Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes

Salinity tolerance is an important quality for European rice grown in river deltas. We evaluated the salinity tolerance of a panel of 235 temperate japonica rice accessions genotyped with 30,000 SNP markers. The panel was exposed to mild salt stress (50 mM NaCl; conductivity of 6 dS m-1) at the seedling stage. Eight different root and shoot growth parameters were measured for both the control and stressed treatments. The Na+ and K+ mass fractions of the stressed plants were measured using atomic absorption spectroscopy. The salt treatment affected plant growth, particularly the shoot parameters. The panel showed a wide range of Na+/K+ ratio and the temperate accessions were distributed over an increasing axis, from the most resistant to the most susceptible checks. We conducted a genome-wide association study on indices of stress response and ion mass fractions in the leaves using a classical mixed model controlling structure and kinship. A total of 27 QTLs validated by sub-sampling were identified. For indices of stress responses, we also used another model that focused on marker × treatment interactions and detected 50 QTLs, three of which were also identified using the classical method. We compared the positions of the significant QTLs to those of approximately 300 genes that play a role in rice salt tolerance. The positions of several QTLs were close to those of genes involved in calcium signaling and metabolism, while other QTLs were close to those of kinases. These results reveal the salinity tolerance of accessions with a temperate japonica background. Although the detected QTLs must be confirmed by other approaches, the number of associations linked to candidate genes involved in calcium-mediated ion homeostasis highlights pathways to explore in priority to understand the salinity tolerance of temperate rice.

耐盐性是河流三角洲种植的欧洲水稻的重要农艺性状。本研究以235份经30000个单核苷酸多态性（SNP）标记完成基因分型的温带粳稻种质群体为材料，对其耐盐性进行评价。该群体在幼苗期接受轻度盐胁迫处理（50 mM氯化钠（NaCl），电导率为6 dS·m⁻¹）。分别设置对照组与胁迫处理组，测定了8项根系及地上部生长参数。采用原子吸收光谱法测定了胁迫处理植株的钠离子（Na⁺）与钾离子（K⁺）质量分数。盐胁迫处理显著抑制了植株生长，其中地上部相关参数受影响尤为显著。该群体的Na⁺/K⁺比值分布范围广泛，温带粳稻种质沿耐盐性梯度呈连续分布，覆盖从最耐盐到最敏感的对照材料区间。本研究采用经典混合模型，通过控制群体结构与亲缘关系，对叶片中的胁迫响应指标及离子质量分数开展全基因组关联研究（genome-wide association study）。经子抽样验证，共鉴定出27个数量性状位点（QTL）。针对胁迫响应指标，我们还采用了另一种聚焦于标记×处理互作的分析模型，共检测到50个QTL，其中3个可通过经典方法重复鉴定。我们将显著QTL的位点位置与约300个已知参与水稻耐盐调控的基因位置进行了比对。结果显示，多个QTL的位点与参与钙信号转导及代谢过程的基因位置邻近，另有部分QTL则与激酶编码基因位置相近。本研究结果揭示了温带粳稻背景种质的耐盐性特征。尽管本研究检测到的QTL仍需通过其他实验手段进一步验证，但与钙介导的离子稳态调控相关的候选基因关联位点数量较多，提示我们可优先探索这些通路，以深入解析温带水稻的耐盐调控机制。