Identifying candidate genes related to rice ML under salt-alkali tolerance

Rice stands as one of the world’s most essential cereal crops, underpinning global food security and economic stability. Salinity-alkalinity stress represents a major environmental constraint that severely impairs rice growth, with mesocotyl elongation being particularly vulnerable. Despite its agronomic importance, the genetic basis of mesocotyl tolerance to combined saline-alkaline stress remains largely unexplored. In this study, we measured mesocotyl length (ML) and relative ML traits under salt-alkali stress and control conditions in a 148-line doubled haploid (DH) population constructed from Sea Rice 86 and Nipponbare (Nip) plants. By constructing a high-density genetic map, we identified two loci significantly associated with mesocotyl elongation under stress, one governing salt tolerance and the other conferring alkali tolerance. Through integrative gene functional annotation and haplotype analysis, we identified two key candidate genes (LOC_Os03g49260 and LOC_Os03g49500) regulating ML, three genes (LOC_Os04g52479, LOC_Os04g52510, and LOC_Os04g52725) linked to salt tolerance, and one pivotal gene (LOC_Os03g01410) associated with alkali tolerance. An effective strategy for enhancing rice ML under salt-alkali stress could be the pyramiding of favorable haplotypes from multiple candidate genes to achieve an optimal haplotype combination. These findings not only provide critical insights into the genetic mechanisms of salinity‒alkalinity tolerance in rice but also provides a functional roadmap for developing resilient rice varieties equipped with superior mesocotyl traits and improved stress adaptability.