Spotlight: Professor Andy Jones - international rice research

Posted on: 9 October 2020 by Louise Colley in October 2020 posts

Rice Diversity.  Part of the image collection of the International Rice Research Institute (IRRI)

This edition of Spotlight focuses on Professor Andy Jones from the Department of Biochemistry, Cell and Systems Biology. Andy is joint Director of the Computational Biology Facility and is one of the founders of the UK Rice Research Consortium (UKRRC).

Global challenge

A major global challenge is how to feed a rapidly growing population, whilst also mitigating the effects of climate change. Rice provides the major calorific need for around 50% of the global human population. The genus as a whole, including the two main branches of domesticated rice (Oryza sativa Japonica and Indica), and a huge variety of wild relatives, has the capacity to grow within an exceptionally wide range of environments. Research teams across the world have been working closely with breeders to help identify desirable traits, such as resistance to droughts, flooding or high temperatures, with the aim to transfer these traits into high yielding and widely distributed varieties of rice.

Genomic science is now central to research and development efforts.  The genome of one reference variety of Japonica and one of Indica were sequenced around 15 years ago.  However, rice gene annotation efforts have suffered from a lack of international coordination, leading to several different efforts to annotate rice genes using different methods, which persist in different databases today. Plant scientists and breeders find it very challenging to interpret and compare information collected from different rice varieties and as new genomes for wider varieties of rice are now becoming available, this problem will get rapidly worse.

Developing tools

The PanOryza project, aims to solve this issue. It brings together an international consortium from the UK, USA and the Philippines, aimed at creating the pan gene, protein and pathway set for Asian cultivated rice (Orzya sativa) and its wild Oryza relatives, using newly developed software to produce consistent gene models across all varieties and species. 

Andy commented: "We are delighted to receive funding from BBSRC / NSF to work on the rice pan genome and pan gene set annotation with our international partners. Our first task is to catalogue consistently what genes are present in the main cultivated and wild rice varieties, and provide the data in intuitive ways for researchers and breeders to mine. Ultimately, we hope this will lead to the discovery of genetic variants that enable cultivation of high yielding rice, resistant to an unpredictable climate, in order to mitigate the impact of global climate change on food security."

The results of the project will be shared through partner platforms, including Ensembl, UniProt, Planteome and SNP-Seek to reach different types of audiences. Community contributions to the rice genome annotation are encouraged and online workshops in the coming year to gain input.

BBSRC press release