Comparative Genomics of Legume Disease Resistance Gene Homologs

豆科，或豆科，是最大和最多样化的植物科之一。三个种，紫花苜蓿，莲花和大豆，已经成为研究豆科植物属特性的参考物种。该项目的研究利用从参考豆科植物中获得的知识，为比较基因组学建立了广泛的基础设施，包括来自蝶形科亚科关键系统发育节点的代表，几乎所有经济上重要的豆科物种都居住在这些亚科中。了解蝶形虫的基因组进化，特别是抗性基因的进化，是这项工作的主要目标。其中的成果将是一份路线图，将相关物种之间的祖先基因组地标联系起来，提供对这些物种进化的洞察，并产生用于基础研究的遗传工具。其中一个这样的产品将是每个目标物种中大多数抗病基因的克隆和遗传作图，从而产生一个全面的核苷酸结合位点富含亮氨酸重复序列(NBS-LRR)蛋白质候选基因资源。我们期望深入了解与物种形成相关的抗性基因辐射的时间；鉴定古老和稳定的抗病基因与最近衍生和快速进化的抗病基因；特定进化过程的性质以及它们是否在分类群中对称地运作；抗病基因和豆科抗病基因簇变异的特定机制的历史和频率。该项目将产生的资源包括：(1)基于同源基因标记的豆科植物基因组之间的比较遗传图谱，(2)深度覆盖的细菌人工染色体(BAC)文库和中等覆盖的BAC末端序列数据，以便于基因发现，(3)将BAC克隆与遗传区间联系起来的物种特定遗传标记，以及(4)每个豆科植物的抗性基因同源物的完整清单。豆类对人类社会的重要性从它们在美国作为大宗商品的重要性可见一斑；例如，大豆和苜蓿是主要的经济实体，而各种谷物豆类占据了美国公民主食的一部分。尽管对基因组内容和结构的了解可以改进各种豆科植物的基础和应用研究战略，但它们的数量太多，无法对它们的每一个基因组进行系统的深入分析。为该项目选择的每一个物种在美国和/或非洲发展中国家和印度都具有重要的经济意义。该项目的一个辅助目标是增加豆类作物基因组学育种和生物技术的机会。获得项目成果项目数据将存储在国家生物技术信息中心的公共数据库中(网址：www.ncbi.nlm.nih.gov)，并可从项目网站访问，可通过http://medicago.ucdavis.edu.访问亚利桑那州基因组研究所(http://www.genome.arizona.edu/).)将提供BAc文库

The legume family, or Fabaceae, is one of the largest and most diverse plant families. Three species, Medicago truncatula, Lotus japonicus and soybean, have emerged as reference species for investigating the generic properties of legumes. The research in this project leverages knowledge gained in the reference legumes to develop a broad infrastructure for comparative genomics, including representatives from the key phylogenetic nodes of the Papilionoid subfamily in which reside almost all of the economically important legume species. Understanding Papilionoid genome evolution, particularly the evolution of resistance genes, is the primary goal of this work. Among the outcomes will be a road map that links ancestral genomic landmarks between related species, providing insight into the evolution of these species and yielding genetic tools of use to basic research. One such product will be the cloning and genetic mapping of the majority of disease resistance genes in each of the target species, resulting in a comprehensive candidate gene resource of nucleotide binding site - leucine-rich repeat (NBS-LRR) proteins. We expect to gain insight into the timing of resistance gene radiation relative to speciation; the identification of ancient and stable, versus recently derived and fast-evolving, resistance genes; the nature of specific evolutionary processes and whether they operate symmetrically across taxa; the history and frequency of specific mechanisms for resistance gene and resistance gene-cluster variation across the legume family. Resources to be generated by the project include: (1) comparative genetic maps between legume genomes based on orthologous gene markers, (2) deep coverage Bacterial Artificial Chromosome (BAC) libraries and moderate coverage BAC end sequence data to facilitate gene discovery, (3) species-specific genetic markers that link BAC clones to genetic intervals, and (4) a complete inventory of resistance gene homologs for each of give legume species.Broader ImpactsCurrently legumes provide an estimated 33% of the protein in the human diet. The significance of legumes to human society is evidenced by their importance as commodities in the US; soybean and alfalfa, for example are major economic entities, while a diversity of grain legumes occupy part of the staple diet of US citizens. Although knowledge of genome content and structure could enable improved strategies for basic and applied research in each of the various legume species, their sheer number precludes a systematic in-depth analysis of each of their genomes. Each species selected for this project is of economic importance in the US and/or in the developing countries of Africa and in India. An ancillary goal of this project is to enhance opportunities for genomics-enabled breeding and biotechnology in legumes generally.Access to project outcomesProject data will be deposited in public databases at the National Center for Biotechnology Information (http:www.ncbi.nlm.nih.gov) and available from a project web site accessible through http://medicago.ucdavis.edu. BAC libraries will be available from the Arizona Genomics Institute (http://www.genome.arizona.edu/).