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 Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR’s 147 chickpea accessions from Turkey and Ethiopia, representing chickpea’s center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic ‘agro islands’, and in genotype-to-phenotype relationships resembling widespread pleiotropy.

Invasive plants impose threats to both natural and managed ecosystems. Downy brome is among the most aggressive invasive weeds that has infested the shrub-steppe ecoregion of eastern Washington. Hyperspectral remote sensing has potential for early detection and for monitoring the spread of downy brome—information that is essential for developing effective management strategies. Two airborne hyperspectral Advanced Visible Infrared Imaging Spectrometer (AVIRIS) images (electromagnetic spectrum ranging from 400 to 2,500 nm) were acquired at a nominal 4-m ground resolution over a study area in south-central Washington on July 27, 2000 and May 5, 2003. We used a mixture-tuned matched filtering (MTMF) algorithm to classify downy brome and predict its percent cover in each dataset plus a merged multiseasonal dataset using the transformed bands from a minimum noise fraction (MNF) output. The correlation coefficient was 0.79, calculated for the multidate MTMF predicted downy brome abundance, compared to 0.41 and 0.51 derived from the July 2000 and May 2003 data, respectively. Although this study used high spatial resolution (∼3 to 4 m) hyperspectral imagery, this result shows that data acquired in different seasons is more effective for detection of downy brome invasion, compared to single-date datasets. These results support expanded use of multitemporal data for weed mapping to capitalize on spectral differences between seasons for weeds, in this case downy brome, and the surrounding environment.