The genetic dissection of wheat root phenotypes using forward and reverse genetics approaches

Lead Research Organisation: University of Cambridge
Department Name: Plant Sciences


Theme: Agriculture and Food Security

The genetic dissection of root traits initiated during the rotation project would be expanded upon, providing multiple forward and reverse genetic lines of investigation for a comprehensive package of root traits to be prioritised for further investigation. Possible approaches include development of precise genetic stocks, combined homeologous TILLING mutations, and CRISPR/Cas9 targeted genome editing lines for fine-scale (eg CT-scanning, laser ablation tomography) and field-scale (eg shovelomics, qPCR root detection) phenotyping approaches, and associated molecular genetic investigation (eg GbyS, GWAS, RNAseq). Ultimately, this PhD aims to identify and characterise multiple root pathway QTL and genes in wheat, helping to unlock yield potential, and helping to understand and harness the role of roots in plant adaptive strategies. Based at NIAB, a UK centre for wheat research and pre-breeding, the PhD would provide expertise in a range of cutting-edge wheat genetic, genomic, molecular and phenotyping approaches highly relevant to the crop R&D sector. With established links to the wheat research, breeding and growing communities, the working environment provides unique experience at the interface between crop science and translation. Combined with the resources, knowledge and training provided by Cambridge University, this PhD provides a timely opportunity to deliver industry-relevant advances within the Food Security sector.

I will be generating a large dataset of root phenotypic data, including images, which I will process and use for QTL analysis. I will use integrated software for building genetic linkage maps and mapping quantitative trait genes. I will be accessing genome databases such as Ensembl and the Wheat Target Induced Local Lesions In Genome (TILLING) database. Furthermore, I will generate qPCR data which will require analysis. I will be using R package throughout this PhD.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011194/1 01/10/2015 30/09/2023
1804473 Studentship BB/M011194/1 01/10/2016 31/12/2020 Emily Cathy Marr
Description I have identified regions of the genome in wheat that regulate root system architecture. More specifically, I have identified regions of the genome that regulate the angle at which roots grow in the soil. This has significance in relation to water and nutrient uptake. Climate change models project increases in drought incidence while soil nutrient losses contribute to environmental damage and lost profits (N fertilisers are ~30% of cereal production costs). It is estimated that global fertiliser production releases 575 MT of greenhouse gases each year, and P fertilisers are made from finite reserves that may be exhausted in the next 50-100 years. Nutrient losses can be reduced and water capture increased by developing more resilient and efficient crop cultivars with improved root systems.

Another aspect of the work relates to the microbiology of the rhizosphere (soil around the roots). Microorganisms exert a significant effect on diverse aspects of plant health, growth and development, including nutrient acquisition. Plants are thought to release compounds favouring microbes that are beneficial to plant health. Testing for an overlap between the root exudate profile, the microbial profile and the promotion of the rhizosheath could pave the way to developing a drought resilient rhizosphere. Thus I am using whole genome sequencing of rhizosheath soil samples to examine the microbiome of the Avalon x Cadenza population.
Exploitation Route Currently, I have identified a fairly large region of the genome, delimited by DNA markers associated with steep root growth angles. Breeders can screen wheat varieties for these markers in order to select wheat varieties with deep roots. This will enable the development of lines with enhanced root systems. I hope to narrow the region of the genome to fewer genes so as to better target the genes responsible for the desirable root traits.
I am also investigating the genetic control of the formation of the rhizosheath - the soil that adheres to the root. This will have benefits with regard to drought tolerance and can be another characteristic to select for when developing drought-resistance wheat.
Sectors Agriculture, Food and Drink,Education,Environment

Description (i) NIAB (National Institute of Agricultural Botany) holds open days with breeders and farmers. I have presented my work there and raised awareness and understanding about the importance of roots for contributing to yield. (ii) I have talked about my work at the University of Cambridge Science Festival to educate the public about crop root systems, sustainability and agriculture.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Education
Impact Types Cultural,Societal

Description GARNet travel award
Amount £200 (GBP)
Organisation GARNet 
Sector Learned Society
Country United Kingdom
Start 04/2019 
End 04/2019
Description Travel Award for ISRR10 Conference
Amount £800 (GBP)
Organisation University of Cambridge 
Department Christ's College
Sector Academic/University
Country United Kingdom
Start 07/2018 
End 07/2018