Leaf Na+ effects and multi-trait GWAS point to salt exclusion as the key mechanism for reproductive stage salinity tolerance in rice

Since salinity stress may occur across stages of rice (Oryza sativa L.) crop growth, understanding the effects of salinity at reproductive stage is important although it has been much less studied than at seedling stage. In this study, lines from the Rice Diversity Panel 1 (RDP1) and the 3000 Rice Genomes (3KRG) were used to screen morphological and physiological traits, map loci controlling salinity tolerance through genome-wide association studies (GWAS), and identify favorable haplotypes associated with reproductive stage salinity tolerance. Salt exclusion was identified as the key tolerance mechanism in this study based on reduced panicle length as flag leaf Na+ increased, and a lack of effect of trimming the leaves in the salinity treatment on genotypic rankings. Since larger biomass showed a negative effect on the number of filled grains in multiple experiments, future studies should investigate the effect of whole-plant transpiration levels on salt uptake. In addition to genome-wide significant peaks identified in the single trait GWAS analyses, six loci showed colocations for multiple traits across experiments. Among these co-locating loci, three candidate loci that exhibited favorable haplotypes were also characterized to be involved in co-expression networks among which apoplast and cell wall functions had been annotated – further highlighting the role of salt exclusion. The loci identified here could be considered as potential sources for improving reproductive stage salinity tolerance in rice.由于盐胁迫可能在水稻（Oryza sativa L.）生长的各个阶段发生，尽管相较于苗期，人们对生殖阶段盐胁迫效应的研究相对较少，但解析该阶段的盐胁迫效应仍具有重要意义。本研究以水稻多样性面板1（Rice Diversity Panel 1, RDP1）和3000份水稻基因组（3000 Rice Genomes, 3KRG）的材料为研究对象，对形态及生理性状进行筛选，通过全基因组关联分析（Genome-Wide Association Studies, GWAS）定位耐盐相关位点，并鉴定与生殖阶段耐盐性相关的优良单倍型。本研究基于剑叶钠离子浓度升高导致穗长缩短，且盐处理下剪叶对基因型排名无影响的结果，将排盐作用确定为该研究中的关键耐盐机制。鉴于在多个试验中，更大的生物量会对饱粒数产生负面影响，未来研究应探究整株蒸腾水平对盐分吸收的影响。除单性状全基因组关联分析中鉴定到的全基因组显著峰值外，另有6个位点在不同试验中表现出多性状共定位现象。在这些共定位位点中，3个携带优良单倍型的候选位点还被证实参与共表达网络，其中已注释到质外体和细胞壁相关功能——这进一步凸显了排盐机制的作用。本研究鉴定的位点可作为提升水稻生殖阶段耐盐性的潜在遗传资源。