Skip to main content Skip to navigation

Understanding genetic mechanisms of complex traits to improve potato breeding

Primary Supervisor: Dr Lindsey Compton, School of Biosciences

Secondary supervisor: Dr Estrella Luna-Diez

PhD project title: Understanding genetic mechanisms of complex traits to improve potato breeding

University of Registration: University of Birmingham

Project outline:

Cultivated potato (Solanum tuberosum) plays a crucial role in addressing world food security in the current food security crisis. With the need to feed a growing population under changing climatic conditions comes the need for development of better adapted varieties. These varieties need to have higher yield and quality, but these traits must also become more stable in response to increasingly variable environmental conditions, including biotic and abiotic stresses.

Potato breeding requires an understanding of the genotype-phenotype relationship to facilitate the development of improved varieties. Breeding has typically focused on time-consuming and labour-intensive traditional phenotyping techniques and their use in selection for improving commercial traits, particularly yield. This has made the development of new and improved varieties a very lengthy process. In addition, while there have been major developments in the ability to create genetic profiles of potato varieties, there have been very few genomics-assisted breeding programs due to limited understanding of the molecular basis of traits. There is therefore an urgent need to develop novel methodological approaches to improve our ability to measure complex traits in large-scale field studies and to understand their molecular basis from multi-omics perspectives.

Together with national collaborators, we undertake field trials with a diverse germplasm collection of more than 250 tetraploid potato varieties to understand the genetic basis of a variety of commercial and underlying physiological traits and their interactions with environmental factors. To do this, we combine statistical genetics with multi-omics approaches and advanced high throughput phenotyping techniques. Building on these approaches, this project is designed to provide opportunities to contribute to world food security in diverse topic areas including:

1) Characterising varietal variation in resistance to disease. The most serious disease affecting potato production worldwide is late blight, the burden of which is expected to increase due to lack of availability of environmentally damaging chemical controls and the conditions brought about by climate change. This work involves a broad set of methods including Genome-Wide Association Study (GWAS) and multi-omics approaches (e.g. transcriptomics, metabolomics) to understand the dynamics and components of potato resistance responses. 

2) Development of new methods to improve genotype-phenotype association studies in autotetraploid species such as potato, including imaging techniques for high throughput phenotyping in the field and new statistical methods to facilitate high-resolution trait mapping. 

3) Characterising the phenotypic response of potato to an organic farming system to facilitate omics-informed breeding of new varieties adapted to low-input systems.

4) Unravelling the genetic and physiological mechanisms of tuber greening in potato, by bringing together developments using multispectral imaging techniques with genome-wide association and transcriptomic approaches. This will be a key step towards the molecular marker-assisted breeding of low-greening varieties, thus cutting serious losses in the supply chain and reducing food waste.

In summary, this project will contribute essential new techniques and knowledge to inform the development of robust new varieties in the face of climate change.

References.

  1. Colwell F, Soutar J, Compton L, Bryan GJ and Prashar A (2021) Development and validation of methodology for estimating potato canopy structure for field crop phenotyping and improved breeding. Frontiers in Geneticshttps://doi.org/10.3389/fpls.2021.612843  
  2. Jing Chen, Lindsey Leach, Jixuan Yang, Fengjun Zhang, Tao Qin, Zhenyu Dang, Yue Chen and Zewei Luo A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species. New Phytologist https://doi.org/10.1111/nph.16413.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science & Understanding the Rules of Life: Plant Science

    Techniques that will be undertaken during the project:

    Experimental techniques include: plant pathology techniques and protocols, molecular biology and genetic analysis, next generation sequencing including RNA-seq, potato field trials, high throughput phenotyping, remote sensing, fluorescence microscopy.

    Computational techniques include: development of code in a variety of languages, including bash script, R and Python, for a variety of purposes e.g. statistical data analysis and visualisation and development of pipelines for image analysis and omics data analysis.

    Contact: Dr Lindsey Compton, University of Birmingham