Less than 5 years ago collection of genotype data was the primary bottleneck in assessing phenotype-genotype associations, whether for applied studies of agronomic traits or for population-level analyses in wild species. Today it is feasible to collect genotype data for gigabase-sized genomes involving thousands of individuals, and, despite challenges of scale and resources, the bottleneck has shifted to different arenas. Of particular importance is whether other aspects of the study system, such as phenotyping, can be of sufficient scale and precision to match the power of the genomic analyses. Equally important are the power of the experimental design and the appropriateness of the question under study. In our case, we combine whole genome genotyping, ecology, population genetics and phenotyping to deduce the history of chickpea and its wild progenitor Cicer reticulatum. We focus in two areas: (1) basic questions regarding symbiotic nitrogen fixation, and (2) the applied goal of re-domesticating wild chickpea for climate resilience. Chickpea and its wild relatives have a natural capacity for nitrogen fixation, reducing their dependence on exogenous nitrogen. Nevertheless domesticated legumes, including chickpea, often suffer from low and/or variable rates of nitrogen fixation. Recent results from our laboratories identify phenotypic and genomic shifts in domesticated chickpea. In particular, we observed that wild and domesticated species differ in their responses to Mesorhizobium (the chickpea symbiont) and to soil nitrogen, and efforts are underway to identify the responsible genes. In parallel, we combined phenotyping and genotyping-by-sequencing to identify candidate genes for domestication-related traits, including nodule number, and also flower color, seed coat tannins, flowering time and plant architecture. More recently we are using ecology, population genetics and whole genome genotyping to characterize evolutionary events in wild Cicer species. Twenty-three populations, surveyed by population biological criteria from throughout south-eastern Turkey, provide the basis for an evolutionary genomics approach to understand the evolution of symbiotic performance and environmental adaptations in the wild progenitors and the ways in which human selection has reshaped this potential during domestication. Results from this ongoing project, as well as a related project to re-domesticate wild chickpea for climate resilience, will be presented.