过GO和KEGG分析挖掘候选基因。【结果】共检测到6个耐储性QTL，分布在1、3、6、7、9号染色体上，每个QTL可解释3.3%~21.0%的表型变异。其中，主效QTL qASS1.1/qNSS1.1在两种老化处理中均稳定检测到，且野生稻等位基因显著提高种子耐储性。转录组分析共鉴定出人工老化下2077个DEG、自然老化下1468个DEG，两种处理下共有733个DEG。GO富集和KEGG代谢途径分析显示，人工老化下DEG可富集到1428个GO条目和97个代谢途径；自然老化下分别为1199个条目和85个代谢途径。在最显著富集的10个生物学过程和30个代谢途径中，昼夜节律调控翻译和过氧化氢分解过程等生物学过程以及MAPK信号传导通路、细胞分裂素生物合成、组氨酸代谢、抗坏血酸和醛糖酸代谢等代谢是两种老化处理共有的富集通路，表明种子耐储性可能受抗氧化系统调控、能量代谢及种子储藏物质积累等机制影响。基于这些富集通路，经RT-qPCR验证，初步筛选到主效QTL qASS1.1/qNSS1.1的5个候选基因，包括Os01g0842400与Os01g0842500(编码漆酶前体蛋白)、Os01g0847800(编码醛酮还原酶家族蛋白)、Os01g0855900(编码CDC6-DNA复制起始蛋白)和Os01g0860400(编码糖基水解酶)。【结论】本研究挖掘到耐储性QTL并筛选出多个候选基因，揭示了不同老化处理下水稻种子主要通过调节抗氧化防御、维持细胞稳定性和代谢过程来提高其耐储性，为水稻耐储性改良提供了新的基因资源和理论支持。

关键词: 野生稻, 渗入系, QTL, 耐储性, 转录组, 差异表达基因

LIAO Zhengming, GUO Liang, PAN Xiaowu, LI Yongchao, DONG Zheng, LI Xiaoxiang. Identification of Genes for Rice Seed Storability and Transcriptome Analysis Under Different Aging Conditions[J]. Chinese Journal OF Rice Science, 2026, 40(1): 95-105.

廖政明, 郭梁, 潘孝武, 黎用朝, 董铮, 李小湘. 水稻种子耐储性基因的挖掘及不同老化方式的转录组分析[J]. 中国水稻科学, 2026, 40(1): 95-105.

Figures/Tables 8

References 35

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染色体 Chr	QTL	处理 Treatment	标记区间 Marker region	物理区间 Interval (Mb)	LOD	R² (%)	加性效应 Additive effect	前人研究 Previous study
1	qASS1.1	人工老化（三亚）	Bin147-Bin152	37.73-38.68	7.28	19.0	0.13	qSS1.1^[19]
1	qASS1.1	人工老化（长沙）	Bin147-Bin152	37.73-38.68	11.60	15.5	0.16	qSS1.1^[19]
1	qASS1.2	人工老化（长沙）	Bin154-Bin160	38.73-40.29	3.90	4.5	−0.09
1	qNSS1.1	自然老化（三亚）	Bin147-Bin152	37.73-38.68	19.04	21.0	0.13	qSS1.1^[19]
1	qNSS1.2	自然老化（三亚）	Bin154-Bin160	38.73-40.29	7.19	5.8	−0.08
3	qASS3	人工老化（长沙）	Bin333-Bin340	50.15-67.74	3.00	3.3	0.12
6	qNSS6	自然老化（三亚）	Bin580-Bin612	1.56-13.19	9.76	9.2	0.40	qSS-6^[15]
7	qNSS7	自然老化（三亚）	Bin662-Bin669	6.16-17.35	8.40	8.1	0.15	qSS7.1^[17]
9	qASS9	人工老化（三亚）	Bin813-Bin819	8.04-10.05	6.96	17.7	0.16	qRC9-2^[14], qSS-9^[15]

染色体 Chr	QTL	处理 Treatment	标记区间 Marker region	物理区间 Interval (Mb)	LOD	R² (%)	加性效应 Additive effect	前人研究 Previous study
1	qASS1.1	人工老化（三亚）	Bin147-Bin152	37.73-38.68	7.28	19.0	0.13	qSS1.1^[19]
1	qASS1.1	人工老化（长沙）	Bin147-Bin152	37.73-38.68	11.60	15.5	0.16	qSS1.1^[19]
1	qASS1.2	人工老化（长沙）	Bin154-Bin160	38.73-40.29	3.90	4.5	−0.09
1	qNSS1.1	自然老化（三亚）	Bin147-Bin152	37.73-38.68	19.04	21.0	0.13	qSS1.1^[19]
1	qNSS1.2	自然老化（三亚）	Bin154-Bin160	38.73-40.29	7.19	5.8	−0.08
3	qASS3	人工老化（长沙）	Bin333-Bin340	50.15-67.74	3.00	3.3	0.12
6	qNSS6	自然老化（三亚）	Bin580-Bin612	1.56-13.19	9.76	9.2	0.40	qSS-6^[15]
7	qNSS7	自然老化（三亚）	Bin662-Bin669	6.16-17.35	8.40	8.1	0.15	qSS7.1^[17]
9	qASS9	人工老化（三亚）	Bin813-Bin819	8.04-10.05	6.96	17.7	0.16	qRC9-2^[14], qSS-9^[15]

候选基因 Candidate gene	功能注释 Functional annotation	Ra32 vs Ra146 ¹⁾	GO富集通路 GO enriched pathways	KEGG富集通路 KEGG enriched pathways
Os01g0842400	漆酶前体蛋白 Laccase precursor protein	下调 Down-regulated	木质素分解过程、氧化还原酶活性 Lignin catabolic process, oxidoreductase activity
Os01g0842500	漆酶前体蛋白 Laccase precursor protein	下调 Down-regulated	木质素分解过程、氧化还原酶活性 Lignin catabolic process, oxidoreductase activity
Os01g0847800	醛酮还原酶家族蛋白 Aldo-keto reductase family protein	上调 Up-regulated		糖酵解/糖异生、抗坏血酸和醛糖酸代谢、丙酮酸代谢Glycolysis/gluconeogenesis, ascorbate and aldarate metabolism, pyruvate metabolism
Os01g0855900	CDC6-DNA复制起始蛋白 CDC6-DNA replication initiation protein	下调 Down-regulated	细胞分裂、有丝分裂细胞周期 Cell division, mitotic cell cycle
Os01g0860400	糖基水解酶 Glycoside hydrolase	上调 Up-regulated	壳聚糖分解过程、多糖分解过程 Chitosan catabolic process, polysaccharide catabolic process	氨基糖和核苷酸糖代谢 Amino sugar and nucleotide sugar metabolism

候选基因 Candidate gene	功能注释 Functional annotation	Ra32 vs Ra146 ¹⁾	GO富集通路 GO enriched pathways	KEGG富集通路 KEGG enriched pathways
Os01g0842400	漆酶前体蛋白 Laccase precursor protein	下调 Down-regulated	木质素分解过程、氧化还原酶活性 Lignin catabolic process, oxidoreductase activity
Os01g0842500	漆酶前体蛋白 Laccase precursor protein	下调 Down-regulated	木质素分解过程、氧化还原酶活性 Lignin catabolic process, oxidoreductase activity
Os01g0847800	醛酮还原酶家族蛋白 Aldo-keto reductase family protein	上调 Up-regulated		糖酵解/糖异生、抗坏血酸和醛糖酸代谢、丙酮酸代谢Glycolysis/gluconeogenesis, ascorbate and aldarate metabolism, pyruvate metabolism
Os01g0855900	CDC6-DNA复制起始蛋白 CDC6-DNA replication initiation protein	下调 Down-regulated	细胞分裂、有丝分裂细胞周期 Cell division, mitotic cell cycle
Os01g0860400	糖基水解酶 Glycoside hydrolase	上调 Up-regulated	壳聚糖分解过程、多糖分解过程 Chitosan catabolic process, polysaccharide catabolic process	氨基糖和核苷酸糖代谢 Amino sugar and nucleotide sugar metabolism

基因ID Gene ID	正向引物 Forward primer	反向引物 Reverse primer
Os01g0842400	ATCTTCGGCGAGTGGTGGA	TGTCTTGGGCAGAGCAGTTG
Os01g0842500	CTTCTCCGTTCCTCCATCCT	ACGTTCGTCGTTTTCACATCGA
Os01g0847800	TGGCGTTCATCTCTCTGCGTA	CTGACCCTGCTGAAGACCC
Os01g0855900	CCATACCCGCGAAGCATTAAG	AGAGCCAAGCCCGCCAAAG
Os01g0860400	GACCTCGCCAGGGATCTGA	CGAACAGCCCCGTGCTGAT