Characterising rice genetic diversity in the mekong delta to sustain future crops

DEVEGA_E22DTP

Rice is a versatile carbohydrate essential to diets worldwide and a staple for over 50% of the human population. Rice production in Vietnam is of enormous value, both as an export commodity and a daily food staple for more than 96 million people in Vietnam. However, climate change is threatening rice’s wide availability. In Vietnam, the highest rice production areas are in the low-lying deltas of the Mekong and Red rivers which are particularly exposed to drought and increased salinity from seawater due to climate change.

Plant genetic resources provide the reservoir of adaptive and productive genes free of deleterious mutations needed to develop the improved cultivars that help ensure future crop production. Vietnam’s rice diversity constitutes a significant and precious genetic resource. The highly productive Mekong Delta is a cultural and agricultural hotspot in Southeast Asia, where a unique and rich diversity of rice landraces developed through centuries (Gutaker et al. 2020; Higgins et al. 2021a). These locally adapted and inherited rice varieties constitute a highly valuable genetic resource for breeders to address increasing threats from climate change in the Mekong Delta. However, the growing adoption for high-yielding rice varieties in the Mekong Delta in the last five decades has driven the progressive replacement of locally adapted landraces.

This PhD aims to understand better the changes in rice genetic diversity in the region and the extent of potential genetic erosion from the loss of adapted local landraces. The student will quantify the genetic diversity in local landraces and admixed accessions, investigate their genetic make-up, and quantify deleterious mutations that hinder the further improvement of rice and its adaptation to future climates. The introduction and later widespread displacement of local landraces left us with a limited understanding of the extent of loss in genetic diversity and adaptive potential available to breeders in admixed elite varieties that retain local adaption.

This is a joint-studentship with Royal Botanic Gardens, Kew based at De Vega’s lab at the Earlham Institute (Y1 and Y2) and Gutaker’s group at Kew (Y3 and Y4). The student will have access to Earlham Institute’s and Kew’s state-of-art high-performance computing, horticultural infrastructure, herbarium and seed collections.

References 

Gutaker et al. (2020) Genomic history and ecology of the geographic spread of rice. Nature Plants 6: 492-502.

Latorre et al. (2020) Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA. Curr Protocols Plant Biol 5(4): e20121.

Higgins et al. (2021) Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam. Rice, 14: 52.

Higgins et al. (2021) Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam. bioRxiv, 2021.08.04.455072v1