Sequencing and exploitation of the Brassica A genome

芸苔A基因组的测序和开发

• 批准号: BB/E017363/1
• 负责人: Ian Bancroft
• 金额: $ 114.72万
• 依托单位: John Innes Centre
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE017363%2F1
• 关键词: Sequencing; exploitation; Brassica; genome

Brassica crops are major contributors to healthy human diet and agricultural economies worldwide. They include oil crops such as oilseed rape (B. napus) and vegetables such as cabbage, cauliflower, broccoli (B. oleracea) and Chinese cabbage and turnip (B. rapa). The UK provides 5% of worldwide production of rapeseed, the oil from which has important nutritional properties and has potential as a biofuel or a renewable resource for industrial applications. Brassica vegetables are rich sources of vitamins, minerals and compounds that help protect against cancer. Despite the importance of Brassica crops in the UK, efforts to develop their potential further are hampered by the complexity of their genetic composition. This is the result of hybrid formation in their ancestry, resulting in amplification of their genomes. For B. oleracea and B. rapa, this results in there typically being 2 copies of each unique gene in closely related species, such as the widely studied Arabidopsis thaliana. In B. napus, the situation is worse still as this species is the result of a very recent hybridization between B. oleracea and B. rapa, resulting in an additional doubling of gene numbers. Fortunately, all of the cultivated Brassica species are closely related and genome structure is very highly conserved between them. This means that detailed knowledge of genome structure and composition in any one species can be readily exploited in the others, providing the necessary data interpretation and information-sharing resources are put in place. A worldwide consortium has initiated the Brassica rapa Genome Sequencing Project, with ongoing activity in Korea, Australia, Germany, Canada, USA and elsewhere. All 10 chromosomes of the homozygous genotype to be sequenced, (Chiifu-401, a Chinese cabbage) have been adopted for sequencing by members of the consortium. The sequencing of two of them is underway in Korea and proposals are being developed to sequence the remainder. In all cases, the methods and standards to be adopted have been agreed. We have established an alliance with scientists in China and the USA, exploiting the complementary expertise available from the partners, to sequence two chromosomes. In addition, we will develop resources to facilitate the exploitation of the entire B. rapa genome sequence, which we expect to be available at the end of 2009. These include systematic annotation of the genome sequence, obtaining sequences from oilseed rape to enable the identification of corresponding regions of its genome, and a database system with displays tailored to enhance the ability of the various user communities to exploit the sequence data for research and the improvement of the Brassica crops of importance in the UK.

芸苔属作物是全球人类健康饮食和农业经济的主要贡献者。它们包括油料作物，如油菜（B。napus）和蔬菜如卷心菜、花椰菜、花椰菜（B. oleracea）和大白菜和萝卜（B. rapa）。英国提供了全球油菜籽产量的5%，油菜籽油具有重要的营养特性，并具有作为生物燃料或工业应用可再生资源的潜力。芸苔属蔬菜富含维生素、矿物质和有助于预防癌症的化合物。尽管芸苔属作物在英国很重要，但由于其遗传组成的复杂性，进一步开发其潜力的努力受到阻碍。这是他们祖先杂交形成的结果，导致他们的基因组扩增。为了B。oleracea和B. rapa，这导致在密切相关的物种中通常存在每个独特基因的2个拷贝，例如广泛研究的拟南芥。在B。napus，情况更糟，因为这个物种是B之间最近杂交的结果。oleracea和B. rapa，导致基因数量增加一倍。幸运的是，所有栽培的芸苔属物种都是密切相关的，并且它们之间的基因组结构非常高度保守。这意味着，只要有必要的数据解释和信息共享资源，任何一个物种的基因组结构和组成的详细知识都可以很容易地用于其他物种。一个世界性的联盟已经启动了芜菁基因组测序项目，目前正在韩国、澳大利亚、德国、加拿大、美国和其他地方开展活动。待测纯合基因型（Chiifu-401，大白菜）的所有10条染色体已被该财团成员用于测序。韩国正在对其中两个进行测序，并正在制定对其余部分进行测序的建议。在所有情况下，应采用的方法和标准均已商定。我们与中国和美国的科学家建立了联盟，利用合作伙伴的互补专业知识，对两条染色体进行测序。此外，我们将开发资源，以促进整个B的开采。rapa基因组序列，我们预计将在2009年底提供。这些包括基因组序列的系统注释，从油菜中获得序列以识别其基因组的相应区域，以及具有定制显示的数据库系统，以增强各种用户社区利用序列数据进行研究的能力，并改善英国重要的芸苔属作物。

项目成果

Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.).

• DOI: 10.1093/dnares/dsu002
• 发表时间: 2014-08
• 期刊: DNA research : an international journal for rapid publication of reports on genes and genomes
• 作者: Li F;Chen B;Xu K;Wu J;Song W;Bancroft I;Harper AL;Trick M;Liu S;Gao G;Wang N;Yan G;Qiao J;Li J;Li H;Xiao X;Zhang T;Wu X
• 通讯作者: Wu X

Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus.

• DOI: 10.1186/1471-2164-13-247
• 发表时间: 2012-06-15
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Higgins J;Magusin A;Trick M;Fraser F;Bancroft I
• 通讯作者: Bancroft I

Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order.

• DOI: 10.1016/j.dib.2015.01.004
• 发表时间: 2015-06
• 期刊: Data in brief
• 影响因子: 1.2
• 作者: Bancroft I;Fraser F;Morgan C;Trick M
• 通讯作者: Trick M