Breeding by the numbers
EiB Annual Report 2020-21
Photo: CIFOR
The numbers are in. And together with our CGIAR and national breeding partners, EiB is delivering real results.
Of course, breeding is about much more than numbers. But as the domain becomes increasingly data driven, numbers play a growing role. Numbers help breeders set goals, make better decisions, and measure progress. And numbers help tell stories -- stories about aspirations, results and achievements.
Find here, 27 vital numbers that drove forward CGIAR breeding over the past year, along with 10 success stories and 20 of EiB's most accessed resources.
"To battle hunger, poverty and climate change, farmers in low- and middle-income countries need a genetically diverse portfolio of continually improving crop varieties.
EiB helps breeders meet this challenge through coordinating efforts and supporting partners to modernize practices and technologies. We aim to help deliver farmers the seeds they need and will use."
Breeding needs to constantly replace currently grown varieties with new and improved ones. To achieve this, Crops to End Hunger (CtEH) funders have six requests to CGIAR breeding programs. EiB leads and supports efforts to respond to these. This report shows how EiB and partners are making progress on the following six requests, including:
Two major goals have been broadly adopted by CGIAR and NARS breeding: increased rates of genetic gain (≥1.5% p.a.) and reduced area weighted average age of varieties in farmers’ fields (<10 years).
Throughout this report, you will find evidence of processes that are beginning to transform CGIAR breeding into a cohesive program targeted toward genetic gain increases, through:
This transformation will result in crop varieties that are more likely adopted by farmers and consumers, driving down the age of varieties in farmers’ fields. This means greater impact on incomes, nutrition, gender equality, and climate adaptation.
EiB has captured some progress on this goal through its Stories of Excellence, delivered at Virtual Meeting 2020.
EiB is realizing the full potential of Crops to End Hunger (CtEH) investments by overseeing funds to help CGIAR and NARS breeding programs implement major improvements to meet the six requests from CtEH funders.
These funds are laying the groundwork for a successful transition to the One CGIAR model. 12 projects are underway with others set for implementation. Highlights include:
EiB will continue to determine where funds are most needed and oversee grants to help partners meet the six requests.
EiB’s success depends on the best technical skills and the strongest relationships. Indeed our greatest asset is our people. EiB’s expertize supports partners through five interlinked modules: Product design & management, Breeding scheme optimization, Genotyping & sequencing, Operations & phenotyping, Breeding informatics.
You will find numbers and success stories throughout this report showing how they are teaming with partners to catalyze change.
EiB’s expertise now includes a Crop Market Economist, Quantitative Genetics Specialists, and Mechanization Support Specialists for Africa. EiB teams collaborate to work across our talented partners to boost capacity for delivering CGIAR’s promised results. And partners expressed high trust in the team’s mandate, skills and expertise in an EiB partner survey. With real talent, comes real results!
Vital to EiB’s goals is making it easier for CGIAR to develop the right product for the right customers. And understanding gender-differentiated trait preferences is critical to ensuring priorities are demand-led and investment decisions are smart.
CGIAR celebrates its 50th anniversary by naming its top 50 innovations in 50 years. The G+ approach for gender-responsive breeding is among them. These tools offer an integrated, systematic and evidence-based approach for breeding new crop varieties with desirable traits.
EiB is supporting the CGIAR Research Program on Roots, Tubers and Bananas’ (RTB) Gender & Breeding Initiative (GBI) to validate the tools and deliver data to improve them. GBI are also developing a Guide to Gender Responsive Product Profile Development and a training program.
Breeding for better gender equity is a priority for EiB, and CGIAR breeding programs are including gender in product profiles through the G+ tools and other methods.
“Historically breeding programs didn’t properly consider gender, or included it late in the process,” says EiB Director Michael Quinn. “But now we are ensuring breeders develop gender responsive product profiles up-front so we know the varieties developed will be adopted.”
To better target investments, EiB and partners set out to understand the characteristics and needs of the markets in their low- and middle- income target regions. By collecting and analyzing data from CGIAR programs, national partners, and international bodies, EiB identified and described 320 ‘market segments’ across 26 crops. Each market segment reflects a unique combination of grower and consumer needs, including gender considerations.
EiB calculated the value of each market segment based on data such as number of hectares, average crop yield, and average selling price. Potential impact was then calculated using numbers of people, of people in poverty and of undernourished people in each segment.
Existing target product profiles will be updated based on this analysis. This work will allow clear metrics to be established for monitoring and reporting progress.
In order to maximize investments and impact, CGIAR needed to identify and describe all of its current breeding pipelines. Working with partners at all CGIAR Centers, EiB characterized 120 breeding pipelines in 2020.
The analysis found that not all market segments were being served by a breeding pipeline, and many breeding pipelines aligned to several market segments. The team then turned to aligning these pipelines to market segments, as not all market segments were associated with a pipeline and some pipelines were associated with multiple market segments.
“This data uncovers potential to reorient some pipelines for greater impact and efficiency,” explains EiB’s Peter Coaldrake, EiB’s Product Design and Management module lead. “As we move toward a One CGIAR model, the data puts us in a good position to make sure breeding programs can target less well-served farmers and consumers.”
CGIAR breeding efforts have a record of high ROI. EiB is enhancing that by working to ensure donor investments are targeted toward crops and regions that will show the most impact on food security, poverty reduction and nutrition. The team has begun developing pipeline investment cases that compare the current level of investment with the potential to make an impact.
The analysis looks at the level of investment per person, per person in poverty, and other breakdowns. This helps us see if the way today’s dollars are allocated are appropriate to the potential impact. Or if investments should be shifted to target one market segment over another.
Pipeline investment cases are developed based on current pipeline investment and the 12 values used to describe market segment/s served by the pipeline. These values include: total population, rural population, number of people in poverty, number undernourished, hectares, tons of production, value of production.
The work means decision-makers can look at the data by crop or region, and act to achieve the greatest impact per dollar. It sets the groundwork for breeding pipeline investment cases to become the new unit of investment in breeding.
EiB ran 45 simulations to test ways in which breeding programs can optimize their activities. In 2020, EiB partnered with the Roslin Institute, University of Edinburgh to bring computer simulations to breeding programs.
EiB's dedicated optimization team worked with breeders to map their programs and identify areas that could be improved on. Simulations were then used to predict the impact of these decisions on breeding program performance over time.
Ten CGIAR breeding programs have implemented 12 optimizations as a result of collaboration with EiB.
This includes optimizing the size of breeding programs to attain the highest performance over time, finding the best strategies to select varieties that have the most potential for farmers, or deciding whether to invest in genomic selection or hybrid breeding. Another 36 optimizations remain to be implemented by the 17 breeding programs.
The EiB breeding optimization toolbox contains 9 manuals and guidelines to manage genetic diversity, evaluate and select promising materials, and track the performance of breeding programs by calculating predicted and actual genetic gains. Libraries of breeding program simulations and software are also available for breeding programs to optimize their operations.
These were the most actively used and shared resources within the Toolbox, which saw a 55% increase in users over 2019.
EiB maintains a reliable collection of marker data for plant and fish varieties that are key to meeting UN development and sustainability goals. This data is a key resource for breeding programs and a step towards centralized genotyping services aligned with OneCGIAR.
The new Mid-density SNP Genotyping (MDSG) service has the capacity to analyze 2.4 million samples per year. The service offers a low cost (as low as $10 per sample) and highly scalable genotyping service for applications such as DNA profiling and routine genomic selection. Users can expect reliable results, fast turnaround time, zero equipment setup costs and data compatibility with various genotyping platforms.
The number of samples processed and overall business volume of the Low-density SNP Genotyping (LDSG) service is increasing at an average of 25% each year.
Contingency plans were made to ensure the robustness of the LDSG service to meet demand and maintain marker-assisted selection and genetic quality control activities in breeding programs affected by COVID-19. This meant that LDSG maintained the level of business volume required to remain a self-sustaining service with no external funding.
EiB found five new ways to increase the adoption of shared genotyping services:
EiB assesses agronomic practices, seed processing, planting and harvesting, phenotyping and continuous improvement practices for partners. EiB finalized the last of these Breeding Operations and Phenotyping assessments, and several partners began implementing recommendations. For example, the EiB team finalized assessments with visits to stations, and delivered final assessment results to AfricaRice (two stations in Senegal and Ivory Coast) and Crop Research Institute (two NARS stations in Ghana).
Assessing the current capacity of CGIAR/NARS breeding operation supports centers and breeding programs helps prioritize improvements. This deep-dives into high-level recommendations developed through the Breeding Program Assessment Tool (BPAT).
Many improvements were implemented by Centers / programs based on the EiB assessments, e.g.:
EiB made progress in supporting technical initiatives for priority crops in 2020. Technical support provided by EiB to CGIAR/NARS breeding programs in 2020 included:
EiB is supporting partners to improve operations through embedding the use of the Continuous Improvement (CI) methodology in their work. The goal is to assure implementation of the breeding programs’ improvement plans. This aims to reach the operational staff as an important support component.
In 2020 EiB worked with the IRRI breeding team to create a CI system that can potentially be deployed in other CGIAR/NARS centers. This first round included some key progress:
In total, EiB trained 50 CGIAR staff in lean methodologies, and over 120 NARS staff participated in a continuous improvement webinar. With these new champions, adopting continuous Improvement could mean a cultural transformation that brings CGIAR to the next level.
EiB is providing breeding programs with equipment to help speed up and enhance the accuracy of various breeding processes including seed preparation, data collection, data analysis and inventory management. With Crops to End Hunger support, EiB acquired and organized the distribution of nearly 400 digitization devices to 24 breeding programs. These included:
This support for mechanization and technology upgrades will continue in 2021. "We want to do more to support centers to improve their operations so they can achieve the most effective and cost efficient phenotypic processes - agronomic practices, seed processing and other areas," says Operations and Phenotyping module lead Gustavo Teixeira. "We aim to expand to more programs and partners."
EiB will continue to support NARS across Africa and beyond to digitize their operations, and is working with partners to secure more equipment, training and resources. With this Digitization project, EiB has targeted 24 breeding programs in 14 countries in Africa.
In collaboration with ICRISAT, CIMMYT and CGIAR’s Big Data platform, EiB coordinated the pilot effort to deploy digital phenotyping as a service for breeding programs. The aim is to federate efforts across CGIAR centers, in the scope of an “Asia hub.” The first phase of this project started at ICRISAT-Patancheru where a wide array of CGIAR crops are currently represented. The work started with four crops before scaling up to more: maize, sorghum, chickpea, and pigeonpea.
The project has delivered:
The second phase aims to deliver a streamlined process and implementation plans for considering other crops and regions.
The Enterprise Breeding System (EBS) is available to 63 users in the CIMMYT Wheat, CIMMYT Maize, IITA Maize and IRRI Rice breeding programs. These power users and early adopters support development by providing input into the functions needed by breeders. More users and crops will be added as EBS development progresses; meanwhile, EiB is supporting breeding programs with training, data curation and integration of digitization equipment.
Over 14 million germplasm records have been curated and loaded to the EBS: 1.4 million maize, 6.6 million rice and 6 million wheat entries. This forms the basis for maize, rice and wheat breeders to start running new trials and nurseries from within the EBS. Soon, this germplasm data will be integrated with phenotypic data that is currently being loaded, enabling use cases such as easily calculating genetic gains.
The Training and Adoption (TrAiN) team has 12 active digitization specialists working across CGIAR and NARS centres to operationalise newly purchased digitization equipment within breeding workflows, and across crops and software systems (EBS, BMS, Breedbase).
The Breeding Informatics Network (BrIN) is a community of around 30 implementers that includes biometricians, quantitative geneticists, bioinformatics, the EBS Analytics Framework development team, and external partners from Bayer Crop Science, the USAID Feed the Future Innovation Lab for Crop Improvement (ILCI), Innovat, BreedBase, Breeding Insight and VSN International. BrIN creates working groups to address topics of common interest for CGIAR breeding programs, with the results being incorporated into development of the EBS software. In the future, BrIN will become a global team serving One CGIAR.
As part of EiB’s support for national breeding programs to modernize practices, EiB completed baseline assessments and developed customized improvement plans for 11 NARES breeding programs for CtEH priority crops in Africa and South Asia.
With support from Crops to End Hunger and EiB’s technical teams, partners have begun implementing improvement plans. Efforts are underway to implement product profiles (for seven breeding programs), access and apply genotyping data for quality control / quality assurance (QC/QA) and profiling of elite parents, improve program costing, adopt data management platforms and more.
For example, Kenya’s KALRO highland maize program carried out its first-ever full program costing, is expanding early stage testing, developing product profiles, digitizing operations, and switching to a double haploid breeding scheme, supported by EiB and AGG / CIMMYT MAIZE.
EiB launched resources and a new webinar series to support NARES and improve collaboration toward a One CGIAR-NARES network.
Over 300 NARES partner participants engaged in webinars on genetic gain enhancement and calculation, data management platforms, the continuous improvement methodology and more. The efforts will continue on key issues such as program costing, market segment definition, and product profile development. Webinars are open to broad audiences, but EiB also provides in-house consultancies and resources for core NARS partners to implement these best practices.
When this knowledge is applied, we can see impressive results, such as those in Ghana. The rice breeding program at CSIR have developed product profiles, identified their target market segments, costed out their program, digitized their operations, and have even deployed molecular markers for selection.
EiB and their partners co-developed a new model for CGIAR/NARES collaboration. It provides clearer definitions of roles and responsibilities in breeding, along with a network of regionally based specialists that will directly support the modernization of NARS breeding.
EiB works with 28 NARES breeding programs in 11 countries, and the model will help streamline processes and relationships across the CGIAR. Collaborations are already supporting NARES to apply genotyping services, access digitization equipment, improve knowledge about best practices, and other improvements.
CGIAR-NARES networks are complex, with crop specific challenges and myriad partners at different stages. The model will help these networks define a route to delivering sustained genetic gain in public breeding programs.
Manuals, guides and examples that describe how to put quantitative genetics principles into practice to optimize breeding schemes.
Simulations performed using the AlphaSimR software that answer important questions facing different crop breeding programs. Includes scripts and reports.
A complete pre-flight checklist for any breeding program looking to incorporate UAV phenotyping, with best practices and equipment recommendations for the capture, processing and extraction of data.
A collection of tools compiled by EiB to support adoption and mainstreaming of routine data management, field apps and molecular breeding tools.
A shared KASP genotyping platform serving all CGIAR centers and their partner program, cost-effective up to 200 markers. Suitable for QC analysis, drop-down selection, marker assisted selection and forward breeding. The markers available for use are known, validated and in use.
A shared DArTAg genotyping method primarily suited to genomic selection applications, but that can also be used for diversity studies, material fingerprinting or background recovery in marker assisted selection (MAS) to complement low-density genotyping.
