Novel QTLs for salinity tolerance revealed by genome-wide association studies of biomass, chlorophyll and tissue ion content in 176 rice landraces from Bangladesh

Farmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earth’s people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 11 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Our explorations yielded 13 QTLs related to various traits in multiple trait classes. 10 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes potential novel functionality for a number of candidate genes. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.