Delivering Genetic Gain in Wheat (DGGW)

Project Overview

The Delivering Genetic Gain in Wheat (DGGW) project, launched in 2016, was a global initiative led by Cornell University to develop new varieties of wheat with improved agronomic traits, climate resilience and disease resistance so that smallholder farmers, especially in East Africa and South Asia, can improve their livelihoods and food security. The collaborative effort — coordinated by the Borlaug Global Rust Initiative at Cornell’s College of Agriculture and Life Sciences — grew and strengthened the international community of wheat scientists and farmers committed to improving the disease resistance of wheat.

Among its achievements, the project upgraded technical capacity and infrastructure in national wheat research centers; created one of the world’s first and most digitally robust crop surveillance and monitoring networks; boosted the capacity of wheat screening nurseries in Mexico, Africa and Asia; increased the number and visibility of women wheat scientists around the world; and created numerous training opportunities for early-career male and female wheat scientists.

The success of DGGW built on the Durable Rust Resistance in Wheat (DRRW) project funded from 2008 to 2016 by the Gates Foundation over two grant phases. DRRW was managed by Cornell University with 24 sub-grantees and an approximate investment of $8 million annually, of which $3 million annually was provided by UK aid from the British people through the Foreign, Commonwealth and Development Office.

At the start of the DRRW project, an estimated 80% of the world’s cultivated wheat was susceptible to epidemic yield losses from a highly virulent stem rust fungus called Ug99, spreading out of East Africa. This threat galvanized a collaborative global response coordinated by the BGRI at Cornell University to protect wheat production. To respond to the challenge, the BGRI was especially focused on smallholder farmers in East Africa and South Asia where dependence on wheat is high, food insecurity is critical, and the risk of rust is greatest.

The Delivering Genetic Gain in Wheat project (2016-2021) focused on strengthening the pipeline for delivering new varieties of wheat with disease resistance for all rusts (stem, stripe and leaf), septoria and spot blotch and improved heat tolerance, and increasing wheat yields for smallholder farmers in Ethiopia and South Asia. The DGGW supported increased rates of genetic gain for wheat by investing in modernized breeding programs at CIMMYT and national programs in East Africa and South Asia, incorporating guidance from a review of the CIMMYT wheat program utilizing a Breeding Program Diagnostic Tool (BPDT) provided by the Bill & Melinda Gates Foundation.

To maintain and increase the annual rates of genetic gains, the DGGW engaged in more targeted crossings, rapid cycling of segregating populations through two-generations-per-year field selection for spring bread and durum wheat, single seed descent method for winter/facultative wheat, application of molecular markers, and new approaches in conjunction with testing of larger number of progenies for yield performance, and precise characterization at phenotyping platforms for key traits.

The approach was divided into nine objectives, with a strong emphasis on gender awareness and long-term sustainability throughout all of them.

Advocacy

Scope and Approach:
Working together with CIMMYT and stakeholders at targeted National Agricultural Research Systems (NARS), the Advocacy objective aims to secure additional funding for durable wheat and create communication and advocacy infrastructures that will sustain the wheat research and development community of scientists and would-be beneficiaries beyond the duration of this four-year grant. Creating stable funding sources will help CIMMYT develop and sustain its position as the world leader of wheat initiatives for global food security. Communications networks will: enable scientists to track and monitor diseases and develop disease-resistant and climate-smart varieties of wheat; provide farmers with information to replace non-durable varieties of wheat with more durable varieties; inform the entire wheat community about emerging threats, whether biotic or abiotic; build the case for continued investment in wheat research. Activities will include: coordinating communications among multiple international wheat organizations, providing communication and advocacy training for young wheat scientists, and interacting with wheat scientists, farmers, and potential donors.

Goals:

  • Facilitate communication of DGGW project outputs to internal and external audiences, particularly in regard to CIMMYT’s activities increasing genetic gains in global wheat yields.
  • Facilitate communication of DGGW project outputs to internal and external audiences, particularly in regard to global wheat partners’ activities to increase genetic gains in wheat yields. Promote stories in B&MGF and DFID networks.
  • Support communication among the wheat community, NARS, and other stakeholders with BGRI website, blogs and newsletter.
  • Strengthen and expand global wheat community among individuals and organizations internally and externally.
  • Enhance and integrate communication infrastructures in Ethiopia and other target areas for rapid dissemination of information regarding possible outbreaks, disease hotspots, etc. to relevant stakeholders.

Objective Leader:
Linda McCandless, Cornell University

Surveillance

Scope and Approach:

The project would give priority to surveillance activities that maintain and improve established and successful core surveillance platforms for stem rust, with some inclusion of stripe rust. They would include: 1) maintaining and enhancing the information platform and core databases for tracking and monitoring wheat rust diseases; 2) delivering accurate and timely information on wheat rust diseases; 3) Expanding and enhancing national capacity to undertake disease surveillance; 4) completing targeted barberry surveillance in Ethiopia and Kenya; 5) characterizing pathogens through traditional race analyses in Ethiopian national laboratories and backstopped by ARIs; 6) Enhancing stem, yellow and leaf rust race analysis in Ethiopia; and 7) Expanding the use of molecular diagnostic tools. The project also would provide advanced warning of vulnerability to emerging rust races through enhanced host surveillance and linking breeding with pathology with an improved resistance knowledge base for released cultivars and advanced breeding materials. 

Activities: 

Activities would include:

  • maintaining and enhancing the information platform and core databases for tracking and monitoring wheat rust diseases;
  • delivering accurate and timely information on wheat rust diseases;
  • characterizing pathogens through traditional race analyses in Ethiopian national laboratories and backstopped by ARIs;
  • expanding the use of molecular diagnostics and genotyping of stem rust in East Africa;
  • determining host resistance of commercial cultivars and advanced lines;
  • developing a vulnerability assessment tool.

More support will be required to address areas identified as priority gaps and national priorities from the previous DRRW project as well as to sustain the systems in place. Those key activities would include:

  • expanding the existing surveillance and monitoring system to include other high priority wheat diseases (i.e., stripe rust, leaf rust, Septoria and spot blotch);
  • expanding and enhancing national capacity to undertake disease surveillance and monitoring in East Africa and South Asia;
  • completing targeted barberry surveillance in East Africa and South Asia;
  • expanding the use of molecular diagnostics and genotyping of stem, stripe and leaf rust in East Africa and South Asia;
  • enhancing host resistance determination and new marker development;
  • conducting a feasibility study on the use of remote sensing for disease monitoring.

The project also would develop an advanced wheat rust early warning and forecasting system, using Ethiopia as a test case. Associated activities would be the development of a robust modeling and forecasting toolbox, development of a seasonal forecast system, establishment of an in-country central early warning/control unit, and messaging and capacity building for extension agents and farmers. Several activities are potentially appropriate for innovative funding approaches:

  • advanced international training in stem and stripe rust race analysis, whereby participants would only qualify for selection based on demonstrated performance and commitment (e.g., sending viable samples and isolating rusts in national labs);
  • strengthening the ICARDA Regional Rust Laboratory, Izmir, if operational race analysis and receipt of regional rust samples was demonstrated;
  • completion of a pilot study on the use of remote sensing for disease detection, if the remote sensing feasibility study indicated viable methods and approaches.

Goals:

  • Important wheat diseases tracked and monitored, critical information provided for disease control through a functional Key Wheat Disease Surveillance & Monitoring System
  • Advanced warning of vulnerability to emerging rust races through enhanced host surveillance and linking breeding with pathology

Objective Leader:
Dave Hodson, CIMMYT

Breeding Pipeline

Scope and Approach:
The breeding activities are central to providing the genetic gain in wheat that the Delivering Genetic Gain in Wheat project proposes. Breeding activities will be a targeted crossing program to combine targeted traits and genes and the selection of the best individuals from the segregating populations, through field phenotyping and application of molecular markers. Shuttle breeding between different field sites will achieve two generations per year for capturing targeted traits as well as enhancing the wide adaptation of resulting lines.

International yield trials and nurseries will be distributed to national partners for global performance testing and utilization in breeding and release as new superior varieties. Targeted breeding to develop high-yielding spring wheat germplasm by utilizing a Mexico-Kenya shuttle-breeding scheme.

This activity has been very successful in incorporating stem rust resistance into CIMMYT breeding materials and identifying high yielding wheat lines that combine rust resistance with other important traits and are distributed globally as International Trials and Nurseries. A portion of the budget for durum and winter /facultative wheat activities is included in this proposal to the foundation. Data generation and sharing will be encouraged and facilitated through the utilization of an open access database and direct interaction with national partners. New tools such as an open access data management platform will be integrated into the program. The breeding program also will focus on training scientists and technical staff in Mexico as well as in target regions, with special emphasis on empowering young women staff members.

Activities:
The breeding activities are central to providing the genetic gain in wheat that the Delivering Genetic Gain in Wheat project proposes. Breeding activities will be a targeted crossing program to combine targeted traits and genes and the selection of the best individuals from the segregating populations, either through field phenotyping or application of molecular markers. Shuttle breeding between different field sites will achieve two generations per year for capturing targeted traits as well as enhancing the wide adaptation of resulting lines. International yield trials and nurseries will be distributed to national partners for global performance testing and utilization in breeding and release as new superior varieties.

Targeted breeding to develop high-yielding spring wheat germplasm by utilizing a Mexico-Kenya shuttle-breeding scheme. This activity has been very successful in incorporating stem rust resistance into CIMMYT breeding materials and identifying high yielding wheat lines that combine rust resistance to rusts and other agronomic traits and are distributed globally as International Trials and Nurseries A portion of the budget for durum wheat activities are included this proposal to the foundation.

Data generation and sharing will be encouraged and facilitated through the utilization of open access database and direct interaction with national partners. New tools such as the Breeding Management System will be integrated into the program.

The breeding program also will focus on training scientists and technical staff in Mexico as well as in target regions, with special emphasis on empowering young women staff.

Goals

  • Spring bread wheat varieties produced with annual genetic yield gains resistant/ tolerant to relevant biotic/abiotic stresses and with appropriate quality characteristics.
  • Spring durum wheat varieties produced with annual genetic yield gains, resistant/ tolerant to relevant biotic/abiotic stresses and with improved quality characteristics acceptable by the local industries.
  • Winter/facultative bread wheat varieties produced with annual genetic yield gains, resistant/ tolerant to relevant biotic/abiotic stresses and with appropriate quality

Objective Leader:
Ravi Singh, CIMMYT

Genomic Selection & High Throughput Phenotyping

Scope and Approach:
Achieving adequate levels of genetic gain for yield and all target traits is increasingly difficult, but effective strategies for implementing the new technologies of genomic selection (GS) and high-throughput phenotyping (HTP) can help predict and identify the best lines and parent combinations. The Delivering Genetic Gain in Wheat approach will: 1) develop and implement a practical prediction-based selection strategy using remote sensing, genomic, and pedigree data in order to accurately select for yield prior to yield testing where seed is limited; 2) develop and evaluate methodologies for selecting the best parent combinations from prediction data. The prediction-based selection strategy developed and implemented in the CIMMYT spring wheat breeding program will provide proof of concept and is expected to deliver greater rates of genetic gain.

Activities:
The GS and HTP objective will initiate a genomic selection and high-throughput phenotyping prediction methodology, integrating remote sensing, genomic, and pedigree data, that will be developed specifically for breeding candidates prior to yield testing where selection accuracies for yield are currently low due to smaller field plots and limited seed availability. Developing methodologies for HTP on small plot sizes and with no replication of breeding candidates will be critical. Methodologies developed will be validated using replicated yield trials data to identify a suitable HTP methodology for these early stage breeding candidates. One of the novel proposed methodologies, the Wheat Walker, is a new low-cost field mobile robot platform being developed by Dr. Joshua Peschel at the University of Illinois at Urbana-Champaign and field implemented and assessed on wheat by Dr. Michael Gore and Ph.D. Student Ms. Margaret Krause at Cornell University. Specially, the Wheat Walker is a small tactical and semi-autonomous, ground-based robotic platform with sensors capable of mapping the physical structure of a cereal canopy in situ and measuring its local climatic parameters.

Using the same set of data from the small plot HTP experiment, prediction models incorporating HTP and pedigree data will be compared with models integrating HTP and genome-wide marker data. These models will also be compared to conventional genomic and pedigree prediction models that do not incorporate HTP data. For each combination of HTP method and prediction model, prediction accuracies and cost per line will be considered to determine the expected rate of genetic gain from each scenario given a fixed budget. The methodology that maximizes genetic gain will be identified. The best selection methodology in terms of expected genetic gain assuming a fixed budget will be implemented at the F4:F5 stage. For each trait that is part of the breeding goal, general functions relating the trait value with the net merit will be identified. Using these functions, methods for optimizing cross combinations will be evaluated using simulation. The best methods will be identified for further testing.

Goals

  • Develop and validate prediction-based selection methodology integrating HTP, pedigree, and genomic data to accurately predict grain yield on vast numbers breeding lines at the pre-yield trial stage.
  • Prediction-based selection strategy developed for CIMMYT breeding program based on genetic gain assuming a fixed budget
  • Best, validated selection methodology implemented into the CIMMYT wheat improvement program

Objective Leader:
Jesse Poland, Kansas State University

Phenotyping Platforms

Scope and Approach:
This objective will increase the capacity of the Delivering Genetic Gain in Wheat project to produce reliable phenotypic data for reaction to stem rust races and other biotic and abiotic stresses to facilitate the development of improved wheat germplasm. An integrated approach will combine biotic and abiotic stress tolerances to address key wheat production constraints in target countries. Phenotyping Platforms will be established (or expanded) to generate precision data for resistance to stem and yellow rust races in Kenya and Ethiopia. Testing sites at the Kenya Agricultural and Livestock Research Organization (KALRO) in Njoro, and the Ethiopian Institute of Agriculture Research (EIAR), in Debre Zeit, are already central to the DRRW project, and benefit the entire global wheat community. Holeta, Ethiopia will serve as the screening platform for Septoria resistance.

Over 600,000 and 87,000 wheat accessions from 25 countries / institutions have been evaluated in Kenya and Ethiopia, respectively, since 2008. This massive screening effort has greatly facilitated the pre-breeding and breeding efforts of CIMMYT, ICARDA and NARS programs in developing and promoting wheat lines with resistance to rusts.

Seedling evaluation at KALRO in Kenya and Ambo in Ethiopia will facilitate gene characterization studies in breeding materials and identify new sources of resistance to incorporate in breeding programs and deploy as durably resistant varieties.

Functional greenhouses complemented by expert staff will enable race identification and characterization studies on stem and yellow rust at KALRO in Njoro, and EIAR in the Kulumsa and Ambo research centers. This will facilitate the identification of potential new races and accelerate pre-emptive breeding efforts to develop and deploy resistant varieties in target regions.

Activities:
Activities within the phenotyping platforms will increase the capacity to produce reliable phenotypic data for stem and yellow rust, and Septoria. The data generated will be compiled and shared with collaborators, major stakeholders, and the international community and made available in an open access database.

Activities will include the use of improved greenhouses at KALRO (Njoro) and EIAR (Ambo, Kulumsa and Debre Zeit) for race characterization, seedling evaluation of breeding lines and gene postulation studies focusing on stem rust (Ambo), yellow rust (Kulumsa) and leaf rust (Debre Zeit). This activity complements field screening by testing for race specific genes and APR genes. The platforms will provide high quality phenotypic data useful in identifying new sources of resistance. Resistance will be characterized and confirmed in both bread wheat and durum wheat lines being considered for release in Kenya, Ethiopia, and at-risk countries. Survey and surveillance data will be used to identify new races, conduct preemptive breeding and inform decisions on varietal release.

In Ethiopia, activities will focus on resistance to three major biotic constraints of wheat: stem rust, yellow rust, and Septoria. The Holeta research center has been identified as a hot spot for evaluating bead wheat wheat accessions against Septoria. Activities there will facilitate screening of wheat breeding lines/accessions resistant to Septoria and the use of those lines in breeding programs and release for use by farmers. The Kulumsa research station will evaluate breeding lines and accessions identified resistant to the combined disease complex of YR/SR/Septoria. These activities will ensure development and release of high yielding wheat germplasm combining resistance to the major biotic constraints in East Africa. The partial support for the phenotyping platform in Izmir, Turkey will complement the yellow and stem rust resistance screening and pathogen characterization activities supported in Ethiopia.

Other activities will focus on training events, exchange visits to enhance the capacity of national programs, and special initiatives to provide opportunities for early career female researchers in wheat. These activities under the phenotyping platforms objective serve not only the global wheat community, but also have a direct benefit to East African and South Asian wheat growers, producers and consumers, especially in Kenya, Ethiopia, India, Nepal and Bangladesh.

Goals:

  • Stem and yellow rust resistant bread wheat accessions identified, characterized, used in breeding programs and /or released for use in farmers fields
  • Stem rust resistant durum wheat accessions identified, characterized, used in breeding programs and /or released for use in farmers fields.
  • Ethiopia positioned to conduct gene postulation studies.
  • Ethiopian farmers grow cultivars that are resistsant to disease complex consiting of stem and yellow rust and septoria tritici.
  • Phenotyping Platform operation established for septoria in Holetta (Bread wheat).

Objective Leader:
Sridhar Bhavani, CIMMYT-Kenya

Seed Multiplication

Scope and Approach:
Farmers’ ability to meet current and future demand for wheat is hampered by the slow dissemination and popularization of released varieties in South Asia and Africa. The Seed objective will address the major bottleneck between the time that elite lines are identified on an experiment station and the time that the variety is grown in farmers’ fields. Since seed multiplication usually starts only once a variety is registered, this process can take 5 to 8 years. One approach is to initiate pre-release seed multiplication at the time a breeding line is submitted for registration trials, which can shorten the period by two years. More importantly, it provides protection from rust and other diseases and enhanced yield potential to farmers two years earlier. Pre-release seed multiplication is often not done, since there is the risk a line will be dropped from registration trials due to poor performance. Another approach will be to select best (not more than 5) lines from CIMMYT and ICARDA’s international yield trials based on yield performance, general adaptation (height and maturity) and resistance to diseases for promotion in regional yield trials conducted by NARS cooperators. These lines have been already intensively tested by CIMMYT and ICARDA for yield potential, disease resistance, and end-use quality. Outstanding performance relative to local checks warrants inclusion in regional trials. This can shorten the usual testing period by 2 years since the lines skip preliminary and 1-year yield trial testing. This approach will be done initially on a line-by-line basis under consideration of urgency and feasibility in targeted countries. In South Asia an enhanced public-private seed dissemination system will reduce redundancies and gain efficiencies from a market-based approach.

Special approach will be taken for earthquake-affected districts in Nepal to replace older varieties in farmers’ fields with agronomically superior seed and rust resistant varieties, through fast track variety testing and release created by accelerated multilateral plant breeding, and delivered through optimized developing country seed sectors.

Activities:
In order to create accessibility to quality certified wheat seed to smallholder farmers in the region, the DGGW project will focus on developing a seed village model in Nepal. Activities will focus in Nepal at the Agriculture and Forestry University with the construction of a seed processing unit and the training of personnel to multiply and distribute Foundation and Breeder Seed. Under this model, AFU will engage small farmers in wheat seed multiplication and production. AFU will have access to superior wheat germplasm with traits for increased productivity and disease resistance that will be provided to the smallholder farmers for seed multiplication. The harvested seed from the farmers will be routed back to the university, where the seed will be processed in the seed-processing unit that would be funded through the DGGW project. The wheat seed after processing and treatment will be distributed to the farmers through the university extension system and also through small private seed enterprises in the region.

Goals:

  • Installation of Seed processing and seed testing unit at AFU
  • Training of personnel at AFU
  • Distribution of Foundation Seeds to network farmers to produce certified seed
    Multiplication of Breeder Seed at AFU for seed dissemination
  • Training of farmers at AFU

Objective Leader:
Sathguru

Data Management

Scope and Approach:
The scope is to integrate wheat breeding related data to the inter-operable phenotypic and genotypic databases and apply management tools that are under development/implementation in other initiatives, allowing the use of these open access data to accelerate genetic gains in (wheat) breeding programs.  The approach is to: 1) link wheat breeders with strategic partners who are developing key components of the informatics platform; 2) involve CIMMYT, ICARDA, and NARS scientists in defining user requirements and testing/validating functionality of the tools before their deployment; 3) train CIMMYT, ICARDA and NARS partners in adopting and utilizing the database and management tools (BMS and GOBII).
Activities:
Activities to integrate wheat breeding related data to the inter-operable phenotypic and genotypic databases will include 1) identify and develop management tools with the involvement of CIMMYT, ICARDA, and NARS scientists in defining user requirements and testing/validating functionality of the tools before their deployment; 2) train CIMMYT, ICARDA and NARS partners in adopting and utilizing the database and management tools; and 3) ensure sustainability of the system with the user group, including training, and pursuing independent financing.
Goals
  • Wheat database management system established and used by CIMMYT and project partners
  • System is sustained throughout project and beyond

Objective Leader:
Stefan Einarson, Cornell University

Talent Pipeline

Scope and Approach:
Training the next generation of wheat researchers, especially in the developing world, will be essential to sustaining the effort to develop durably resistant wheat varieties and making certain that resource-constrained, smallholder farmers are the beneficiaries. Though the Talent Pipeline objective, tomorrow’s researchers will gain additional training in data management, gender-awareness, interdisciplinary collaboration, resource management, communication, and leadership. The Talent Pipeline will include both hands-on and online training modules, including a PhD program in Ethiopia for Ethiopian scientists. Delivering Genetic Gain in Wheat will track the progress of these scientists and evaluate the impact of training. Because access to scientific training for early- to mid-career women is often limited, every training module will have a gender component designed to engage women scientists in the global wheat system..
Activities:
This objective will design, coordinate, and facilitate training modules and sessions with emphasis on increasing access to younger scientists in the developing world, particularly women scientists. We will track the status and progress of each scientist trained with a single database system. We will be able to measure the impact of the training as well as avoid potential overlaps. A special focus will be on retaining talent in Ethiopia, including supporting MSc students in Ethiopian universities.. MSc students will be co-mentored by DGGW scientists in Ethiopia and abroad. Additionally, support will be provided for three students from Ethiopia to obtain PhD degrees in US universities to increase the change of retaining the talent in Ethiopia, the students research will be focused on Ethiopia wheat breeding and pathology issues and field research activities will be done in the country. A surveillance training course on wheat blast will be held in Bangladesh to prepare scientists to deal with this new threat to wheat production in the SAARC region.
Goals:
  • Graduate students and early-career wheat scientists empowered to work effectively and become leaders within the project and the larger wheat community
  • Increased access to scientific training, data, and other information for early-career scientists so that individuals learn the latest techniques and bring those skills back to their home country.
  • Training videos from project affiliated trainings available online in order to increase access for scientists not able to travel
  • Improved gender representation and responsiveness among project and greater wheat community to lessen institutional barriers against gender balance.
  • Increase data management skills and open access data sharing awareness and practice in wheat community
  • Integrate all identified scientists from Talent Pipeline objective into a single database system to better measure and evaluate impact

Objective Leader:
Maricelis Acevedo. Cornell University

Project Management

Objective Leader:
Cornell University

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Project Duration

2016-2021

Funded by

Bill & Melinda Gates Foundation

UK Foreign, Commonwealth & Development Office

Project

35

Total funding (USD)

5

Duration of project (2016-2021)
Project Impact

A sample of achievements from the DGGW project

155+

Improved wheat varieties released to farmers in 11 at-risk countries

31

Early-career women scientists selected as WIT Awardees

43

Countries with geo-referenced rust survey records as part of our global wheat rust monitoring system, one of the largest and most informative operational crop disease surveillance systems in the world
Associate Director for Science

Maricelis Acevedo, Cornell University

External Project Advisory Committee

– Bill Angus, Angus Wheat, UK
– Usha Barwale Zehr, Mahyco, India
– Richard Michelmore, UC-Davis, USA
– Robert Park, University of Sydney, Australia