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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.
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.
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.
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.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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