SNP-based markers have been widely used to identify tolerant varieties harboring major genes related to abiotic stress tolerance. Here, we developed Fluidigm markers for the core set of SNPs underlying tolerance to abiotic stresses such as salinity, drought, anaerobic germination and submergence. The core set of SNPs was selected from the major genes and/or QTLs for the abiotic stresses previously reported in rice; Saltol for salinity, qDTY2.2 and qDTY4.1 for drought, OsTPP7 for anaerobic germination, and Sub1A for submergence tolerance. First, a total of 17 KASP markers were developed and converted to Fluidigm markers. The developed Fluidigm markers were applied to genotypic screening of 172 domestic and abroad varieties. The phylogenetic analysis has revealed that the majority of varieties can be largely grouped into two clusters, which correspond to domestic and foreign categories. This observation could be attributed to the fact that most tolerance genes for abiotic stresses have been inherited from indica varieties. The developed Fluidigm marker set would be used for screening genotypes tolerant to major abiotic stresses in the rice plant breeding process.

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