IWYP Call 2: Rooty-A root ideotype toolbox to support improved wheat yields

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Genetics and Breeding

Abstract

This project assembles a world-class team of leaders in root research and wheat genetic improvement from seven institutes and five breeding companies, and brings this expertise into the IWYP programme. Our goal of optimising root systems is a critical component of the overarching IWYP aim of raising yield potential: higher yielding crops developed through IWYP will most likely demand more water and nutrients to support those yields, and roots must supply these in an efficient manner without draining any more carbon away from grain formation than is necessary to provide this function. The project builds on state-of-the-art developments in wheat genomic tools, germplasm resources, 'Speed Breeding', physiological and genetic understanding of root growth/development, high-throughput root phenotyping methods and the creation of novel genetic variation ready for exploitation. We establish a pipeline to validate the impact of root ideotype on yield, based on the use of: (1) recently cloned genes, (2) known QTL, and (3) de novo natural and artificial allele discovery. This pipeline provides staggered delivery of validated root ideotypes that will feed the breeding activities carried out by the IWYP Hub, participating breeding companies, and wider wheat breeding networks. By focusing on the often ignored 'invisible half' of the crop, this approach complements IWYP work on above ground traits, ultimately providing the knowledge and resources to allow above and below ground approaches to be combined in the future to maximise yield genetic gains.

Technical Summary

Rooty is a multidisciplinary project with 6 workpackages:

WP1-Fast track stacking of cloned root angle gene and known QTLs into elite CIMMYT, EU and Australian wheat germplasm
WP2-Exploiting novel genetic variation for beneficial root phenotypes via TILLING
WP3-Genome editing to create novel variation for deep, narrow root systems
WP4-Genetic characterisation of novel root architecture genes
WP5-Testing yield x root trait interactions using lines with high yield potential
WP6-Field validation of root phenotypes and yield

The project will establish a pipeline of materials and knowledge that allow root architecture alleles/allelic combinations to be precisely assessed for root architecture and its impact on yield in elite genetic backgrounds adapted to three broad wheat growing regions: countries within CIMMYT's remit; Australia; NW Europe (focussed on winter wheat). The research pipeline (WPs 1 to 5), serving the validation phase (WP6), is organised into four overarching Tiers, providing a framework for continued research and translation post-project:

Tier 1-Cloned wheat root genes and well-characterised QTL.
Tier 2-Characterisation of novel alleles: artificial variants. Includes allele discovery/creation via TILLING and genome editing.
Tier 3-Characterisation of novel alleles: natural variants. Allele discovery via forward genetic screens of mapping populations created from genetically diverse wheat germplasm.
Tier 4-Forward scanning for sources of novel root architecture alleles/phenotypic diversity.

Work is predominantly focused on near-term validation (Tier 1), but reflects the increasing timescales of mid- (Tiers 2 and 3) and long-term (Tier 4) validation objectives. Accordingly, this project will provide the IWYP Hub, partner breeding companies, and the wider wheat breeding community with a phased release of validated near isogenic material & knowledge in regionally adapted genetic backgrounds for subsequent breeding activities.

Planned Impact

The research will benefit wheat improvement programmes in developed and developing countries because there is global interest in understanding how to optimise root systems for a range of environments. Improved root systems should increase the capture and utilisation of nutrients and water, and decrease losses of nutrients to groundwater through leaching. These factors will contribute to the sustainability of growing wheat in both high input and low input farming systems. In this project we aim to collaborate where possible with other initiatives and projects aimed at improving root systems within the CG centres and by academic groups around the world. Specifically, information on controlled environment and field phenotyping of root ideotypes to support yield potential will foster collaboration across IWYP Programme projects focussed on above-ground traits. Communication and sharing of ideas, results, markers and germplasm with other research efforts will provide mutual benefits.
The potential impact on livelihoods is extensive, as the project's pipeline of tools (e.g. molecular markers and germplasm) to improve wheat varieties is delivered to plant breeders in the public and private sector. The commercial breeding companies involved in the project sell seed for food production in many LMICs, taking advantage of large distribution networks, and their markets are not limited to Europe and North America. In the public sector, by using elite (high yielding) lines currently used by CIMMYT breeders in Mexico and Turkey as recurrent parents for the proposed backcrossing programme, the resulting lines produced in the project should feed directly into their variety improvement programmes.

Publications

10 25 50
 
Description Genomic regions that control root architectural traits, such as seminal root angle and seedling root biomass have been discovered in bread wheat and durum (pasta) wheat by the project team members. Using a combination of these molecular markers to assist a backcrossing programme (MAB), these traits have been introgressed into four elite hexaploidy (bread) wheat backgrounds: two high-yielding CIMMYT lines used by breeders to make new varieties (Borlaug100 and Kingbird), and two elite Australian lines (Suntop and Mace). An effective shuttle system of KASP marker development at JLU and selections of lines carrying the marker for root biomass at UQ was established, which aided the MAB. In the same crosses, phenotypic selection for root angle was made, such that four ideotypes were selected: high and low root biomass combined with shallow and narrow root angle. This will allow testing of the hypotheses of which root traits confer yield advantages. The material is now at BC2F3 and will soon go into multiplication so that sufficient seed quantities for field trials will be produced by October 2020. Five NILs of each ideotype are slated for planting in replicated yield plots at the CIMMYT Hub in Obregon in early December, 2020.
The Julich group have built and designed an improved field phenotyping platform for obtaining soil cores and counting roots at the core break interface under blue light illumination (to increase contrast for the imaging). This system is slated to be built at Obregon for the field trials.
Exploitation Route Markers, germplasm, know-how will be disseminated to the academic and breeding communities.
Sectors Agriculture, Food and Drink

 
Description Improving root systems to support yields in unpredictable environments and poor soils of South Africa
Amount £19,828 (GBP)
Organisation Cambridge-Africa Alborada Trust 
Sector Academic/University
Country United Kingdom
Start 01/2020 
End 07/2024
 
Description South African Wheat breeding collaboration 
Organisation Sensako
Country South Africa 
Sector Private 
PI Contribution NIAB contributes expertise in root phenotyping, quantitative genetics
Collaborator Contribution Sensako contributes germplasm for testing, expertise in breeding, access to field trial sites
Impact disciplines: crop physiology, genetics, breeding, agronomy
Start Year 2020
 
Description South African Wheat breeding collaboration 
Organisation University of Stellenbosch
Country South Africa 
Sector Academic/University 
PI Contribution NIAB contributes expertise in root phenotyping, access to UK funding sources
Collaborator Contribution Stellenbosch contributes expertise in wheat genetics, agronomy, field trial sites and technical staff
Impact disciplines: crop physiology, genetics, agronomy, genetics, breeding
Start Year 2020
 
Description Testing commercial pre-breeding germplasm 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution NIAB provides data on root phenotypes and yield performance of KWS pre-breeding line
Collaborator Contribution KWS provides germplasm and knowledge/expertise in pre-breeding
Impact Results of experiments on seedling root phenotypes, root architecture and yield from field plot disciplines: genetics, breeding, crop physiology
Start Year 2019
 
Description Talk given to visitors: "Root- soil interactions for sustaining crop productivity" 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk given to a small delegation of visiting scientists from the Chinese Academy of Sciences
Year(s) Of Engagement Activity 2010,2019
 
Description Talk to Farming Group. Title: "Water stress and plant breeding-where next?" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Invited talk given to a regional farming group in the 'Arable Horizons' seminar series sponsored by Farmers Weekly magazine and Syngenta.
Year(s) Of Engagement Activity 2019
 
Description Workshop talk title: "Understanding the genetic components of deep root phenes, and developing a toolbox for breeders" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk given at the 'Deep Roots Frontiers' workshop at the University of Copenhagen
Year(s) Of Engagement Activity 2019