Sequencing and exploitation of the genetic diversity in Vietnamese native rice lines to serve research and breeding programs

对越南本土水稻品系的遗传多样性进行测序和利用，为研究和育种计划服务

• 批准号: BB/N013735/1
• 负责人: Mario Caccamo
• 金额: $ 55.01万
• 依托单位: National Institute of Agricultural Botany
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN013735%2F1
• 关键词: Sequencing; exploitation; genetic; diversity; Vietnamese

We propose to develop a modern platform for rice breeding in Vietnam focused on traits of agronomic interest. Rice is a staple food for a population of 90 million in Vietnam and it is also one of the main exporter commodities of the country. Vietnam is experiencing an exceptional growth in its economic output and population rising as a global leading agricultural country. There is, however, an increasing threat from climate change such as emerging pathogens, periods of droughts and rising sea levels. The areas under greatest risk are the deltas of the Red and Mekong rivers, which represent the major rice growing regions of Vietnam. The rapid selection of rice varieties that are tolerant and resilient to these conditions will help to mitigate some of these challenges and contribute to ensure food security in Vietnam. The Genome Analysis Centre (TGAC) in the UK and the Agricultural Genetics Institute (AGI) in Vietnam initiated a collaboration to sequence the genome of a reduced number of Vietnamese rice varieties with the purpose to characterise the genetic variations in native lines and develop molecular markers that could be used to accelerate rice breeding. The application of new genomics technologies to improve crop breeding is one of the priorities at the National Institute of Agricultural Botany (NIAB) at UK. The proposed project continues the partnership initiated between TGAC and AGI as a collaboration with NIAB. We aim at expanding the pilot project phase I to complete the re-sequencing of around 600 lines. We will complement the generation of these data with the development of databases and the application of bioinformatics pipelines to identify associations of alleles with specific phenotypes. We expect to characterise markers that will enable more efficient rice breeding. The application of modern technologies to rice breeding will also provide an excellent example of how these strategies could be applied to other plant species such as wheat and barley. Rice has a simple genome for which many genomics resources have been already generated and it offers an excellent model for the evaluation and assessment of new strategies for breeding that could later be applied to more complex crops. This collaboration with Vietnam will also open opportunities to work with world leading scientists with experience in rice breeding and agronomy.

我们建议在越南建立一个以农艺性状为重点的现代水稻育种平台。大米是越南9000万人口的主食，也是越南的主要出口商品之一。作为一个全球领先的农业国家，越南正在经历经济产出和人口的异常增长。然而，气候变化带来的威胁越来越大，例如新出现的病原体、干旱期和海平面上升。风险最大的地区是红色和湄公河三角洲，它们是越南主要的水稻种植区。快速选择对这些条件具有耐受性和适应力的水稻品种将有助于减轻其中一些挑战，并有助于确保越南的粮食安全。英国的基因组分析中心（TGAC）和越南的农业遗传研究所（AGI）发起了一项合作，对数量减少的越南水稻品种的基因组进行测序，目的是表征本地品种的遗传变异，并开发可用于加速水稻育种的分子标记。应用新的基因组学技术来改进作物育种是英国国家农业植物学研究所（NIAB）的优先事项之一。拟议的项目延续了TGAC和AGI之间的合作关系，并与NIAB合作。我们的目标是扩大试验计划的第一阶段，完成约600个品种的重新排序。我们将通过数据库的开发和生物信息学管道的应用来补充这些数据的生成，以确定与特定表型的等位基因的关联。我们希望鉴定出能够提高水稻育种效率的标记。将现代技术应用于水稻育种也将提供一个很好的例子，说明如何将这些策略应用于小麦和大麦等其他植物物种。水稻有一个简单的基因组，许多基因组学资源已经产生，它为评估和评估新的育种策略提供了一个很好的模型，这些策略以后可以应用于更复杂的作物。与越南的这种合作还将为与具有水稻育种和农学经验的世界领先科学家合作提供机会。

项目成果

Whole Genome Sequencing Reveals the Islands of Novel Polymorphisms in Two Native Aromatic Japonica Rice Landraces from Vietnam.

• DOI: 10.1093/gbe/evx135
• 发表时间: 2017-06-01
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Trung KH;Nguyen TK;Khuat HBT;Nguyen TD;Khanh TD;Xuan TD;Nguyen XH
• 通讯作者: Nguyen XH

Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

• DOI: 10.1111/eva.13433
• 发表时间: 2022-07
• 期刊: Evolutionary applications
• 影响因子: 4.1

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.

• DOI: 10.1186/s12284-021-00481-0
• 发表时间: 2021-06-10
• 期刊: Rice (New York, N.Y.)
• 作者: Higgins J;Santos B;Khanh TD;Trung KH;Duong TD;Doai NTP;Khoa NT;Ha DTT;Diep NT;Dung KT;Phi CN;Thuy TT;Tuan NT;Tran HD;Trung NT;Giang HT;Nhung TK;Tran CD;Lang SV;Nghia T;Van Giang N;Xuan TD;Hall A;Dyer S;Ham LH;Caccamo M;De Vega JJ
• 通讯作者: De Vega JJ

Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

• DOI: 10.1101/2020.07.07.191981
• 发表时间: 2020-07
• 期刊: bioRxiv
• 作者: J. Higgins;B. Santos;T. Khanh;K. H. Trung;T. D. Duong;Nguyen Thi Phuong Doai;N. T. Khoa;D. Ha;N. T. Diep;K. T. Dung;Cong Nguyen Phi;T. Thủy;N. T. Tuan;H. Tran;N. Trung;H. T. Giang;Ta Thi Kim Nhung;C. Tran;S. Lang;L. T. Nghia;N. Giảng;T. Xuan;Anthony Hall;S. Dyer;L. Hàm;M. Cáccamo;J. D. Vega

Additional file 3 of Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

对 672 个本地水稻品种进行重新测序以探索越南遗传多样性和性状关联的附加文件 3

• DOI: 10.6084/m9.figshare.14767051
• 发表时间: 2021
• 作者: Higgins J