Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.

No abstract

Summary Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought‐responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.

Crop wild relatives are a reservoir of phenotypic variation not present in the germplasm of cultivated species and thus have great potential for crop improvement. However, issues of genetic compatibility often interfere with effective utilization of crop wild relative taxa. Among chickpea (Cicer arietinum L.) crop wild relatives, Cicer echinospermum P.H. Davis is the sole species in the secondary genepool, being partially compatible with the primary genepool that is composed of the cultigen and its progenitor wild species Cicer reticulatum Ladizinksy. We report results from genetic studies among interspecific hybrids between cultivated chickpea and accessions from six recently identified wild C. echinospermum sites in southeastern Turkey, encompassing the known genetic diversity of the secondary genepool. Our studies indicate that both hybrid sterility and hybrid breakdown occur and are associated with distinct subgroups of C. echinospermum. Analysis of early‐generation progenies suggests that both hybrid sterility and hybrid breakdown are conditioned by one to few genetic loci. These results clarify ambiguity in the nature of the hybridization barriers of reduced fertility in interspecific crossing of cultivated chickpea with C. echinospermum and should foster a more systematic and wider use of C. echinospermum for base broadening of cultivated chickpea.

No abstract