Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.

低温作为一种重要的非生物胁迫因素，对水稻（Oryza sativa L.）的形态发育和种子产量产生负面影响。在秧苗阶段，低温胁迫会导致发芽不良、秧苗损伤和成苗率降低；在生殖阶段，低温会降低种子产量。水稻多样性群体1（Rice Diversity Panel 1，RDP1）是一个全球性的水稻基因型收集，包含超过400个O. sativa品种，代表来自INDICA和JAPONICA品种组的五大主要亚种群，其基因型数据集由70万个单核苷酸多态性（SNP）标记组成。本研究旨在评估RDP1品种在发芽和生殖阶段的复杂、数量性状遗传的耐寒特性，并开展全基因组关联（GWA）分析，以识别与低温胁迫相关的SNPs和候选基因。发芽指数（以低温条件下的发芽率除以温暖处理条件下的发芽率计算）的全基因组关联分析揭示了42个与秧苗阶段耐寒性相关的数量性状位点（QTLs），其中包括在整个群体中18个，温带粳稻7个，热带粳稻6个，JAPONICA品种14个，INDICA品种9个，以及所有亚种群共有的5个。其中22个QTLs与先前报道的32个耐寒性QTLs共定位。生殖阶段的耐寒性全基因组关联分析检测到29个QTLs，包括与百分比不育性相关的7个，每穗种子重量相关的10个，每株种子重量相关的14个，以及两个性状重叠的一个区域。其中15个与先前报道的耐寒性或产量组分QTLs共定位。候选基因本体搜索显示，这些QTLs与与脂质代谢、应激反应、生物应激反应（暗示生物和非生物胁迫之间的相互作用）以及氧结合相关的基因显著富集。总体而言，JAPONICA品种比INDICA品种对低温胁迫更具耐受性。