Integrating IRRI standardized phenotyping and genome-wide association analysis to decipher salinity tolerance and yield responses in rice

Soil salinization poses a severe threat to rice production, and the reproductive growth is particularly sensitive to salt stress. Although the Standard Evaluation System (SES) developed by the International Rice Research Institute (IRRI) provides a rapid visual scoring system for salinity tolerance screening, the relationship between SES scores, final yield components, and their underlying genetic basis remains insufficiently unserstood. In this study, a population of 118 lines from diverse origins was employed for field experiments under salt stress. Salinity tolerance of the materials was classified according to the IRRI-SES standard, key agronomic traits were measured at maturity and quantitative trait loci (QTL) associated with salt tolerance were identified via genome-wide association analysis (GWAS). The 118 lines were categorized into five SES classes, and their agronomic traits were closely correlated with SES scores. Highly significant differences (p < 0.01) were observed between SES 3 (tolerant) and SES 5 (moderately tolerant) groups for plant height and panicle length. while significant differences (p < 0.01) were detected between SES 5 and SES 7 (sensitive) groups for thousand-grain weight. Correlation analysis further indicated that plant height, panicle length, and thousand-grain weight were highly sensitive to salt stress, and subsequent genetic analysis revealed the loci governing these traits. Collectively, our findings demonstrate that SES scoring provides a useful framework for evaluating salt stress responses and predicting variation in agronomic performance among rice genotypes. By integrating standardized phenotypic evaluation with genetic analysis, this approach facilitates the identification of candidate genomic regions associated with salt tolerance, thereby providing valuable molecular markers and genetic resources for breeding salt-tolerant and high-yielding rice varieties.