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

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.

The proposed collaboration will support the development of a modern rice breeding platform in Vietnam that will contribute to ensuring food security in the country. The impacts on research will be delivered within the timeframe of the proposed project and continue thereafter on an international scale. There will be direct impacts on staff through training and outreach activities in bioinformatics and the deployment of modern breeding technologies. The indirect impacts, for example, on the food security agenda and the wider public will take longer.

There is a requirement for bioinformatics expertise in Vietnam, and a shortage of scientists with the required expertise in genomics, computer science and mathematics. Capacity building in bioinformatics will strengthen research into genomics globally to exploit the opportunities presented by big data but this requires good people and requires tapping into reserves of mathematicians, physicists and computer scientists internationally that we can attract to increase the pool of skilled labour Vietnam.