OsMOCSalt as a candidate salt tolerance gene in rice (Oryza sativa) identified through meta-analysis, overview analysis and collinearity analysis.

Salinization poses a critical threat to global crop production, affecting approximately 15% of irrigated land and substantially reducing yields. Therefore, enhancing crop salt tolerance has become extremely urgent. Notably, identifying and utilizing salt-related genes is fundamental to salt tolerance breeding. Rice (Oryza sativa) is an important crop and a staple food worldwide, especially in Asia. However, most cultivated varieties are sensitive to salt stress. Therefore, identifying and applying salt-related genes could facilitate breeding of salt-tolerant varieties. In this study, 265 salt-related QTLs were obtained from the Gramene database and subjected to overview and collinearity analyses. Notably, the QTLs were concentrated on chromosome (Chr) 9, within 12.79-15.29 Mb in the overview analysis and 14.80-18.68 Mb in the collinearity analysis. Additionally, 65 meta-QTLs (MQTLs) were identified through meta-analysis. The candidate interval for MQTL9.4 was 5.2 Mb. Integrating the three analyses, a candidate region associated with salt tolerance was defined on Chr 9, at 14.85-15.21 Mb. A total of 36 genes were identified within this region. Screening based on predicted molecular function, expression profiles across different tissues, and responses to salt stress revealed the candidate gene Os09g0416200, designated OsMOCSalt. This gene had two haplotypes, and OsMOCSaltHap1 was confirmed to positively regulate salt tolerance in transgenic yeast. Additionally, molecular markers associated with the polymorphic sites were developed, and a specific single nucleotide polymorphism was found to be significantly correlated with salt tolerance (P < 0.05). This study identified and validated a salt tolerance-related gene, providing an empirical basis for the molecular breeding of salt-tolerant rice.