Deducing the Genomic Footprint and Functional Impact of Chickpea Domestication on Nitrogen Fixation

PI: Douglas Cook（加州大学戴维斯分校）coPIs: Varma Penmetsa（加州大学戴维斯分校）和Eric von Wettberg（佛罗里达国际大学）合作者：Abdullah Kahraman（土耳其哈兰大学）豆科植物是自然和农业生态系统的关键组成部分。它们的重要性在很大程度上源于它们与土壤细菌共生固氮的能力，使它们能够将重要的氮返回土壤环境，并产生高蛋白含量的种子和饲料。二十年来对模型系统的分子和基因组研究已经揭示了启动共生的精致遗传途径的存在，但尽管这些进展基本上对自然环境中调节共生表现的基因知之甚少。该项目的研究旨在了解豆科作物野生祖先共生表现的进化，以及人类选择在驯化过程中重塑这种潜力的方式。本研究将生态学和种群基因组学与经典分子遗传学和反向遗传分析相结合，推断了嘴豆（Cicer reticulatum）野生种群和其驯化对应物Cicer arietinum（鹰嘴豆）的直立变异的功能后果。项目成果将以新颖的方式扩展我们对共生固氮的认识，并将为植物生物学的新兴范式做出贡献，其中生态学，基因组学和分子生物学的交叉赋予了研究自然和人为环境中基因功能的能力。重要的是，研究结果应该与基础科学和农业相关。豆科植物提供了大约30%的人类营养氮，而在农业系统中，豆科植物的作物轮作是保持土壤肥力的重要手段。尽管豆科植物具有固氮的相对优势，但豆科植物在种植过程中经常添加氮肥，豆科植物在谷物作物之后经常在高残氮条件下生长。这些做法放松了固氮性状的选择，并在很大程度上通过氮径流导致环境退化。提高对自然和农业环境中调节固氮过程的理解将最终使减轻这些情况的基本策略成为可能。更直接的影响是，该项目的研究人员通过参加加州大学戴维斯分校和仙童植物园建立的高中科学项目，指导被忽视的少数民族作为年轻生物学家。该项目将为实验室科学的本科生提供培训，同时指导他们的学术和专业发展。该项目产生的数据和生物资源将通过公共存储库提供，包括国家生物技术信息中心（NCBI）和美国农业部农业研究服务局的种质资源信息网络（GRIN）。还将通过一个具体项目的网站提供信息。

PI: Douglas Cook (University of California - Davis)coPIs: Varma Penmetsa (University of California - Davis) and Eric von Wettberg (Florida International University)Collaborator: Abdullah Kahraman (Harran University, Turkey) 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 genetic pathways that initiate symbiosis, but despite these advances essentially little is known about genes that regulate symbiotic performance in the natural environment. Research under this project strives 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. The research combines 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). Project outcomes 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. Importantly, the outcomes should have relevance to both basic science and to agriculture. 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 are mentoring under-represented minorities as young biologists by participating in established high school science programs at UC Davis and the Fairchild Botanical Garden. The project will provide training for undergraduate students in laboratory science, while mentoring their academic and professional development. Data and biological resources generated under this project will be available through public repositories, including the National Center for Biotechnology Information (NCBI) and through the Germplasm Resource Information Network (GRIN) of the USDA Agricultural Research Service. Information will also be provided through a project-specific web site.