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

耦合表达序列和细菌人工染色体资源以获取大麦基因组

• 批准号: 0321756
• 负责人: Timothy Close
• 金额: $ 243.31万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-01 至 2009-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0321756&HistoricalAwards=false
• 关键词: Coupling; Expressed; Sequences; Bacterial; Artificial

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.

几种具有重要经济和社会意义的谷类作物，包括大麦、小麦、黑麦和黑小麦，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%的人口将其作为主食。 在美国，每年约有8100万英亩的麦类作物播种，平均价值超过90亿美元。 尽管来自小麦族作物的产品多种多样（面包、糕点、意大利面、啤酒、麦芽威士忌、汤配料、动物饲料），但这些物种在遗传上密切相关。 小麦族基因组，每个单倍体基因组的大小约为5 × 109个碱基对，太大了，目前不能认真考虑全基因组测序。 它的大小是大米的12倍。 然而，可以立即采用可靠的方法来获得小麦族基因组中大部分表达的基因。 在过去几年中，在建立大麦基因组学核心公共资源方面取得了相当大的进展。 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、36万多个部分cDNA序列（“表达序列标签; EST），其代表大麦基因组中所有基因的约75%，以及一种微阵列，其使得可以同时监测超过21个，该项目的目的是将这些资源结合起来，以促进美国和世界各地的研究人员对大麦基因组的访问，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理解。 统一的目标是加速过渡到全面的物理作图和测序的大麦基因组的所有基因包含区域。 该项目分为六个渐进的目标，每个目标都以逐步提取大麦基因组的精华为导向。 第一个目标将利用单基因序列的知识来鉴定携带表达基因的大多数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”），并从它们定义代表所有的最小集合。 第三个和第四个目标特别强调1000个基因，与非生物胁迫，包括干旱，低温，热，盐通过添加这些重叠群和基因的大麦遗传连锁图谱。 第五和第六个目标将通过一个数据库浏览器方便地获取这些信息，该数据库浏览器将为用户提供纯粹基于网络的功能选择，或者为那些喜欢更快速度的人提供主要在个人计算机上运行而仅依赖网络获取补充信息的混合软件。 富集基因组的基因丰富部分的整个BAC文库的子阵列将在第2年年底开始可用。 与基因组的这一部分相关的BAC重叠群的物理图谱将从第1年开始提供，直到第2年。 与1000个与非生物胁迫相关的基因相关的BAC重叠群和EST将在第4年锚定到遗传连锁。 在整个项目期间和项目结束后，将通过项目网站（http：//www.example.com）免费提供全部进展情况汇编harvest.ucr.edu