Background

Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species.

Results

The Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to “carbohydrate biosynthesis”, “carbohydrate transmembrane transport”, “small molecule protein modification”, and “plasma membrane” were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to “Golgi apparatus”, “stress response”, “transmembrane transport”, and “signal transduction”.

Conclusions

Taken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.

中文翻译：

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多种耐寒性状的表型分析揭示了水稻的共有定量性状位点。

背景

发展驯化的亚洲水稻的耐冷性品种是作物获得重大改良的潜在来源。热带起源的稻米具有独特的低温敏感性，使其成为最重要的谷物作物，可通过提高对低温的耐受性而显着提高。但是，这种复杂特征的机制尚不完全清楚。水稻具有两个不同的耐冷性水平的亚种，JAPONICA和INDICA，提供了一个理想的工具来研究这种重要农作物中的耐冷性响应机制的差异。

结果

水稻多样性专家组1（RDP1）用于研究稻的核心组加入。该面板可用的工具可对RDP1的354个品种的多个温度下的两个耐冷性进行全面分析。耐冷性状的值分布为大多数特定于亚群的耐性，中度和敏感性种质。使用全部354个种质的全基因组关联研究（GWAS）定位方法共产生了245个定量性状位点（QTL），其中包含178个独特的QTL，覆盖了水稻基因组的25％，而40个QTL被多重性状鉴定。使用水稻种质簇子集的QTL定位又产生了255个QTL，总计500个QTL。分析这些多性状QTL中的基因的基因本体论（GO）术语和潜在途径富集。与“碳水化合物生物合成”有关的术语，“碳水化合物跨膜转运”，“小分子蛋白质修饰”和“质膜”从该列表中得到了丰富。进行过滤以识别出更多可能的耐寒性候选途径，从而增强了与“高尔基体”，“应激反应”，“跨膜运输”和“信号转导”有关的术语。

结论

总而言之，这些GO术语簇揭示了高尔基体介导的亚细胞和细胞外小泡以及细胞内碳水化合物运输的可能参与，作为在寒冷胁迫下实现细胞和代谢稳态的一般寒冷胁迫耐受机制。