Our Research

Our research is in the field of Quantitative and Population Genetics, which deals with the inheritance of complex or quantitative traits which result from the actions and interactions of multiple genes and the environment. By developing new experimental and statistical methods we seek the answers to a range of interesting questions in genomics and evolutionary biology encompassing the following broad areas:

 

(1) Evolution of polyploid plants.

Polyploid organisms have undergone whole genome duplication and so have multiple complete sets of chromosomes, unlike their diploid counterparts which have two chromosome sets. Polyploidy has been a major driving force in the evolution of flowering plants, with most species existing either as current polyploids or palaeopolyploids, having undergone a gradual process of “diploidization,” or reversion to a diploid state over evolutionary time. In fact, many of our most important crop plants are either autopolyploid, such as potato and coffee, or allopolyploid, for example pasta and bread wheats, oat, cotton and canola. Other major crops are palaeopolyploids, including barley, maize and rice. Understanding the evolution of polyploid genomes is therefore an essential component in meeting the global food security challenge.

We are interested in polyploidy as it is an incredibly dynamic process with hallmark features including rearrangements, gene loss, sequence divergence and changes in expression of the component subgenomes. These multiple subgenomes create add an extra layer of complexity in meiosis and lead to more sophisticated patterns of inheritance in polyploid species. This in turn creates challenges for us to solve in order to carry out population genetics analyses and genetic analysis of complex traits in these species.

 

(2) Theoretical and experimental strategies for dissecting the genetic architecture of complex traits in diploids and polyploids.

Almost all organismal traits in nature are complex or quantitative traits, particularly those relevant to plant and animal breeding, and also human health and disease. To unravel the genetic architecture of such traits into underlying Quantitative Trait Loci (QTL), we develop new experimental and statistical methods for constructing genetic marker linkage maps in either diploid or autotetraploid genomes, and for linking quantitative phenotypes to the effects of their underlying genes. We have established several experimental systems for this work, including Arabidopsis thaliana, potato and yeast.

 

(3) Evolutionary and comparative genomics using multi-omics approaches.

In the modern era of large scale data-driven biology, high dimensional ‘omics’ data is rapidly accumulating, particularly from Next Generation Sequencing (DNA-seq, RNA-seq, MethylC-seq, etc.) We are developing statistical methods to integrate data from multiple omics sources, including genomics, epigenomics and transcriptomics, to achieve a detailed understanding of the molecular basis of complex traits in various species.

 

(4) Molecular mechanisms of lung cancer.

Working with our collaborators in Fudan University (Shanghai, China), we carry out experimental analyses using human populations and mouse models to understand the molecular basis of non-small cell lung cancer (NSCLC).

 


Current Projects

Mapping complex agronomic traits in autotetraploid potato

Potato (Solanum tuberosum), an autotetraploid crop, has been selected by the FAO as the world’s 3rd most important food crop. Effective breeding of improved varieties of potato is therefore an important part of the solution to world food security. In this project we are developing a new set of experimental and methodological tools to enable complex traits to be mapped in potato on a theoretically rigorous basis. This work will provide potato breeders with map information of agronomic quantitative traits for performing marker assisted selection and thereby significantly enhancing breeding efficiency. Funded by the BBSRC.