Genome-Wide Association of Drought Stress and Biomass Traits with HapMap SNPs in Medicago truncatula

With the advancement of modern genetic and molecular tools, marker-assisted selection has played an increasingly important role in crop breeding.  In the Medicago truncatula HapMap project, ~300 Medicago inbred lines have been sequenced and a high density haplotype map of SNPs was built.  Here we characterized drought stress and biomass-related traits of 220 Medicagoinbreds, including 30 deeply-sequenced lines (minimum 20X sequence coverage).  Plants were grown in a controlled-environment walk-in growth chamber.  Characterized traits included shoot dry weight, maximum leaf size, specific leaf weight, stomatal density, tricome density, shoot carbon 13 isotope discrimination (water use efficiency), and leaf performance in dehydration stress specified by chlorophyll content and dry weight changes after floating on 25% PEG8000.  Pearson correlation analysis showed that under well-watered conditions plant water use efficiency was negatively correlated with plant shoot size, leaf size, and stomata density.  Genome-wide association analyses of the phenotyping results and HapMap SNPs were carried out using the Multi Linear Model in TASSEL.  For each trait, multiple chromosome regions showing significant marker-trait association and were in high linkage disequilibrium were identified. Top candidate genes were selected and are under further investigation.