Apply Untapped Genetic Diversity of Crop Wild Relatives to Meet Global Challenges

Climate change has generated various critical challenges to agriculture susceptibility and food security. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enable them to thrive in changing environments. Crop wild relatives (CWRs) harbor a much higher level of genetic diversity than cultivated crops and have the potential to meet these challenges. The wild soybean (Glycine soja), from which domesticated soybeans (Glycine max) were derived, is widely distributed throughout diverse habitats in East Asia. We use G. soja as our study system to investigate its genomic diversity, population structure, climate adaptation, and biotic stress resistance, integrating genomic, transcriptomic, and metabolomic approaches. Using ~42,000 genome-wide single nucleotide polymorphism (SNP) data, we estimated that environmental factors contributed 23.6% to population differentiation, much more than that for geographic factors (6.6%). Precipitation variables largely explained the divergence of the groups along longitudinal axes whereas temperature variables contributed more to latitudinal divergence. We also used a genome scan of outlier loci to identify candidate loci involved in climate adaptation. This scan uncovered a total of 32 known genes with diverse functions, seven of which are involved in abiotic stress responses. We also integrated genome-wide association studies, RNA-seq comparisons, and metabolomic comparisons to dissect the genetic basis of wild soybean resistance to soybean cyst nematode (SCN), the most devastating pest of soybean. We identified some candidate genes involved in SCN type-specific resistance, as well as others exhibiting broad-spectrum resistance to multiple types of SCN. These candidate genes will not only shed light on the molecular mechanisms of plant and SCN interactions, but also will facilitate the molecular breeding and development of soybean varieties with improved SCN resistance.