Identification of Candidate Genes for Salinity Tolerance and Their Application in Alfalfa Breeding

Salt tolerance in alfalfa (Medicago sativa L.) is a complex trait controlled by multiple genes, involving different signaling pathways. Although recurrent selection under salt stress is an effective method for improving salt tolerance, molecular markers may be critical for detecting major genes involved in salt tolerance in alfalfa. We identified a total of 237 differentially expressed genes (DEGs) in leaves of the salt tolerant ‘Halo’ alfalfa and salt sensitive ‘ Vernal’ using an RNA-Seq analysis. Of these, 28 salt responsive candidate genes were highly expressed in ‘Halo’ under salt stress. We developed Kompetitive allele-specific Polymerase Chain Reaction (KASP) assay for the SNPs linked to the highly expressed genes. Then we genotyped four salt tolerant alfalfa breeding lines, in addition to ‘Halo’ and salt susceptible cultivar ‘Rangelander’. Our results showed that four cycles of recurrent selection have accumulated certain salt resistant related favorable alleles in the alfalfa breeding lines. Certain KASP markers were able to differentiate the six alfalfa populations used in the study. This indicates that these KASP markers can be used for detecting important alleles frequency associated with alfalfa salt tolerance.