Genetic diversity and population structure studies toward an association mapping approach in globe artichoke

Next-generation sequencing (NGS) technologies have enabled the routine application of genome-wide association (GWA) studies to investigate genotype-phenotype relationships in a number of plant species, by determining the genetic diversity present within an entire germplasm panel. The linkage disequilibrium in a GWA study is influenced not only by recombination frequency but also by factors such as genetic drift, mating system and the history of selection. Population structure can potentially lead to erroneous associations between a candidate marker and a phenotype, particularly when trait means or frequencies differ across subpopulations. However, this risk can be mitigated by inferring the population structure of germplasm collections. Here we i) provide an overview of the current understanding of globe artichoke genome structure; ii) review the research progress in deciphering its gene pools population structure; iii) emphasize the value of deep genotyping in a well-characterized core collection for QTLs identification.