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+, Ca2+, 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.