Chickpea is the world’s second most important pulse legume, with particular importance in the semi-arid tropics of sub-Saharan Africa and South Asia. Like the majority of cultivated legumes, chickpea has exceedingly narrow genetic and phenotypic diversity. This has consequences for breeding of climate-resilient crop varieties, because much of the historical phenotypic plasticity necessary to tolerate environmental extremes may have been lost through domestication. Thus breeding only within cultivated material will have steeply diminishing returns, and there is an urgent need for new sources of diversity.
Breeding for climate resilience as well as other high value traits will be greatly accelerated if we can expand the range of adaptations accessible to breeders. Towards this end, we are characterizing wild Cicer species from a representative range of environments; introducing wild diversity into phenology-normalized backgrounds so that it is amenable for trait assessment and breeding; characterizing the material by systematic phenotyping; developing a digital information network that explicitly identifies and quantifies the contributions of agronomically useful alleles; and developing improved chickpea varieties using an international consortium of chickpea breeders.
Chickpea is also of great scientific importance because of its natural capacity for nitrogen fixation, reducing dependence on exogenous nitrogen. Nevertheless domesticated legumes, including chickpea, often suffer from low and/or variable rates of nitrogen fixation. Multiple factors underlie this situation, including host genetics, the quality of applied and endemic rhizobia, as well as local edaphic and environmental influences. Initial data from our team suggests that shifts in the genetics of domesticated chickpea may have created legume crops that are more reliant on soil nitrogen and likely less able to harness symbiotic nitrogen fixation. Developing a detailed understanding of the genes that underlie these genetic shifts and deducing their evolutionary history and functional consequences are the primary focuses of this project. In the course of this research we expect to reveal novel aspects of the symbiosis. Doing so requires characterizing evolutionary outcomes in both natural and human-built environments, which we achieve by combining the traditionally separate domains of ecology and molecular biology, with genomics and quantitative biology serving as the bridge.
We hypothesize that a range of distinct genetic processes during domestication and recent breeding underlie altered nitrogen responses in chickpea. Among factors that might reduce function are selection trade-offs, selection relaxation, and random demographic processes (e.g., drift). A corollary to this logic is that natural populations of chickpea’s progenitor species, Cicer reticulatum, possess nitrogen fixation traits that are maintained by positive selection. These statements frame the major challenges and opportunities of this project, namely the need to deduce diverse selection histories in the context of natural and human-built environments, and to translate this information into candidate gene identification and stringent tests of gene function.
As important as single genotypes of model systems and forward genetics have been (and continue to be) for gene discovery, they are typically insufficient to inform us about the nature of standing genetic variation from which natural and human selection reshape organismal function. Bridging ecology and molecular biology by means of genomics and quantitative biology will permit identification and subsequent analysis of these evolutionarily active genes. We anticipate that the outcomes will include genes whose functions have not been identified in forward genetic screens. We anticipate describing the molecular genetic basis of long-standing, but poorly understood observations and questions. Is there a genetic basis for the often low and variable rates of nitrogen fixation in legume crops? If so, has domestication contributed to this situation? To what extent does coevolution of plant and microbial populations contribute to efficient symbiosis across environments? What are the underlying genes, and are the “solutions” idiosyncratic or common to different populations? Do such solutions include novel alleles of well-described signaling proteins? Have such interactions been altered during domestication, and are the alterations adaptive or mal-adaptive?
This project incorporates the following objectives:
1. Characterize existing cultivated chickpea across worldwide seed collection.
2. Characterize a comprehensive collection of wild species focused on C. reticulatum and C. echinospermum, the wild progenitors of cultivated chickpea.
3. Create reverse-introgression and advanced backcross introgression lines to (a) remove phenological barriers that otherwise impede the use of wild germplasm in breeding, (b) establish a resource for association mapping of climate-resilience traits, and (c) initiate breeding with superior wild alleles.
4. Phenotype reverse-introgressed and advanced backcross introgression lines for a range of high-priority traits related to developing high-yielding, climate-resilient chickpea.
5. Develop a predictive network of genotype-phenotype associations that identifies genes and genome regions from wild species that improve chickpea’s yield resilience to climatic extremes.
6. Characterize the functional significance of standing variation in wild populations of Cicer reticulatum and its co-occurring bacterial symbionts, using ecology, genomics, and phenotyping.
7. To identify genomic footprints of domestication-associated shifts in genetic/genomic variation.
8. Development of reference genomes for the wild species, Cicer reticulatum and Cicer echinospermum. Developing reference genomes of these two wild species will be important to our activities of association mapping and introgression breeding. Less...