Genome‐wide association analysis of salinity responsive traits in Medicago truncatula

Salinity stress is an important cause of crop yield loss in many parts of the world. Here, we performed genome‐wide association studies of salinity‐stress responsive traits in 132 HapMap genotypes of the model legume Medicago truncatula. Plants grown in soil were subjected to a step‐wise increase in NaCl concentration, from 0 through 0.5% and 1.0% to 1.5%, and the following traits were measured: vigor, shoot biomass, shoot water content, leaf chlorophyll content, leaf size, and leaf and root concentrations of proline and major ions (Na(+), Cl(−), K(+), Ca(2+), etc.). Genome‐wide association studies were carried out using 2.5 million single nucleotide polymorphisms, and 12 genomic regions associated with at least four traits each were identified. Transcript‐level analysis of the top eight candidate genes in five extreme genotypes revealed association between salinity tolerance and transcript‐level changes for seven of the genes, encoding a vacuolar H(+)‐ATPase, two transcription factors, two proteins involved in vesicle trafficking, one peroxidase, and a protein of unknown function. Earlier functional studies on putative orthologues of two of the top eight genes (a vacuolar H(+)‐ATPase and a peroxidase) demonstrated their involvement in plant salinity tolerance.