Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Abstract

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.

The Impact of Genetic Changes during Crop Domestication

“…There appears to be evidence for all these possibilities among our domesticated crops. Chickpea is thought to have a monophyletic origin, given the narrow distribution of its wild progenitor [26] and the limited genetic diversity of the cultigen [7,27]. Domesticated barley (Hordeum vulgare) [28,29] and emmer wheat (Triticum turgidum L.) [23] have more polyphyletic tendencies.…”

“…This human-associated cultivation reshaped the evolutionary trajectories of these species to become transformed into domesticated crops. These crops evolved over time and space as they spread to new areas (e.g., chickpea [41]), sometimes beyond the climatic niche of their wild relatives [7,42]. However, the speed and level of human intentionality during domestication remain topics of discussion [42,43].…”

“…Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication [6]. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops [7].…”

Healthy and sustainable diets for future generations

“…Classically, crop relatives were the source of individual traits, most commonly disease resistance,20 but with recent advances in genome‐scale approaches the stage is set for a more systematic characterization and use of crop wild relatives. Such an approach is being undertaken for chickpea to improve a range of agronomic traits, including tolerance to climatic extremes 21, 22, 23. Similar approaches are feasible to improve the nutritional content of crops, as has been done, for example, in corn for provitamin A.…”

Pod Shattering: A Homologous Series of Variation Underlying Domestication and an Avenue for Crop Improvement

“…In chickpea, although Ladizinsky [111] described several loci putatively controlling shattering, Kazan and colleagues described a single recessive gene [112]. This discrepancy could result from different parents being used in different crosses [e.g., the widely used CRIL2 recombinant inbred population has been created a few times independently [112,113] and other wild-cultivated crosses have been developed with different parents [114]], with post-domestication diversification shifts in modulators of shattering, or differences in dispersal ability among populations of wild Cicer reticulatum. Work utilizing larger numbers of crosses, with distinct wild and cultivated parents and genome-scale genetic maps will be able to clarify the nature of loci involved in shatter in chickpea.…”