Integrative Physical Mapping of the Soybean Genome

对作物基因组科学的投资是合理的，因为存在着未知功能的属、种和栽培特定基因。在这组基因中，预计有一个亚组是具有农艺和经济重要性的基因，如抗病基因、主要产量决定因素和产生特定化学品和成分的基因。传统遗传学和初步基因组学对经济上重要的基因亚群成员的鉴定非常缓慢。美国大豆作物的生产力和国际竞争力的不断提高将依赖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，以加快经济上重要基因的发现速度10-100倍；为EST映射提供框架；并为未来整个大豆基因组的测序提供依据。方法：构建物理图谱的主要方法将是一种改良的基于限制性内切酶的聚丙烯酰胺（测序）凝胶指纹图谱（PAGFP），它能够识别重叠的BAC克隆，形成contigs。通过DNA库组装和筛选，将微卫星标记与基因组进行整合。通过改进指纹识别方法、从BAC末端开发微卫星锚点或对BAC末端克隆进行DNA测序，可以填补基本序列图（2-5千到1-2百）的空白。一些RFLPs和ESTs将与contigs和锚定的基因组区域杂交。其他品种的微卫星、RFLP和EST锚定无性系将进行指纹鉴定。在不同的contigs中重复的标记将以高分辨率识别大豆基因组的同源区域。潜在影响：该研究将为所有大豆研究人员提供一个强大的工具：分离出对大豆生产有重要意义的定位基因和qtl，分离出适合大豆育种中标记辅助选择（MAS）的基因和qtl的DNA标记，在几年内以200 - 2,000 kb的分辨率绘制大部分（80%）大豆ESTs。o开发大豆基因组芯片，从已定位的基因和组态中获得排列的连锁组。最终目标是显著加快对遗传改良和农业生产具有重要农艺意义的大豆基因和qtl的发现、克隆、操作和利用。因此，美国大豆产业的盈利能力将得到保护。可交付成果:1。3个大豆BAC文库，9 -12万个BAC，相当于12-16个大豆单倍体基因组（包括45-6万个能够通过大豆转化直接互补的bibac），指纹形成2-5万个连续的基因组区域（以下简称contigs）。通过PCR扩增或杂交，将BAC序列与大豆分子遗传图谱中500- 1000个微卫星标记进行整合。3 .指纹bac装配物理地图组件的测试方法，分析缺口填充和组件验证的方法。测试这些序列在鉴定重复大豆基因组的同源基因组区域和EST家族在基因组区域的分配方面的效用。5. 为大豆研究人员提供BAC克隆的电子访问途径，这些克隆可能包含具有重要农艺意义的基因和QTL。联系信息：对于Contigs（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 Web 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?source=soybean；name = A1

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