Coupling Expressed Sequences and Bacterial Artificial Chromosome Resources to Access the Barley Genome

几种具有重要经济和社会意义的谷类作物，包括大麦、小麦、黑麦和小黑麦，都是小麦族的成员。这些作物占世界粮食产量的30%以上，超过35%的人口将它们作为主食。在美国，小麦属作物每年播种面积约为8100万英亩，平均价值超过90亿美元。虽然来自小麦类作物的产品多种多样(面包、糕点、意大利面、啤酒、麦芽威士忌、汤料、动物饲料)，但这些物种在遗传上是密切相关的。小麦族每个单倍体基因组的大小约为5×109个碱基对，目前太大了，不能认真考虑全基因组测序。这大约是大米的12倍大小。然而，可靠的方法可以立即获得小麦基因组中的大多数表达基因。在过去的几年里，大麦基因组核心公共资源的建设取得了长足的进展。这些核心资源包括基因组“细菌人工染色体”(BAC)文库和cDNA文库，几个广泛使用的作图群体，超过36万个部分cDNA序列(“表达序列标签”；ESTs)，约占大麦基因组所有基因的75%，以及一个可以同时监测超过21,000个大麦基因表达的微阵列。该项目的目的是将这些资源结合起来，方便美国和世界各地的研究人员访问大麦基因组，从而建立对与农业和生物学相关的谷类植物性状的更全面的了解。统一的目标是加速向全面物理图谱的过渡和大麦基因组所有包含基因的区域的测序。该项目分为六个渐进的目标，每个目标都指向逐步提取大麦基因组的精华。第一个目标将利用Unigene序列的知识来鉴定大多数携带表达基因的BAC克隆，预计约占所有BAC克隆的20%。第二个目标将使用遗传指纹技术来创建这些BAC克隆的数千个连续比对(“重叠群”)，并从它们定义一个代表所有克隆的最小集。第三个和第四个目标特别强调与干旱、低温、高温和盐度等非生物胁迫相关的1000个基因，将这些重叠群和基因添加到大麦遗传连锁图谱中。第五个和第六个目标将通过数据库浏览器方便地访问这些信息，该浏览器将为用户提供纯粹基于网络的功能选择，或者对于那些喜欢速度更快的人，可以选择主要在个人计算机上操作并仅依赖网络获取补充信息的混合软件。可交付关于基因特异性和流行的溢出探针的信息将在第一年提供。整个BAC文库的亚阵列丰富的基因组部分将从第二年开始提供。与基因组这一部分相关的BAC连续序列的物理图谱将从第一年开始提供，与非生物胁迫相关的1,000个基因的BAC重叠群和EST将在第四年被固定在基因连锁上。进展的全部汇编将通过项目网站(http://harvest.ucr.edu))在整个项目过程中和项目结束后免费获得。

Several cereal crops of major economic and social importance, including barley, wheat, rye and triticale, are members of the tribe Triticeae. These crops account for over 30% of the world's grain production, with more than 35% of the human population using them as a staple food. In the United States, Triticeae crops are sown on approximately 81 million acres each year with an average value over 9 billion dollars. Although products derived from the Triticeae crops are diverse (bread, pastries, pasta, beer, malt whiskey, soup ingredients, animal feed), the species are genetically closely related. The Triticeae genomes, each with a size of about 5 x 109 base pairs per haploid genome, are too large to seriously consider whole-genome sequencing at present. This is about 12 times the size of rice. Yet, reliable methods can be immediately employed to gain access to the majority of expressed genes in Triticeae genomes. During the past several years, considerable progress has been made in the establishment of core public resources in barley genomics. These core resources include genomic "bacterial artificial chromosome" (BAC) libraries and cDNA libraries, several widely used mapping populations, more than 360,000 partial cDNA sequences ("Expressed Sequence Tags; ESTs) representing about 75% of all genes in the barley genome, and a microarray that makes it possible to simultaneously monitor the expression of more than 21,000 barley genes.The purpose of this project is to couple these resources to facilitate access of US and worldwide researchers to the barley genome, thereby building a fuller understanding of cereal plant traits that are pertinent to agriculture and biology. The unifying objective is to accelerate a transition to comprehensive physical mapping and the sequencing of all gene-containing regions of the barley genome. The project is structured into six progressive objectives, each oriented toward gradual extraction of the essence of the barley genome. The first objective will utilize knowledge of unigene sequences to identify the majority of BAC clones that carry expressed genes, expected to be about 20% of all BAC clones. The second objective will use a genetic fingerprinting technique to create many thousands of contiguous alignments ("contigs") of these BAC clones, and from them define a minimal set representing all. The third and fourth objectives place special emphasis on 1000 genes that are related to abiotic stress, including drought, low temperature, heat, and salinity by adding these contigs and genes to the barley genetic linkage map. The fifth and sixth objectives will create easy access to this information through a database browser that will offer users a choice of purely web-based functionality or, for those who prefer more speed, hybrid software that operates principally on personal computers and relies on the web only for supplemental information.DeliverablesInformation on gene-specific and popular overgo probes will be available during year #1. Sub-arrays of the entire BAC library enriched for the gene-rich portion of the genome will be available beginning at the end of year #2. Physical maps of BAC contigs related to this portion of the genome will be available starting year #1, with additions through year #2. BAC contigs and ESTs related to 1000 genes pertinent to abiotic stress will be anchored to the genetic linkage through year #4. The total compilation of progress will be freely available through the project web site (http://harvest.ucr.edu) throughout and after the end of the project.