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The Food Security and Farming Challenge

Crop improvement programmes focus on the parts of plants above ground, and have neglected the vital yet hidden half below ground: roots. This project will test the idea that optimising root development and function, particularly when soil moisture and nutrients are limiting, will help stabilise yields in the face of climate change and meet the challenges of low input, regenerative agriculture. The project will make use of newly developed germplasm including near-isogenic lines that differ in root system architecture, and novel molecular markers for important traits such as root biomass and gravitropic response angle.
Farmers consistently mention that yield stability is an important consideration in choosing which variety to grow, and as a major factor contributing to volatility in financial planning for their businesses. With increasing variability in seasonal weather due to climate change, the need to reduce unpredictability in production and improve ‘resilience’ is greater than ever. Low rainfall and light soils found across East Anglia make this an important regional priority. Unfortunately, there is little guidance on which varieties show greater year to year reliability than others. Breeders assess candidate lines across a range of test locations and examine aspects of stability and adaptability, but have little understanding of the genetic basis of superior performance. Given the importance of these challenges to the industry, this PhD project will build the analytical tools required for practical yield stability comparisons, and test hypotheses regarding the genetic, physiological and agronomic factors underlying yield stability, with an initial emphasis on roots and root function.
 

 

Prospects for Scientific Discovery - Fundamental Biological Questions

Studies of genetic populations grown across several environments have shown that some quantitative trait loci for stability co-locate with QTLs for yield, whereas others do not, indicating underlying genes that are responsive to environmental factors. Therefore, at the gene level, ‘stability’ is more than the complex phenomena determining yield, but also gene networks that integrate environmental signals into the expression of traits that modulate yield. The project will rigorously test one set of hypotheses (out of many possible ideas) that should contribute to our understanding of the system: varietal differences in the acquisition of water and nutrients from soil explains a proportion of yield stability differences, and a major factor is differential growth and development of the root system. We posit that a root system architecture that establishes more roots deeper in the soil profile will contribute to better yield in dry years and sites, with little cost when soil moisture is adequate, and greater ‘plasticity’ contributes to more efficient acquisition of water and nutrients from unexploited patches in a heterogeneous soil environment, typical of most fields. Work should fill gaps in our knowledge of ‘plastic’ root behaviour, where the genetically programmed blueprint for a root system is tuned to local conditions.
 

 

Guide Workplan

  1. Develop and apply state-of-the-art statistical tools to existing multi-environment yield trial (MET) datasets from historical and current field trials to derive metrics for stability, relative drought tolerance and yield potential.
     
  2. Measure yield stability and root traits across multiple environments using a set of near-isogenic wheat lines that contrast for root system architecture. Approximately 80 spring wheat lines developed at the Univ. Queensland in the NIAB-led IWYP Rooty project will be available for this work. Initial MET data on these lines from yield trials in Australia will be available by the end of 2021. UK trials will be subject to ‘deep phenotyping’ of above- and below-ground traits. Additional MET data on South African lines will be available from ongoing experiments in a related project in South Africa.
     
  3. Identify wheat lines that exhibit enhanced plasticity in controlled-environment experiments and develop screens for discovery of QTLs controlling plasticity traits.

 

Training and Career-building Opportunities

The student will obtain experience and training in: advanced statistical techniques working with MET data; working with mechanistic crop growth models to calculate environmental and drought indices, and developing algorithms based on machine learning; setting up and operating precision field trials; wheat genetics and crop physiology; field phenotyping and genomics/bioinformatics. The research is highly interdisciplinary, spanning plant biology, agronomy, crop physiology, statistics and modelling (both mechanistic and machine learning based). The project involves substantial global collaboration, including partners in Australia and South Africa. Through the studentship sponsor, TMAF, the student will have ample opportunity to interact directly with farmers and other TMAF PhD students, and spend time at the Morley Farm to understand how a research farm operates.
 

 

Supervision

The primary supervisor, Eric Ober is group leader in crop physiology within the Pre-breeding Department at NIAB. His research focuses on improving crop yields through increased understanding of plant traits that contribute to yield formation, drought tolerance and the efficient use of water. Research is primarily funded by government and the agricultural industry, and work is done in close collaboration with commercial plant breeders. Emphasis is placed on translating fundamental understanding of plant biology into practical field-scale screening methods, and identifying superior germplasm using advanced phenotyping methods. A career focus has been root biology, and an objective of current work is improvement of wheat root systems for climate resiliency through development of an ideotype toolbox for breeders. Novel germplasm and molecular markers stemming from this project will be available for this PhD project.
Supervisory panel: Prof Julia Davies (Univ. Cambridge), Prof Lee Hickey (Univ. Queensland); Dr Steve Rawsthorne (Morley Foundation); Dr Anyela Camargo-Rodriguez (NIAB)
 

 

About NIAB

Historically the National Institute of Agricultural Botany, NIAB’s central research objective is to bridge the gap between the fundamental understanding of plant biology and our ability to apply that knowledge in practice. NIAB is affiliated with the University of Cambridge, and works closely with researchers in a number of areas, including the new joint Crop Science Centre. For individuals desiring not only to learn but to make an impact, this is a vibrant and exciting place to conduct a PhD.
 
 
 

References

 
 
 
 
 
 
 
 
 
 

Application Deadline

This project is now closed for applications

Supervisors

Dr Eric Ober, NIAB

Professor Julia Davies, Department of Plant Sciences, University of Cambridge

Supervisory panel

Professor Lee HickeyUniversity of Queensland
 
Dr Steve RawsthorneThe Morley Agriculture Foundation