Association Genetics in Plant Pathogens: Minding the Gap between the Natural Variation and the Molecular Function

One of the main goal in phytopathology is to better understand the molecular basis of plant–pathogen co-evolution through the identification of effectors and effector targets that play a role in natural phenotypic variation. Fortunately, next generation sequencing (NGS)—which can measure genetic variation at hundreds of thousands of markers across a genome, including for non-model organisms—is now helping to reach this goal. Among all possible strategies using NGS data, we expect that genome-wide association studies (GWAS) have the most potential to revolutionize the field of phytopathology. In contrast to QTL mapping, GWAS use outbred populations to capture the standing genetic variation, thus characterizing the raw material for evolution. By examining the natural phenotypic and genetic variation, association mapping can elucidate the genetic basis underlying complex traits. In the two decades since association mapping successfully detected common variants for human complex diseases (Risch and Merikangas, 1996) and with the publication of the first successful GWAS in humans in 2005 (Klein et al., 2005), the number of published GWAS keeps increasing. Researchers in the field of plant pathogens are now embarking on GWAS, with the promise to open new frontiers of research