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Understanding genetic mechanisms of complex traits to improve potato breeding.

Principal Supervisor: Dr Lindsey ComptonLink opens in a new window

Co-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:

1. Project outline describing the scientific rationale of the project (max 4,000 characters incl. spaces and returns). There is no need to be too detailed about individual projects – general background, objectives and methods should suffice. One or two key references for potential applicants would be useful.

Cultivated potato (Solanum tuberosum) plays a crucial role in addressing world food security. With the need to feed a growing population under rapidly changing climatic conditions comes the need to develop better adapted potato varieties. These varieties need to have higher yield and improved quality traits, but also a more stable performance in response to increasingly variable environmental conditions, including diverse biotic and abiotic stresses.

Potato breeding requires an understanding of the genotype-phenotype relationship to facilitate the development of improved varieties. Breeding has typically relied on the use of traditional phenotyping methods that are usually insufficiently quantitative and labour-intensive, limiting the accuracy of genetic analysis while making the development of new and improved varieties a lengthy process. Moreover, 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. Therefore, we need to develop novel methodological approaches for high-throughput, accurate and continuous detection of quantitative traits in real farm environments and to understand the molecular basis of these traits from multiple ‘omics’ perspectives.

Together with national collaborators, we conduct large-scale field trials using a diverse germplasm collection of more than 250 tetraploid potato varieties. Using data from these trials, we seek to understand the genetic basis of a variety of commercial and underlying physiological traits and their interactions with environmental factors in different farming systems. 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. Late blight is the most serious disease affecting potato production worldwide, causing more losses than any other pathogen, while the disease burden is expected to increase due to 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 response of diverse potato varieties to this highly destructive pathogen and thus how to create varieties with a more durable disease resistance.

2) Development of new methods to improve genotype-phenotype association studies in crops such as potato, including remote sensing based imaging techniques for high-throughput phenotyping in the field and new statistical methods and data analysis pipelines to facilitate high-resolution trait mapping.

3) Characterising the phenotypic responses 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, bringing together advanced multispectral imaging techniques with genome-wide association and omics 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 new potato varieties with a more robust performance in the face of climate change.

References:

1). Ponce P, Torres Y, Prashar A, Buell R, Lozano R, Orjeda G, Compton L (2022) Transcriptome Profiling Shows a Rapid Tissue-Specific Response in Two Andigenum Potato Varieties Under Drought Stress. Frontiers in Plant Science. In press.

2) 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 Genetics https://doi.org/10.3389/fpls.2021.612843.

BBSRC Strategic Research Priority: Sustainable agriculture and food – Plant and crop 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-based omics 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 data analysis and omics data analysis.

 

Contact: Dr Lindsey ComptonLink opens in a new window