QTL detection and genomic prediction for resistance to anthracnose in alfalfa (Medicago sativa)

Forage production, persistence, and associated ecosystem services provided by the major forage legume, alfalfa (Medicago sativa), may be affected by disease susceptibility. Resistance to anthracnose, caused by Colletotrichum trifolii, has been described as an oligogenic trait, but the precise location of resistance genes on the alfalfa genome is not known. Therefore, we phenotyped a set of 417 alfalfa accessions for anthracnose resistance as the frequency of resistant plants. With available genotyping by sequencing data for 380 accessions from this collection, we performed quantitative trait locus (QTL) detection by genome-wide association study (GWAS) and genomic prediction using a validation set of 97 accessions randomly selected. A wide range of variation for anthracnose resistance was observed, with newer varieties and breeding materials exhibiting greater resistance than old varieties and landraces. Accessions from America showed the highest resistance, although some European accessions also displayed notable resistance. Six QTLs, controlling 58% of the variation, were identified by GWAS. Two major QTLs were found on chromosome 8, within a region already identified in an alfalfa mapping population. Four other QTLs, each controlling less than 5% of the variation, were also found, including one near a major QTL on chromosome 4 in the model species M. truncatula. The predictive ability of our set of accessions was surprisingly high: 85%. These results are promising and highlight the potential of molecular markers and genomic prediction to improve anthracnose resistance in alfalfa breeding programs.