Mapping early responses to salt stress in Arabidopsis thaliana

Abstract

Salt stress is a global problem that limits agricultural production. The early responses to salinity, independent of toxic shoot-ion accumulation, are still largely unknown. Here, optimised salt treatment and high-throughput phenotyping protocols were developed and used to examine the natural variation in the early responses to salt stress of 191 Arabidopsis thaliana accessions. Common and novel traits of plants grown under salt treatment were captured through time using RGB and chlorophyll fluorescence imaging. Phenotypic data was combined with the Arabidopsis 10M SNP markers for genome-wide association studies to identify genetic components underlying the early responses to salt stress. The most promising candidate loci were selected based on association strength, allele frequency and number of traits associating to the same locus. In silico analysis highlighted interesting allelic variations across the identified loci, and by phenotypically characterising the candidate gene mutants under salt stress, the associations were experimentally validated. This work comprises a detailed study of the natural variation in the early responses to salt stress, which can give insights into the mechanisms contributing to salinity tolerance and provide the fundaments for crop improvements under saline conditions across the globe.