Prospecting for Gene Function in Complex Natural Environments and Their Derived Agricultural Systems.

We are characterizing the potential of chickpea’s wild relatives for crop improvement. We focus on climate resilience, nitrogen fixation and seed nutrient density, with the goal of more sustainable and stable production systems. We combine upstream ecology and genomics to assemble and characterize wild germplasm; population development to remove barriers to use of wild alleles; phenotyping and modeling of trait-gene associations to enhance the precision and rate with which wild alleles are applied. We have completed ecological characterization and genetic resource collection for ~2,000 wild accessions, used genotyping by sequencing to deduce population genetic parameters, initiated whole genome re-sequencing of 1,100 accessions, collected co-occurring bacterial symbionts, surveyed seed and flowering phenotypes, and initiated development of nested association mapping and backcross introgression panels for trait dissection and breeding. In parallel to the analysis of plant populations we have initiated genomics and community ecology of legume-associate microbes from both wild species at their center of origin and their domesticated counterparts globally. We are particularly interested in understanding both positive and negative consequences of domestication on the function of these complex, multi-species systems. For example, sequencing the genome of ~800 Mesorhizobium individuals reveals a history of horizontal gene transfer of symbiotic genes from the natural symbiont of Cicer spp to atypical genomic backgrounds outside the center of origin, presumably to balance adaptation to agricultural situations (e.g., soil, competing microbes) with the need for symbiotic competency. We have also initiated culture-independent metagenomic studies of rhizosphere and phylosphere microbial communities throughout the plant species’ center of origin, to investigate the biogeography of plant-associate microbes. We are testing the hypothesis of plant-microbiome coevolution in a range-wide study system, as well as characterizing the population genetics of key crop pathogens in wild systems.