Project: Deducing the genomic footprint and functional impact of chickpea domestication on nitrogen fixation

, ,

, , , ,

Principal investigators: Douglas Cook, University of California – Davis; Varma Penmetsa, University of California – Davis; Eric von Wettberg, Florida International University

Associated with: National Science Foundation Plant Genome Research Program

Project Summary:

Legume species are key components of both natural and agricultural ecosystems. Their importance derives in large part from their capacity for symbiotic nitrogen fixation with soil bacteria, enabling them to return vital nitrogen to the soil environment and to create seed and forage of high protein content. Two decades of molecular and genomic studies in model systems have revealed the presence of exquisite signal transduction and developmental pathways that initiate symbiosis, but despite these advances we have essentially no understanding of genes that regulate symbiotic performance in the environment.

Here we present a strategy to understand the evolution of symbiotic performance in the wild progenitors of legume crops and the ways in which human selection has reshaped this potential during domestication. Specifically, we propose to combine ecology and population genomics with classical molecular genetics and reverse genetic assays to deduce the functional consequences of standing variation in wild populations of Cicer reticulatum and its domesticated counterpart Cicer arietinum (chickpea).  Doing so will expand our knowledge of symbiotic nitrogen fixation in novel ways, and will contribute to an emerging paradigm in plant biology where the intersection of ecology, genomics and molecular biology empowers the study of gene function in natural and human-built environments.

This proposed research builds on observations in soybean and chickpea indicating that domestication has caused significant shifts in symbiotic performance and nitrogen responsiveness. Impacted phenotypes suggest shifts in bacterial strain discrimination by the host, nodule number changes related with symbiotic efficiency, and the acquisition of soil N responsiveness in domesticated genotypes. Among the objectives of this research are to identify the impacted genes and pathways, and also to understand the relative contributions of specific evolutionary processes (i.e., random demographic processes such drift, direct selection including selection tradeoffs, and selection relaxation) to altered symbiotic function.

The specific objectives of this study are:

  1. To characterize the functional significance of standing variation in wild populations of Cicer reticulatum and its co-occurring bacterial symbionts, using ecology, genomics, and phenotyping.
  2. To identify genomic footprints of domestication-associated shifts in genetic/genomic variation.
  3. To identify the genes that underlie domestication-related shifts in nodule number and responsiveness to soil nitrogen, as well as of selected phenotypes and pathways discovered in Objectives 1 and 2.

Legumes provide an estimated 30% of humankind’s nutritional nitrogen, while in agricultural systems crop rotations with legume species provide an important means to maintain soil fertility. Despite legumes’ comparative advantage of N-fixation, nitrogen fertilizers are often added during legume cultivation and legumes are often grown under high residual nitrogen following cereal crops. These practices relax selection on nitrogen fixation traits and contribute in a substantial way to environmental degradation through nitrogen runoff. Improved understanding of the processes that regulate N-fixation in natural and agricultural environments will ultimately enable rationale strategies to mitigate these situations. Of more immediate impact, researchers on this project will mentor under-represented minorities as young biologists by participating in established high school science programs at UC Davis and the Fairchild Botanical Garden. We will also train undergraduate students in laboratory science, while mentoring their academic and professional development.