Genetic Diversity in Vietnam Native Rice Lines

Professor Mario Caccamo
Characterisation and exploitation of the genetic diversity in Vietnam native rice lines.

Participating Institutions: NIAB (Cambridge, UK), Agriculture Genetics Institute (AGI, Hanoi, Vietnam), Earlham Institute (Norwich, UK)

In this project a panel of 619 rice lines from Vietnam’s national seedbank have been sequenced using low-pass coverage whole genome sequencing performed at the Earlham Institute. Sequencing data has been analysed using a bioinformatics pipeline for variant discovery. The resulting variants (single nucleotide polymorphisms) were then subsequently filtered and combined with those from IRRI’s 3,000 Rice Genomes Project (3K-RG).
Vietnamese native lines are currently underrepresented in the reference rice collections: only 38 lines from Vietnam were included in the 3K-RG project. The collection used in this project is comprised of varieties that exhibit key agronomical traits including draught and salt tolerance cultivars. We combined the unfiltered variants from Vietnam’s collection (16m) with those from the 3K-RG project (29m). The admixture and phylogenetic analyses of the integrated dataset suggest novel varietal groups in addition to the ones characterised by the 3K-RG project.
An initial genome-wide association study also points at regions in the genome that are expected to support the acceleration of the breeding of new cultivars. As part of the project we have made available this variants to breeders at AGI (Vietnam) and also train them in the use of bioinformatics tools. The rapid selection of rice varieties to counteract challenges linked to climate change will greatly contribute to food security in Vietnam and enhance current breeding programmes.