Kim Chun Ae, Chen Wenqiang, Zhu Shuangbing, Zhang Guogen, Shen Congcong, Chen Kai, Zhao Xiuqin, Zheng Tianqing, Wang Wensheng, Xu Jianlong
State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Molecular Plant Breeding Lab, Branch of Biotechnology, Democratic, State Academy of Sciences, Pyongyang, Democratic People's Republic of Korea.
BMC Genomics. 2025 Aug 19;26(1):756. doi: 10.1186/s12864-025-11937-8.
Rice, being a thermophilic crop, exhibits high sensitivity to low-temperature stress throughout its growth and development. Consequently, enhancing cold tolerance (CT) has been a paramount objective in rice breeding programs. The budding and seedling stages are particularly susceptible to low-temperature damage, making it crucial to improve CT during these stages to ensure the stable establishment and development of the rice population.
In this study, we exposed the parental lines Nipponbare (NIP) and Searice 86 (SR86), along with their derived 170 doubled-haploid (DH) population lines, to cold treatments during both the budding and seedling stages. Quantitative trait locus (QTL) mapping was performed using statistical indices such as the survival rate at the budding stage (SRBS), severity of damage at the budding stage (SDBS), survival rate at the seedling stage (SRSS), and wilting degree at the seedling stage (WDSS). This analysis identified four QTLs at the budding stage and eight QTLs at the seedling stage. Furthermore, by integrating differentially expressed genes (DEGs) from transcriptomic data with genes located within the QTL regions, we identified 10 candidate genes for the budding stage and 11 candidate genes for the seedling stage. Based on DNA sequence variations between the parental lines, changes in gene expression under cold treatment, and haplotype analyses, the key candidate genes were ultimately determined to be Os02g0250600 for the budding stage and Os06g0696600 for the seedling stage. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of transcriptomic data from both stages revealed significant differences in the regulatory pathways involved in CT between the budding and seedling stages.
The results indicate that Os02g0250600 is the pivotal gene responsible for CT at the budding stage, with haplotype 4 exhibiting the highest level of CT. Meanwhile, Os06g0696600 plays a crucial role in CT at the seedling stage, where haplotypes 2 and 4 have been identified as advantageous. A comprehensive analysis integrating QTL and transcriptome data from both stages revealed distinct differences in CT mechanisms, highlighting stage-specific variations. This study provides valuable theoretical insights and practical references for the cloning of CT genes and the development of cold-tolerant rice varieties during the budding and seedling stages.
水稻作为一种喜温作物，在其整个生长发育过程中对低温胁迫表现出高度敏感性。因此，提高耐寒性一直是水稻育种计划的首要目标。发芽期和苗期尤其容易受到低温伤害，在这些阶段提高耐寒性对于确保水稻群体的稳定建立和发育至关重要。
在本研究中，我们将亲本系日本晴（NIP）和丝苗86（SR86）及其衍生的170个双单倍体（DH）群体系在发芽期和苗期进行冷处理。使用发芽期存活率（SRBS）、发芽期损伤严重程度（SDBS）、苗期存活率（SRSS）和苗期萎蔫程度（WDSS）等统计指标进行数量性状位点（QTL）定位。该分析在发芽期鉴定出4个QTL，在苗期鉴定出8个QTL。此外，通过将转录组数据中的差异表达基因（DEG）与位于QTL区域内的基因整合，我们鉴定出发芽期10个候选基因和苗期11个候选基因。基于亲本系之间的DNA序列变异、冷处理下基因表达的变化以及单倍型分析，最终确定关键候选基因在发芽期为Os02g0250600，在苗期为Os06g0696600。此外，对两个阶段转录组数据的基因本体论（GO）和京都基因与基因组百科全书（KEGG）富集分析揭示了发芽期和苗期在耐寒性调控途径上的显著差异。
结果表明，Os02g0250600是发芽期负责耐寒性的关键基因，单倍型4表现出最高水平的耐寒性。同时，Os06g0696600在苗期耐寒性中起关键作用，其中单倍型2和4已被确定为有利单倍型。综合两个阶段的QTL和转录组数据进行的全面分析揭示了耐寒机制的明显差异，突出了阶段特异性变化。本研究为发芽期和苗期耐寒基因的克隆以及耐寒水稻品种的培育提供了有价值的理论见解和实践参考。
