Integrative Physical Mapping of the Soybean Genome

大豆基因组的综合物理作图

• 批准号: 9872635
• 负责人: David Lightfoot
• 金额: $ 130.37万
• 依托单位: Southern Illinois University at Carbondale
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-10-01 至 2004-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9872635&HistoricalAwards=false
• 关键词: Integrative; Physical; Mapping; Soybean; Genome

Investment in crop genomic science is justified by the existence of genus, species and cultivar specific genes with no known function. A subgroup, within this group of genes, is expected to be genes of agronomic and economic importance such as disease resistance genes, major yield determinates and genes that produce specific chemicals and components. Identification of members of the economically important gene subgroup has been painstakingly slow by conventional genetics and preliminary genomics. The continuously enhanced productivity and international competitiveness of the US soybean crop will depend on applications of biotechnologies in genetic improvement Proposed is the development of a physical map of the soybean genome to accelerate the rate of economically important gene discovery 10-100 fold; to provide a framework for EST mapping; and to provide for the future sequencing of the whole soybean genome. Methods: The primary method for physical map construction will be a modified restriction enzyme based polyacrylamide (sequencing) gel based fingerprinting (PAGFP) that enables the identification of overlapping BAC clones to form contigs. Microsattellite markers will be integrated with the contigs by DNA pool assembly and screening. Some gaps in the basic contig map (1-2 hundred from 2-5 thousand) will be filled by improving fingerprinting methods, developing microsattelite anchors from end-BACs or DNA sequencing of BAC end clones. Some RFLPs and ESTs will be hybridized with contigs and anchored genomic regions. Some microsatellite, RFLP and EST anchored clones from other cultivars will be fingerprinted. Duplicated markers in separate contigs will identify homeologous regions of the soybean genome at high resolution.Potential Impact: The proposed research will provide all soybean researchers with a powerful tool to:o Isolate the mapped genes and QTLs important to soybean production,o Isolate DNA markers for genes and QTLs that are well-suited for marker-assisted selection (MAS) in soybean breeding, o Map most (80%) of the soybean ESTs at a resolution of 200 - 2,000 kb within a few years.o Develop soybean genome chips with arrayed linkage groups from the mapped genes and contigs.The ultimate goal is to significantly accelerate discovery, cloning, manipulation, and utilization of soybean genes and QTLs of agronomic importance for genetic improvement and agricultural production. Thereby, the profitability of the US soybean industry will be protected. Deliverables:1. Fingerprint three soybean BAC libraries of 90-120 thousand BACs, equivalent to 12-16 x soybean haploid genomes (including 45-60 thousand BIBACs that are capable of direct complementation by soybean transformation) to form 2-5 thousand contiguous genomic regions (hereafter, contigs).2. Integrate the BAC contigs with 500-1,000 microsattelite markers from the soybean molecular genetic map by PCR amplification or hybridization.3. Test methods for assembling the fingerprinted BACs into the physical map contigs, analyze methods for gap filling and contig verification.4. Test the utilility of the contigs for identifying homeologous genomic regions of the duplicated soybean genome and for the assignment of EST families to genomic regions . 5. Provide soybean researchers with electronic access to BAC clones encompassing regions likely to contain genes and QTL of agronomic importance.Contact Information:For Contigs (mirror sites):http://www.siuc.edu/~pbgc/htmls/link.htm andhttp://hbz7.tamu.edu/homelinks/phymap/soybean/soy_home.htmhttp://www.siuc.edu/~meksem/htmls/link.htmFor Web FPC:http://hbz7.tamu.edu/homelinks/phymap/soybean/soy_home.htmFor the DAS enabled Soybean Genome Browser:http://www.siuc.edu/soybeangenome.infohttp://www.langin.com/soybean/gbrowse?source=soybean;name=A1

对作物基因组科学的投资是合理的，因为存在属、种和栽培品种特异性基因，但功能未知。在这组基因中的一个亚组预期是具有农学和经济重要性的基因，例如抗病基因、主要产量决定因素和产生特定化学物质和组分的基因。通过传统遗传学和初步基因组学，对具有重要经济意义的基因亚组成员的鉴定一直进展缓慢。 美国大豆产量的持续提高和国际竞争力将取决于生物技术在遗传改良中的应用。建议开发大豆基因组物理图谱，以加快10-100倍的经济重要基因发现速度;为EST作图提供框架;并为未来的大豆全基因组测序提供基础。研究方法：物理图谱构建的主要方法是基于聚丙烯酰胺（测序）凝胶指纹图谱（PAGFP）的改良限制性内切酶，其能够鉴定重叠BAC克隆以形成重叠群。微卫星标记将通过DNA池组装和筛选与重叠群整合。基本重叠群图中的一些空白（从2-5千个中的1-2百个）将通过改进指纹方法、开发来自末端BAC的微卫星锚或BAC末端克隆的DNA测序来填补。一些RFLP和EST将与重叠群和锚定基因组区域杂交。对其他品种的微卫星、RFLP和EST锚定克隆进行指纹分析。分离重叠群中的重复标记将以高分辨率识别大豆基因组的同源异型区域。潜在影响：拟议的研究将为所有大豆研究人员提供一个强大的工具，以：o分离对大豆生产重要的定位基因和QTL，o分离非常适合大豆育种中标记辅助选择（MAS）的基因和QTL的DNA标记，o以200 - 2的分辨率定位大多数（80%）大豆EST，o利用已定位的基因和重叠群，开发具有排列的连锁群的大豆基因组芯片，最终目标是显著提高大豆基因组的表达水平。加速发现、克隆、操作和利用对遗传改良和农业生产具有重要意义的大豆基因和QTL。美国大豆产业的盈利能力将得到保护。1. 指纹鉴定三个90-120千BAC的大豆BAC文库，相当于12-16 X大豆单倍体基因组（包括45-60千能够通过大豆转化直接互补的BIBAC），以形成2-5千个连续的基因组区域（下文称为重叠群）。 将BAC重叠群与500- 1000个来自大豆分子遗传图谱的微卫星标记通过PCR扩增或杂交进行整合. 测试将带指纹的BAC组装成物理图重叠群的方法，分析空位填充和重叠群验证的方法.测试重叠群用于鉴定复制的大豆基因组的同源异型基因组区域和用于将EST家族分配到基因组区域的效用。5. 为大豆研究人员提供BAC克隆的电子访问，包括可能包含基因和农艺学重要性QTL的区域。联系信息：对于重叠群（镜像站点）：http://www.siuc.edu/~pbgc/htmls/link.htm和http：hbz7.tamu.edu/homelinks/phymap/soybean/soy_home.htmhttp://www.siuc.edu/~meksem/htmls/link.htmFor网络FPC：http://hbz7.tamu.edu/homelinks/phymap/soybean/soy_home.htmFor启用DAS的大豆基因组浏览器：http://www.siuc.edu/soybeangenome.infohttp://www.langin.com/soybean/gbrowse?来源=大豆;名称=A1