Comparative Genomics of Legume Disease Resistance Gene Homologs

豆科，或豆科，是最大和最多样化的植物家族之一。作为研究豆科植物属特性的参考种，已经出现了苜蓿、日本莲子和大豆三种。该项目的研究利用在参考豆类中获得的知识，为比较基因组学开发广泛的基础设施，包括凤蝶亚科关键系统发育节点的代表，其中居住着几乎所有具有重要经济意义的豆类物种。了解凤蝶基因组的进化，特别是抗性基因的进化，是这项工作的主要目标。其中的成果将是一个路线图，将相关物种之间的祖先基因组标志联系起来，为这些物种的进化提供深入的见解，并为基础研究提供遗传工具。其中一个成果将是对每个目标物种中大多数抗病基因的克隆和遗传定位，从而获得核苷酸结合位点-富亮氨酸重复（NBS-LRR）蛋白的综合候选基因资源。我们期望深入了解抗性基因辐射相对于物种形成的时间；鉴定古老且稳定的抗性基因与新近衍生且快速进化的抗性基因；特定进化过程的性质以及它们是否在分类群中对称运作；豆科植物抗性基因和抗性基因簇变异的历史和频率。该项目将产生的资源包括：(1)基于同源基因标记的豆类基因组遗传图谱比较，(2)深度覆盖细菌人工染色体（BAC）文库和中等覆盖BAC末端序列数据，以促进基因发现，(3)将BAC克隆与遗传间隔联系起来的物种特异性遗传标记，以及(4)每个给定豆类物种的抗性基因同源物的完整清单。更广泛的影响目前，豆类提供了人类饮食中约33%的蛋白质。豆类对人类社会的重要性可以从它们在美国作为商品的重要性得到证明；例如，大豆和苜蓿是主要的经济实体，而多种谷物豆类占据了美国公民主食的一部分。虽然对基因组内容和结构的了解可以改善对各种豆科植物的基础和应用研究策略，但它们的数量之多阻碍了对每个基因组的系统深入分析。为该项目选择的每个物种在美国和/或非洲和印度的发展中国家都具有经济重要性。该项目的一个辅助目标是增加基因组学育种和豆类生物技术的机会。获取项目成果项目数据将存入国家生物技术信息中心的公共数据库（http:www.ncbi.nlm.nih.gov），并可通过http://medicago.ucdavis.edu访问项目网站。BAC库可从亚利桑那基因组研究所（http://www.genome.arizona.edu/）获得。

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/).