Molecular Markers Associated with Resistance to Drought and High Salinity in Alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is the most important worldwide grown forage crop. Changing trends to multipurpose uses increases demand for alfalfa. However, the production of alfalfa is challenged by adverse environmental factors. Identification of molecular markers linked to stress resistance will facilitate breeding for improving alfalfa production. In the present investigation, we applied an integrated framework of genome-wide association with high-throughput genotyping by sequencing for identifying resistance loci associated with abiotic stress in alfalfa populations. Different bioinformatics pipelines were used for SNP discovery. Agronomic and physiological traits including biomass yield, drought/salt resistance index, relative water content and leaf senescence were evaluated in the field and greenhouse. Marker-trait association by linkage disequilibrium identified a group of SNP markers significantly associated with drought and salt tolerance. Alignment of their sequence tags to the reference genome revealed multiple chromosomal locations. Markers associated with drought tolerance were located on all chromosomes. Most loci identified in this work overlap with the reported QTLs associated with biomass under drought in alfalfa. Marker associated with salt tolerance shared few resistance loci with drought but most of them are independent. With further investigation, these markers may be used for marker-assisted selection for breeding alfalfa with resistance to abiotic stress.