Cristobal Uauy, Philippa Borrill and Ricardo H. Ramirez-Gonzalez

As part of the IWGSC RefSeq v1.0 project, Cristobal, Philippa and Ricardo worked on the transcriptome analysis. They used both publicly available data and those made available by IWGSC members to analyze RNA-Seq samples and develop a wheat expression atlas, an invaluable resource for the wheat research community. Through the web resource www.wheat-expression.com researchers and breeders will, upon publication of the RefSeqv1.0, be able to access information and analysis from over 850 RNA-Seq data sets and to compare these with their own data sets to facilitate in-depth research and analysis. This web resource will play a critical role in advancing plant breeding.

The value of the group’s work is best demonstrated in their development of networks which assign genes to co-expression modules associated with specialized roles in in wheat such as floral development. Cristobal and colleagues have moved the wheat community beyond relying on phylogenetic relationships between wheat and Arabidopsis / rice orthologs to develop functional predictions for wheat genes based on their expression profiles. Using 850 diverse RNA-Seq samples, the team assigned 55% of transcribed genes (54,401) to 38 modules, largely based on tissue specific expression. By relating these modules to phenotypes, such as floral development, it was possible to distinguish between members of a transcription factor family (MADS_II) as to whether or not they could be argued to part of the floral development process, moving beyond the information provided by orthologs in rice and Arabidopsis. The rigor of the group’s bioinformatics analyses, including homeolog expression, has defined a broader process for understanding wheat development.

Cristobal Uauy is a Project Leader in the department of Crop Genetics at the John Innes Centre (JIC) in the United Kingdom. Cristobal’s research is focused on using genetics and genomics to identify genes involved in wheat productivity traits – such as grain size and shape, pre-harvest sprouting, and resistance to the wheat yellow rust pathogen. With his team, he aims to understand the mechanisms by which these genes function and to translate this knowledge into improved wheat varieties for growers, industry, and consumers.

Philippa Borrill is a research fellow in the department of Crop Genetics at JIC. Her research focuses on understanding gene regulatory networks which control important agronomic traits. She is particularly interested in senescence which is an important biological determinant of yield and grain nutrient content in wheat. Through understanding senescence her research aims to improve the nutritional value of wheat for human health.

Ricardo H. Ramirez-Gonzalez is a bioinformatician who has recently graduated with a Ph.D. undertaken as a joint project between the Earlham Institute and JIC. His project focused on design and implementation of tools to make the data produced by high-throughput sequencing accessible to wheat researchers and has been central to the development of web-based portals providing access to marker, tilling and expression data.