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UK's TGAC to Lead Development of Bioinformatics Capabilities for Rice Genomics in Vietnam

Terraced Rice Fields in Vietnam

NEW YORK (GenomeWeb) – Scientists from The Genome Analysis Centre in the UK will work with their counterparts in Vietnam to bring the country's rice genomics programs up to speed as the Southeast Asian nation's staple crop battles climate change, emerging pathogens, and urban development.

TGAC announced this week that it has received £50,000 ($78,000) from the British Council to train bioinformaticians from Vietnam's Agricultural Genetics Institute in Hanoi. TGAC and AGI have worked together for two years to explore the genetic diversity of Vietnamese rice, including the sequencing of 36 accessions.

As part of that ongoing cooperation, TGAC and AGI will sequence an additional 48 rice accessions, with the goal of sequencing 600 lines, according to TGAC's Sarah Ayling, who is leading the project. Ayling, who is crop genomics and diversity group leader at the Norwich-based center, said that TGAC and AGI are now seeking additional funding to carry out the project.

Ayling noted that it was logistically feasible to only sequence these 600 accessions from the approximately 8,000 in the national gene bank. She also noted that the new grant will in part support sequencing of the 48 additional accessions, though most of the money will fund bioinformatics capacity building and training.

"The sequencing is a subset of this training grant, but as part of that we are generating some data to feed the training activities," Ayling said.

The UK-Vietnamese collaboration so far has been supported via The Newton Fund, the UK's £375 million fund for science and innovation partnerships. The British Council manages the fund. According to Ayling, all 600 accessions will ultimately be sequenced at TGAC's facility in Norwich using Illumina machines.

"The idea is that all the sequencing will be done here," Ayling said. "If we can run all of the samples through the same pipeline, that will reduce variation and so forth.

Sequencing Vietnamese rice accessions is just one component of the cooperation between TGAC and AGI, Ayling noted. She said that while AGI has already implemented marker-assisted breeding programs to improve Vietnam's rice production, it does not yet have the bioinformatics capabilities in house to make sense of the NGS data sets.

"AGI are looking to set up their own bioinformatics group, so it is an area of interest for them, it is something they are developing," Ayling said. "Having experienced personnel is difficult because it is not established within the universities. It is common in many countries globally, but the UK is quite advanced in that we have been doing it for the past 10 to 15 years."

Le Huy Ham, director general of AGI, said in a statement that the collaboration with TGAC is of "extreme value" for the institute. "At our institute and in Vietnam in general, we have good rice breeders, including molecular breeders, but we do not have bioinformatics experts who can use data from genomic sequencing for breeding purposes," he said.

To aid AGI toward its goal of creating its own bioinformatics group, TGAC will invite investigators from Hanoi to Norwich for several weeks to run analysis pipelines as they would be run at TGAC. "We are not talking about developing new software,"Ayling noted. "We will use existing tools and we are very much in favor of using open-access software. They won't need to invest in software when they get back. We will be using things that are available to everybody."

While in training at TGAC, AGI investigators will gain experience in running the tools and navigating the size of the data. "As they are making investments in a bioinformatics group, they will need to know what kind of hardware is needed to run things," she said. "These are all discussions they can have when they are here and can see what we are using."

TGAC scientists also intend to visit Vietnam and hold a workshop there, making use of the sequences generated as part of the project. Ayling said that TGAC will develop training materials for their counterparts not only at AGI, but at other universities and institutes in Vietnam. "They can come in and get a feel for what we are doing and what can be done," Ayling said. "Obviously, they are not only working on rice, but genomics is genomics, they can use what we offer to help them with their own projects."

In order to make the data from the project accessible, TGAC will also set up a public database to host the variant data within the context of the latest genome assemblies and annotation, Ayling said.

A final event is planned where a larger group of Vietnamese bioinformaticians will visit TGAC to hold a "train the trainer" workshop. "They will gain more experience conducting the workshop themselves, so they can continue into the future," she said. TGAC's Vietnamese partners might also assist TGAC in the future as they train other collaborators in Southeast Asia, Ayling noted.

"It's a useful opportunity for us," Ayling said. "We can call on them in the future and continue to work together to reach a broader audience," she said.

Vietnam is the second largest rice exporter in the world, and continues to see an average 3 percent annual yield increase in rice production over the past 30 years. This is in spite of rising sea levels that threaten the crop, which is primarily raised in coastal regions, as well as the environmental pressures of urban development.

Ayling said that her counterparts at AGI have been successful in using known markers to improve their rice yields, but that the recent initiatives should enable AGI to make new gains in its rice breeding programs.

"It's about expanding the possibility for the markers that are out there and bringing in more information from more diverse materials than they can use in the breeding programs," said Ayling. She noted that AGI scientists are already investigating some genes of interest identified from the sequencing of the initial 36 accessions two years ago.