Domestication has resulted in reduced salt tolerance in tomato. To identify the genetic components causing this deficiency, we performed a genome-wide association study (GWAS) for root Na + /K + ratio in a population consisting of 369 tomato accessions with large natural variations. The most significant variations associated with root Na + /K + ratio were identified within the gene SlHAK20 encoding a member of the clade IV HAK/KUP/KT transporters. We further found that SlHAK20 transports Na + and K + and regulates Na + and K + homeostasis under salt stress conditions. A variation in the coding sequence of SlHAK20 was found to be the causative variant associated with Na + /K + ratio and confer salt tolerance in tomato. Knockout mutations in tomato SlHAK20 and the rice homologous genes resulted in hypersensitivity to salt stress. Together, our study uncovered a previously unknown molecular mechanism of salt tolerance responsible for the deficiency in salt tolerance in cultivated tomato varieties. Our findings provide critical information for molecular breeding to improve salt tolerance in tomato and other crops.

Terrestrial plants must cope with drought stress to survive. Under drought stress, plants accumulate the phytohormone abscisic acid (ABA) by increasing its biosynthesis and decreasing its catabolism. However, the regulatory pathways controlling ABA catabolism in response to drought remain largely unclear. Here, we report that the flowering repressor SHORT VEGETATIVE PHASE (SVP) is induced by drought stress and associates with the promoter regions of the ABA catabolism pathway genes CYP707A1, CYP707A3 and AtBG1, causing decreased expression of CYP707A1 and CYP707A3 but enhanced expression of AtBG1 in Arabidopsis leaves. Loss-of-function mutations in CYP707A1 and CYP707A3 or overexpression of AtBG1 could rescue the drought-hypersensitive phenotype of svp mutant plants by increasing cellular ABA levels. Collectively, our results suggest that SVP is a central regulator of ABA catabolism and that a regulatory pathway involving SVP, CYP707A1/3, and AtBG1 plays a critical role in plant response to water deficit and plant drought resistance.

Arabidopsis PICKLE (PKL) is a putative CHD3-type chromatin remodeling factor with important roles in regulating plant growth and development as well as RNA-directed DNA methylation (RdDM). The role of PKL protein in plant abiotic stress response is still poorly understood. Here, we report that PKL is important for cold stress response in Arabidopsis. Loss-of-function mutations in the PKL gene lead to a chlorotic phenotype in seedlings under cold stress, which is caused by the alterations in the transcript levels of some chlorophyll metabolism-related genes. The pkl mutant also exhibits increased electrolyte leakage after freezing treatment. These results suggest that PKL is required for proper chilling and freezing tolerance in plants. Gene expression analysis shows that CBF3 , encoding a key transcription factor involved in the regulation of cold-responsive genes, exhibits an altered transcript level in the pkl mutant under cold stress. Transcriptome data also show that PKL regulates the expression of a number of cold-responsive genes, including RD29A, COR15A , and COR15B , possibly through its effect on the expression of CBF3 gene. Mutation in PKL gene also results in decreased cotyledon greening rate and reduced primary root elongation under high salinity. Together, our results suggest that PKL regulates plant responses to cold and salt stress.