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Outline
Low-temperature stress poses a significant threat to rice production, and the development of cold-tolerant varieties through the identification of cold resistance-related genes represents a critical strategy to address this challenge. Meta-QTL analysis offers a powerful approach to integrate quantitative trait loci governing complex agronomic traits, such as cold tolerance, across diverse genetic backgrounds. By improving the precision and reliability of candidate gene localization, this method provides a robust foundation for the cloning and breeding application of cold tolerance genes in rice.
We conducted a comprehensive meta-analysis of 353 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, derived from 38 independent studies. These QTLs were integrated using BioMercator 4.2, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to identify candidate genes within the Meta-QTL regions.
A total of 82 Meta-QTLs were identified, of which 67 (81.71%) had confidence intervals of less than 1 Mb. These regions encompassed 9282 annotated genes, including 25 previously reported genes associated with cold tolerance at the seedling stage. GO analysis revealed 99, 230, and 119 genes associated with abiotic stress response, environmental stress response, and transcription factors, respectively. KEGG enrichment analysis further identified 27, 69, and 9 significantly enriched genes related to abiotic stress response, stress response, and transcription factors, respectively.
Through the integration and analysis of 353 QTLs related to cold tolerance at the seedling stage, 82 Meta-QTLs were identified. GO analysis pinpointed 448 candidate genes, while KEGG analysis further refined this list to 105 differentially enriched candidate genes. These findings provide valuable insights for molecular marker-assisted breeding and gene cloning for cold tolerance at the rice seedling stage.
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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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