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.

Cleistogamous species present strong evidence for the stability of mixed mating, but are generally not considered in this context. Individuals of cleistogamous species produce both obligately selfing cleistogamous flowers (CL) and potentially outcrossed chasmogamous flowers (CH) with distinct morphologies. Greater energetic economy and reliability of CL relative to CH suggest that forces that maintain selection for outcrossing may be stronger in these species than in mixed maters with monomorphic flowers. We reviewed data from 60 studies of cleistogamous species to evaluate proposed explanations for the evolutionary stability of mixed cleistogamous and chasmogamous reproduction and to quantify the magnitude of selection necessary to account for the maintenance of CH. We found circumstantial support for existing hypotheses for the stability of cleistogamy, and that forces that maintain CH must account for a 15-342% advantage of reproduction via CL. We suggest that heterosis and the effects of mass action pollination should be considered.

BackgroundTransgenerational plasticity provides phenotypic variation that contributes to adaptation. For plants, the timing of seed germination is critical for offspring survival in stressful environments, as germination timing can alter the environmental conditions a seedling experiences. Stored seed transcripts are important determinants of seed germination, but have not previously been linked with transgenerational plasticity of germination behavior. In this study we used RNAseq and growth chamber experiments of the model legume M. trucantula to test whether parental exposure to salinity stress influences the expression of stored seed transcripts and early offspring traits and test for genetic variation.ResultsWe detected genotype-dependent parental environmental effects (transgenerational plasticity) on the expression levels of stored seed transcripts, seed size, and germination behavior of four M. truncatula genotypes. More than 50% of the transcripts detected in the mature, ungerminated seed transcriptome were annotated as regulating seed germination, some of which are involved in abiotic stress response and post-embryonic development. Some genotypes showed increased seed size in response to parental exposure to salinity stress, but no parental environmental influence on germination timing. In contrast, other genotypes showed no seed size differences across contrasting parental conditions but displayed transgenerational plasticity for germimation timing, with significantly delayed germination in saline conditions when parental plants were exposed to salinity. In genotypes that show significant transgenerational plastic germination response, we found significant coexpression networks derived from salt responsive transcripts involved in post-transcriptional regulation of the germination pathway. Consistent with the delayed germination response to saline conditions in these genotypes, we found genes associated with dormancy and up-regulation of abscisic acid (ABA).ConclusionsOur results demonstrate genetic variation in transgenerational plasticity within M. truncatula and show that parental exposure to salinity stress influences the expression of stored seed transcripts, seed weight, and germination behavior. Furthermore, we show that the parental environment influences gene expression to modulate biological pathways that are likely responsible for offspring germination responses to salinity stress.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0322-4) contains supplementary material, which is available to authorized users.

Summary• Phenotypic traits differ between plants in different environments and within individuals as they grow and develop. Comparing plants in different environments at a common age can obscure the developmental basis for differences in phenotype means in different environments. Here, we compared trait means and patterns of trait ontogeny for perennial ( Viola septemloba ) plants growing in environments that differed in quality either naturally or due to experimental manipulation.• Consistent with predictions for adaptive stress resistance, plants grown in lowerquality environments allocated proportionately more biomass to roots and rhizomes, and produced smaller, thicker and longer-lived leaves. The developmental trajectory of almost all traits differed between environments, and these differences contributed to observed differences in trait means.• Plants were able to alter their initial developmental trajectory in response to an increase in resources after 8 wk of growth. This result contrasts with previous findings, and may reflect a difference in the way that annual and perennial species respond to stress.• Our results demonstrate the complexity of interactions between the environment and the development of the phenotype that underlie putatively adaptive plastic responses to environment quality.

Previous studies have quantified variation in environmental maternal effects (EME) within populations, but these effects could differ among populations as well. In this study we grew clonal replicates of individuals from three populations of the annual plant Diodia teres in their native and non‐native environments. Our goal was to estimate the effects of maternal environment and maternal population on seed and seedling traits. Seeds that were produced in this field study were then planted in two soil types to quantify effects of the offspring environment on seedling traits. There was substantial variation among populations for seed weight. We found population variation for EME, and maternal environment by offspring environment interactions. We conclude that variation among populations in EME may be an unrecognized component of local adaptation, and that attempts to control maternal effects by statistically accounting for variation in seed weight may be ineffective.