A Whole Genome Association Study on Verticillium Wilt Resistance in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.)

Verticillium wilt (VW) of alfalfa is a soilborne disease causes severe yield loss in alfalfa production.  Identification of genes involved in VW resistance will facilitate breeding for improving resistance to the disease in alfalfa. In the present investigation, we applied an integrated framework of genome-wide association with high-throughput genotyping by sequencing for identifying VW resistance loci in two alfalfa populations selected for the disease resistance.  Phenotyping was done by inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association by linkage disequilibrium identified a group of SNP markers significantly associated with VW resistance.  Alignment of their sequence tags to the M. truncatula genome revealed multiple chromosomal locations, including chromosomes 5, 6, 7 and 8 in the Forage Genetics population and 1, 6 and 7 in the S&W population.  Overlaps of the resistance loci were found on chromosomes 6 and 7 between the two populations, and between our prevoius report and the present study. Additional markers were aligned to different contigs whose chromosomal locations are unknown. BLAST search using the flanking sequences of the resistance loci against M. truncatula genome identified candidate genes associated with disease resistance, including TIR-NBS-LRR protein and MDR-ABC transporter.  With further investigation, these markers may be used for marker-assisted selection for breeding VW resistant alfalfa.