Comprehensive analysis and genome-wide association studies of biomass, chlorophyll, seed and salinity tolerance related traits in rice highlight genetic hotspots for crop improvement

Farmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earths 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 15 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 sophisticated fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Candidate genes were sorted by tissue specific gene expression profiles and protein level consequence of existing polymorphisms. Our explorations yielded 17 QTLs related to various traits in multiple trait classes. 12 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes novel functionality for 21 candidate genes on multiple evidence levels. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.