Identifying QTL Associated with Waterlogging Tolerance in Dry Bean (Phaseolus vulgaris L.), Set the Stage for Marker-Assisted Selection

Climate change adversely affects crop production, mostly by altering temperature and rainfall patterns.  Several studies have addressed the devastating effects of heat and drought, however few efforts have been devoted to understand the mechanism by which crops cope with excess precipitation and waterlogging. Legumes, particularly dry bean, are classified as very sensitive crops to excess water, especially during early stages. To identify the loci associated with waterlogging tolerance in dry bean, a Genome-Wide Association Study (GWAS) was conducted using ~600 genotypes belonging to Middle-American and Andean gene pools in the greenhouse. Nine traits were measured from both stress and non-stress conditions including total weight, shoot weight, root weight, chlorophyll content, and adventitious root rate. Genotyping was performed by using a combination of two 6K Illumina iSelect gene chips and Genotyping-by-sequencing (GBS) platforms. Using these two platforms we could cover the dry bean genome with more than 150K SNPs. The results indicate that root is the primary tissue which is affected by waterlogged condition. In the Middle-American gene pool, a signal was detected on Pv08 associated with root weight. This peak is ~53 Kbp far away from Rap2.6L gene, which was shown to be involved in waterlogging tolerance in Arabidopsis. Furthermore, within the Andean gene pool, a peak on Pv09 was detected for adventitious root production. Besides these, at least ten other QTL were detected which contribute to waterlogging tolerance of dry bean. Using the markers linked to these QTL would help breeders for marker-assisted selection and variety improvement.