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CGIAR breeding programs need more than just tech upgrades — they need change management

Shivali Sharma (right), pre-breeding research leader at ICRISAT, explains pearl millet pollination techniques to visitors at the ICRISAT campus. (Photo: Michael Major/Crop Trust)
Shivali Sharma (right), pre-breeding research leader at ICRISAT, explains pearl millet pollination techniques to visitors at the ICRISAT campus. (Photo: Michael Major/Crop Trust)

Did you know that vehicles with steering wheels on the left are often cheaper to make than right hand-drive cars? They are mass-produced in much larger batches. But many drivers and governments were just unwilling to change to this dominant design.

We humans are not so adept at change. Instead of embracing novel ways of thinking, we’d rather stick to the old ones. We cling onto what is safe, what is familiar or what we are already good at. We see this in the workplace, in our personal lives and in society as a whole. The world still can’t agree on using the metric system!

Within the domain of plant breeding, we are both driving and responding to rapid change. It is mesmerizing to visualize the changes gene editing is about to deliver, not to mention what genomic prediction is already delivering. We are being challenged on every single aspect of plant breeding.

Change of a different sort is about to cascade through the world’s main network of agricultural research centers — which includes centers at the global forefront of plant breeding. CGIAR is embarking on a transition into a much more integrated One CGIAR organization.

An overarching goal of this integration is no other than to ensure breeding improvement plans — and the changes they aim to drive — are implemented as seamlessly and quickly as possible. The Excellence in Breeding Platform is both driving and supporting this change among CGIAR centers and international and national partners.

The case for change in plant breeding programs

Plant breeders are in fact missing some vital opportunities. For example, there continues to be a rather limited use of real market insights to inform resource allocation within programs. This in turn results in a selection of traits weighted towards what breeders and associated scientists think are needed, which may not necessarily meet actual market needs.

With new goals and structures foisting change on breeding programs, their success depends on one thing above all else: savvy change management. Fortunately, there are some steps we can take to manage change well.

1. Drive out complacency with a sense of urgency

Most change management efforts fail when insufficient urgency is built early enough in the process. But this urgency can be the most effective antidote against complacency. Organizations that have either secured a very dominant and successful position in the market, or lack effective and threatening competition, can very easily slide into a sense of self-righteousness and an inward-looking perspective.

Although CGIAR breeding efforts could be thought of as an example of the latter — lacking competitors — seasoned managers in industry and marketing like to think that “there is no such thing as a lack of competition.” Funding, for one, is by nature a competition. Funding agencies might look at other fields and/or players to support if they deliver a higher return on investment, not only financially but also socially.

The impact of high complacency cultures can be seen in plant breeding. For instance, a rather large number of breeding programs still lack a high enough rate of what is called “elite x elite crosses.” Unless breeding pipelines run on such crosses, they achieve less than optimal genetic gains and delivery at the field. And donors get a lesser return on investment. Moreover, this complacency means not delivering the best varieties smallholder farmers need to support their families.

The parable of the slowly boiling frog is oftentimes used to portray the consequences of complacency. In any complacency-filled organization, no matter how intelligent, educated and well-intentioned its members are, change is often dead on arrival.

You may already have an inkling of what it takes to create enough urgency: bold and sometimes risk-taking leadership. For instance, some years ago, Unilever was one of the first global companies to decouple its financial growth from its environmental footprint, and it established the then outrageous sounding goal of halving its environmental footprint by 2030.

A good urgency-raising example that could inspire our line of work may be this one: let’s renew at least 50% of a current portfolio of cultivars within the next five years in a given Target Population of Environments (TPE). A second could be: let’s deploy sparse testing in at least 90% of field trials within six months.

To create urgency we need to articulate the gap between opportunities available, and the current ability of the organization to pursue such opportunities. But we must also spell out — upfront — the risks if we don’t bridge such a gap.

2. Build a guiding coalition

These days, driving change is too complex to be led by single individuals. We live in fast-paced times. And situations are full of evident and not-so-evident links among myriad moving pieces. We cannot expect one individual to be able to gather enough information fast enough, and then to consistently make the right decisions. Instead, a guiding coalition is needed, with sufficient determination, commitment and thought diversity. Such coalitions require five traits: a position of power, credibility, leadership, expertise, and individual egos held at bay. Once such teams are assembled, the main drivers of success are having a common goal, and enough trust and safety so the real issues are unearthed and addressed.

3. Develop a vision and a strategy

When leadership tries to drive change by applying dated approaches such as micromanagement or an authoritarian stance, plans are likely to fail upon arrival. These methods may breed compliance, but certainly not a fierce and sincere commitment. Because of the extreme uncertainty and organizational survival being at stake, crafting a vision plays a bigger role during change management than during business as usual.

Two main aspects of developing a vision are especially relevant to CGIAR breeding programs.

Firstly, academic and R&D organizations often keep doing what has worked well in the past. But any change management effort ought to be very explicit about what it is known as “strategic dismissal.” This is the ability to stop and phase out activities no longer providing enough value, or where the outcomes of which are not wanted/needed by funding agencies or beneficiaries. For instance, programs investing in developing hybrid cultivars for the first time in a crop could downsize previous cultivar development efforts. Alternatively, they could scale down efforts in countries that have their own strong local breeding programs. These changes are no small feat, but the inability to phase out activities clashes with the very first posit of any effective strategy: don’t just “keep doing.”

Secondly, a vision provides an invisible fabric that pulls all efforts together in a cohesive way. Therefore, its scope is much wider than most people realize, stretching across strategies, plans, and the budgets and means needed to exert change at the depth and speed needed.

4. Encourage constructive confrontation

One characteristic of a complacent organization stands out: a rather low-candor, low-confrontation culture. No one needs excessively high-confrontation, “take no prisoners”, toxic cultures. But low-confrontation cultures tend to breed under-performance, status quo maintenance and deeply ingrained complacency. And perhaps the most negative consequence is that they fail to instill a strong enough sense of ownership and accountability among its members.

Change is coming (it has arrived already…)

Yes, change is hard, but it is coming. Maybe not for drivers of right-hand drive cars. But certainly for those who want to modernize and optimize their breeding programs. Now is the time for us to invest in a smart and forward-looking change management processes.

Hugo Campos is the Chair of the CGIAR Excellence in Breeding (EiB) Platform Steering Committee and Director of Research for the International Potato Center (CIP). This blog was developed with support from EiB’s communications lead Adam Hunt.This is the second in a series of blogs on change in the breeding domain. See the first.

East Africa partners welcome “new era” in wheat breeding collaboration

Representatives from ministries of agriculture and national agricultural research systems (NARS) in Ethiopia and Kenya recently joined funder representatives and technical experts from the International Maize and Wheat Improvement Center (CIMMYT) to renew a long-standing collaboration under the auspices of an ambitious new project, Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG).

AGG is a 5-year project that brings together partners in the global science community and in national agricultural research and extension systems to accelerate the development of higher-yielding varieties of maize and wheat — two of the world’s most important staple crops. Funded by the Bill & Melinda Gates Foundation, the UK Foreign, Commonwealth, and Development Office (FCDO), the U.S. Agency for International Development (USAID) and the Foundation for Food and Agriculture Research (FFAR), AGG fuses innovative methods that improve breeding efficiency and precision to produce varieties that are climate-resilient, pest- and disease-resistant, highly nutritious, and targeted to farmers’ specific needs.

Ethiopia and Kenya: CIMMYT’s longstanding partners

The inception meeting for the wheat component of AGG in East Africa drew more than 70 stakeholders from Ethiopia and Kenya: the region’s primary target countries for wheat breeding. These two countries have long-standing relationships with CIMMYT that continue to deliver important impacts. Ninety percent of all wheat in Ethiopia is derived from CIMMYT varieties, and CIMMYT is a key supporter of the Ethiopian government’s goal for wheat self-sufficiency. Kenya has worked with CIMMYT for more than 40 years, and hosts the world’s biggest screening facilities for wheat rust diseases, with up to 40,000 accessions tested each year.

AGG builds on these successes and on the foundations built by previous projects, notably Delivering Genetic Gain in Wheat, led by Cornell University. The wheat component of AGG works in parallel with a USAID-funded “zinc mainstreaming” project, meeting the demand for increased nutritional quality as well as yield and resilience.

CIMMYT Director General Martin Kropff gave key remarks at the stakeholder gathering, which took place Thursday, August 20.

“Cooperation between CIMMYT and Ethiopia and Kenya – as in all the countries where CIMMYT works – has had tremendous impact,” he said. “We are proud, not for ourselves, but for the people we work for: the hundreds of millions of poor people and smallholders who rely on wheat and maize for their daily food and incomes.”

“AGG will raise this spirit of global cooperation to a new level.”

AGG Project Leader and CIMMYT Interim Deputy Director General for Research Kevin Pixley introduced the new project as a “unique and important” project that challenges every stakeholder to grow.

“What we would like to achieve is a step change for all of us, he told the stakeholders. “Each of us has the opportunity and the challenge to make a difference and that’s what we’re striving to do.”

Representatives from the agricultural research communities of both target countries emphasized the significance of their long collaboration with CIMMYT and their support for the project.

The Honorable Mandefro Nigussie, Ethiopia’s State Minister of Agriculture, confirmed the ongoing achievements of CIMMYT collaboration in his country.

“Our partnership with CIMMYT […] has yielded several improved varieties that increased productivity twofold over the last 20 years. He referred to Ethiopia’s campaign to achieve self-sufficiency in wheat. “AGG will make an immense contribution to this. The immediate and intermediate results can help achieve the country’s ambitious targets.”

A holistic and gender-informed approach

Deputy Director of Crops at the Kenya Agriculture and Livestock Organization (KALRO) Felister Makini, representing the KALRO Director General Eliud Kireger, noted the project’s strong emphasis on gender-intentional variety development and gender-informed analysis to ensure female farmers have access to varieties that meet their needs and the information to successfully adopt them.

“The goal of this new project will indeed address KALRO’s objective of enhancing food security and nutrition in Kenya,” she said. “This is because AGG not only brings together wheat breeding and optimization tools and technologies, but also considers gender and socioeconomic insights, which will be pivotal to our envisaged strategy to achieve socioeconomic change.”

Funding partners keen for AGG to address future threats

Before CIMMYT wheat experts took the virtual floor to describe specific workplans and opportunities for partner involvement, a number of funder representatives shared candid and inspiring thoughts.

“We are interested in delivery,” said Alan Tollervey of FCDO, formerly the UK Department for International Development. “That is why we support AGG, because it is about streamlining and modernizing the delivery of products […] directly relevant to both the immediate demands of poor farmers in developing countries and the global demand for food – but also addressing the future threats that we see coming.”

Hailu Wordofa, Agricultural Technology Specialist at the Bureau for Resilience and Food Security at USAID highlighted the importance of global partnerships for past success and reiterated the ambitious targets of the current project.

“We expect to see genetic gains increase and varieties […] replaced by farmer-preferred varieties,” he reminded stakeholders. “To make this happen, we expect CIMMYT’s global breeding program to use optimal breeding approaches and develop strong and truly collaborative relationships with NARS partners throughout the entire process.”

“Wheat continues to be a critical staple crop for global food security and supporting CIMMYT’s wheat breeding program remains a high priority for USAID,” he assured the attendees.

He also expressed hope that AGG would collaborate other projects working in parallel, including the Feed the Future Innovation Lab for Applied Wheat Genomics at Kansas State University, and the International Wheat Yield Partnership.

FFAR Scientific Program Director Jeff Rosichan called AGG a “really ambitious project that takes a comprehensive look at the research gaps and challenges and how to translate that research into farmers’ fields.”

Agriculture prevails even under COVID-19

The global COVID-19 pandemic was not ignored as one of several challenges during this time of change and transition.

“As we speak today, despite the challenge that we have with the COVID-19, I am proud to say that work on the nurseries is on-going. We are able to apply [our] skills and deliver world-class science,” said Godwin Macharia, center director at KALRO-Njoro.

“This COVID-19 pandemic has shown us that there is a great need globally to focus on food equity. I think this project allows that to happen,” said Jeff Rosichan from FFAR.

Transformations are also happening at the research organization and funding level. CIMMYT Director General Martin Kropff noted that “demand-driven solutions” for “affordable, efficient and healthy diets produced within planetary boundaries” are an important part of the strategy for One CGIAR, the ongoing transformation of CGIAR, the world’s largest public research network on food systems, of which CIMMYT is a member.

Hans Braun, director of CIMMYT’s Global Wheat Program reminded attendees that, despite these changes, one important fact remains. “The demand for wheat will continue to grow for many years to come, and we must meet it.”

Cover photo: Harvesting golden spikes of wheat in Ethiopia. (Photo: Peter Lowe/CIMMYT)

Massive-scale genomic study reveals wheat diversity for crop improvement

A new study analyzing the diversity of almost 80,000 wheat accessions reveals consequences and opportunities of selection footprints. (Photo: Eleusis Llanderal/CIMMYT)
A new study analyzing the diversity of almost 80,000 wheat accessions reveals consequences and opportunities of selection footprints. (Photo: Keith Ewing)

Researchers working on the Seeds of Discovery (SeeD) initiative, which aims to facilitate the effective use of genetic diversity of maize and wheat, have genetically characterized 79,191 samples of wheat from the germplasm banks of the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA).

The findings of the study published today in Nature Communications are described as “a massive-scale genotyping and diversity analysis” of the two types of wheat grown globally — bread and pasta wheat — and of 27 known wild species.

Wheat is the most widely grown crop globally, with an annual production exceeding 600 million tons. Approximately 95% of the grain produced corresponds to bread wheat and the remaining 5% to durum or pasta wheat.

The main objective of the study was to characterize the genetic diversity of CIMMYT and ICARDA’s internationally available collections, which are considered the largest in the world. The researchers aimed to understand this diversity by mapping genetic variants to identify useful genes for wheat breeding.

From germplasm bank to breadbasket

The results show distinct biological groupings within bread wheats and suggest that a large proportion of the genetic diversity present in landraces has not been used to develop new high-yielding, resilient and nutritious varieties.

“The analysis of the bread wheat accessions reveals that relatively little of the diversity available in the landraces has been used in modern breeding, and this offers an opportunity to find untapped valuable variation for the development of new varieties from these landraces”, said Carolina Sansaloni, high-throughput genotyping and sequencing specialist at CIMMYT, who led the research team.

The study also found that the genetic diversity of pasta wheat is better represented in the modern varieties, with the exception of a subgroup of samples from Ethiopia.

The researchers mapped the genomic data obtained from the genotyping of the wheat samples to pinpoint the physical and genetic positions of molecular markers associated with characteristics that are present in both types of wheat and in the crop’s wild relatives.

According to Sansaloni, on average, 72% of the markers obtained are uniquely placed on three molecular reference maps and around half of these are in interesting regions with genes that control specific characteristics of value to breeders, farmers and consumers, such as heat and drought tolerance, yield potential and protein content.

Open access

The data, analysis and visualization tools of the study are freely available to the scientific community for advancing wheat research and breeding worldwide.

“These resources should be useful in gene discovery, cloning, marker development, genomic prediction or selection, marker-assisted selection, genome wide association studies and other applications,” Sansaloni said.


Read the study:

Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints.

Interview opportunities:

Carolina Sansaloni, High-throughput genotyping and sequencing specialist, CIMMYT.

Kevin Pixley, Genetic Resources Program Director, CIMMYT.

For more information, or to arrange interviews, contact the media team:

Ricardo Curiel, Communications Officer, CIMMYT. r.curiel@cgiar.org

Rodrigo Ordóñez, Communications Manager, CIMMYT. r.ordonez@cgiar.org

Acknowledgements:

The study was part of the SeeD and MasAgro projects and the CGIAR Research Program on Wheat (WHEAT), with the support of Mexico’s Secretariat of Agriculture and Rural Development (SADER), the United Kingdom’s Biotechnology and Biological Sciences Research Council (BBSRC), and CGIAR Trust Fund Contributors. Research and analysis was conducted in collaboration with the National Institute of Agricultural Botany (NIAB) and the James Hutton Institute (JHI).

About CIMMYT:

The International Maize and What Improvement Center (CIMMYT) is the global leader in publicly-funded maize and wheat research and related farming systems. Headquartered near Mexico City, CIMMYT works with hundreds of partners throughout the developing world to sustainably increase the productivity of maize and wheat cropping systems, thus improving global food security and reducing poverty. CIMMYT is a member of the CGIAR System and leads the CGIAR programs on Maize and Wheat and the Excellence in Breeding Platform. The Center receives support from national governments, foundations, development banks and other public and private agencies. For more information visit staging.cimmyt.org.

Breaking Ground: Yoseph Beyene breeds desirable maize varieties for smallholder farmers in sub-Saharan Africa

About 25 years ago, Yoseph Beyene first heard about the International Maize and Wheat Improvement Center (CIMMYT) from one of his professors, back when he was pursuing his undergraduate degree in Plant Science at Haramaya University in Ethiopia. “The professor, whom I regard as a great mentor, (…) always told me that if I ever got an opportunity to work at CIMMYT, I should not hesitate to take it up, as it was a great place to conduct maize breeding,” recollects Beyene, now a maize breeder at CIMMYT. He grew up in Alem Ketema, a village located 190 km north of Addis Ababa, Ethiopia’s capital.

In retrospect, he did not know this would change his perspective on how he viewed crops, especially maize, on smallholder farms. Like many other families in Alem Ketema, his family attended to their small farm to meet their food and nutritional needs. Most people practiced subsistence farming, intertwined with livestock keeping, on small plots that were typically less than 2 hectares. At the backyard of his family’s farm, different crops such as maize, sorghum and teff were grown. As a child, he never quite registered in his mind that farmers grew mainly recycled seed. “In hindsight, I can say that the yield of a crop such as maize was just about 1.5 tons per hectare at the time,” he reckons.

Such low yield potential meant feeding relatively large family sizes of about seven people was a tall order. It did not help that crops such as maize and wheat were frequently affected by diseases and pests and erratic rains, which diminished yields. It was not until his high school days when he had firsthand experience with high-yielding improved crop varieties. As part of the farm management class, he actively participated in the school’s farm management unit. He got to appreciate the yield variation between improved and local varieties, grown on the school plots. These improved seed, he quickly realized, were the ideal antidote to the low yield farmers obtained. 

Struck by an epiphany

“This was like a eureka moment for me. When I realized that it was possible to improve and deliver desirable seed varieties that could double farmers’ yields, I decided to study plant breeding at the university. If only the farmers back in my village knew about the improved seed and adopted them at the time, it could not only have helped solve the problems of food insecurity but also bettered their livelihoods,” he ponders.

When he enrolled for a PhD in Plant Breeding and Genetics at the University of Pretoria, he did his research in highland maize in collaboration with CIMMYT in Ethiopia. Upon completion, he was appointed as a senior cotton breeder at South Africa’s Agricultural Research Council (ARC), where he worked for one and a half years.

“One day, I saw an advertisement in which CIMMYT was looking for a maize breeder. I applied, went for the interview and was happy to get the position. That was in 2008,” he says.

The right tool for the right variety

Biotic and abiotic stresses are becoming more frequent and vicious because of climate change and there is growing urgency to tackle them to avert future potential food crises.

Beyene’s current research focuses on developing high-yielding and climate-resilient maize inbred lines and hybrids for sub-Saharan Africa. He uses  conventional and molecular breeding, including integration of novel tools and techniques, such as doubled haploid, and marker-assisted recurrent section and genomic selection. Over the years, he has developed at least 25 new drought-tolerant maize hybrids recommended for commercialization in Kenya, Mozambique, Uganda, South Africa and Tanzania. Currently, 23 seed companies have been engaged to produce and market the released hybrids through sub-licensing.

Presently, as the Regional Breeding Coordinator for Africa, he is responsible for assessing the progress of implementing product profile-based breeding, appropriate germplasm exchange within and across regional breeding hubs, and ascertaining the progress on new initiatives by regional breeding teams.

A long-term endeavor

Breeding is a costly, time consuming and complex exercise. “It takes at least 10 years from crossing to release using pedigree breeding because the hybrids should be evaluated in multiple years and tested in multiple locations, which increases costs and time of the breeding cycle. You have to appreciate the fact that you are not breeding for now but for the future,” he says.

“As a breeder, you have to keep testing new tools and techniques to make breeding more efficient. Yet, resources are not always constant but inadequate. Stresses are becoming more urgent and vicious, despite increased urgency in tackling them to avert a potential food crises,” he says.

To reduce the time and accelerate genetic gains, Beyene and his colleagues at CIMMYT are currently applying the genomic selection technique for maize breeding, using it to predict the performance of un-phenotyped genotypes at early stage of testing. He and his colleagues recently published their research comparing genomic selection with phenotypic selection, as used by CIMMYT’s maize breeding program in sub-Saharan Africa. They found that the use of genomic selection for yield under optimum and drought conditions in tropical maize can produce selection candidates with similar performance as those generated from conventional phenotypic selection, but at a lower cost. They concluded that this strategy should be effectively incorporated into maize breeding pipelines to enhance breeding program efficiency.

Breeding challenges notwithstanding, Beyene feels fulfilled whenever he sees a farmer has planted a variety that he helped breed. “The epitome of my inspiration is when there is a smile on their face because of the variety’s good performance on their farm,” he says.

Interacting with the farmers and seed companies provides an opportunity for him to learn, understand their varietal preferences as well as appreciate the impact that his work has on their operations. He is also actively engaged in building the capcity of public and private partners, and supervising master’s and doctoral students from various countries. He has published more than 50 articles in journals.

The life of a breeder is not as lonely and boring as some would think. Beyene creates time to be with his three children, playing with them and helping with their homework, taking them out for social events. He also dedicates time to watch football, reality television, comedy and drama with his family.

In the best possible taste

The pursuit for higher and more stable yields, alongside better stress tolerance, has dominated maize breeding in Africa for a long time. Such attributes have been, and still are, essential in safeguarding the food security and livelihoods of smallholder farmers. However, other essential traits have not been the main priority of breeding strategies: how a variety tastes when cooked, its smell, its texture or its appearance.

They are now gradually coming into the mainstream of maize breeding. Researchers are exploring the sensory characteristics consumers prefer and identifying the varieties under development which have the desired qualities. Breeders may then choose to incorporate specific traits that farmers or consumers value in future breeding work. This research is also helping to accelerate varietal turnover in the last mile, as farmers have additional reasons to adopt newer varieties.

In the last five years, the International Maize and Wheat Improvement Center (CIMMYT) has been conducting participatory variety evaluations across East Africa. First, researchers invited farmers and purchasers of improved seed in specific agro-ecologies to visit demonstration plots and share their preferences for plant traits they would like to grow in their own farms.

In 2019 and 2020, researchers also started to facilitate evaluations of the sensory aspects of varieties.

Fresh samples of green maize, from early- to late-maturing maize varieties, were boiled and roasted. Then, people assessed their taste and other qualities. The first evaluations of this kind were conducted in Kenya and Uganda in August and September 2019, and another exercise in Kenya’s Machakos County took place in January 2020.

Similar evaluations have looked at the sensory qualities of maize flour. In March 2020, up to 300 farmers in Kenya’s Kakamega County participated in an evaluation of ugali, or maize flour porridge. Participants assessed a wider range of factors, including the aroma, appearance, taste, texture on the hand, texture in the mouth and overall impression. After tasting each variety, they indicated how likely they would be to buy it.

Participants were asked to rate the texture of different maize varieties, cooked as ugali, at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Participants were asked to rate the texture of different maize varieties, cooked as ugali, at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Participants were asked to rate the smell of different maize varieties, cooked as ugali, at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Participants were asked to rate the smell of different maize varieties, cooked as ugali, at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Ugali made with different maize varieties is served to participants of a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Participants taste ugali at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Cooks prepare ugali, or maize flour porridge, with different maize varieties at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Cooks prepare ugali, or maize flour porridge, with different maize varieties at a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
At a sensory evaluation in Kakamega County, Kenya, different types of ugali were cooked using maize flour from several varieties. (Photo: Joshua Masinde/CIMMYT)
At a sensory evaluation in Kakamega County, Kenya, different types of ugali were cooked using maize flour from several varieties. (Photo: Joshua Masinde/CIMMYT)
Ugali made with different maize varieties is served to participants of a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)
Ugali made with different maize varieties is served to participants of a sensory evaluation in Kakamega County, Kenya. (Photo: Joshua Masinde/CIMMYT)

Tastes differ

“Farmers not only consume maize in various forms but also sell the maize either at green or dry grain markets. What we initially found is green maize consumers prefer varieties that are sweet when roasted. We also noted that seed companies were including the sensory characteristics in the maize varieties’ product profiles,” explained Bernard Munyua, Research Associate with the Socioeconomics program at CIMMYT. “As breeders and socioeconomists engage more and more with farmers, consumers or end-users, it is apparent that varietal profiles for both plant and sensory aspects have become more significant than ever before, and have a role to play in the successful turnover of new varieties.”

For researchers, this is very useful information, to help determine if it is viable to bring a certain variety to market. The varieties shared in these evaluations include those that have passed through CIMMYT’s breeding pipeline and are allocated to partners for potential release after national performance trials, as well as CIMMYT varieties marketed by various seed companies. Popular commercial varieties regions were also included in the evaluations, for comparison.

A total of 819 people participated in the evaluation exercises in Kenya and Uganda, 54% of them female.

“Currently, there is increasing demand by breeders, donors, and other agricultural scientists to understand the modalities of trait preferences of crops by women and men farmers,” said Rahma Adam, Gender and Development Specialist at CIMMYT.

Bags of seeds with a diversity of maize varieties are displayed before being cooked at a sensory sensory evaluation in Kakamega County, Kenya. (Photo: Bernard Munyua/CIMMYT)
Bags of seeds with a diversity of maize varieties are displayed before being cooked at a sensory sensory evaluation in Kakamega County, Kenya. (Photo: Bernard Munyua/CIMMYT)

That’s the way I like it

For Gentrix Ligare, from Kakamega County, maize has always been a staple food in her family. They eat ugali almost daily. The one-acre farm that she and her husband own was one of the sites used to plant the varieties ahead of the evaluation exercise. Just like her husband, Fred Ligare, she prefers ugali that is soft but absorbs more water during preparation. “I also prefer ugali that is neither very sticky nor very sweet. Such ugali would be appropriate to eat with any type of vegetable or sauce,” she said.

Fernandes Ambani prefers ugali that emits a distinct aroma while being cooked and should neither be very sweet nor plain tasting. For him, ugali should not be too soft or too hard. While it should not be very sticky, it should also not have dark spots in it. “When I like the taste, smell, texture and appearance of a particular variety when cooked, I would definitely purchase it if I found it on the market,” he said.

While the task of incorporating all the desired or multiple traits in the breeding pipeline could prove complex and costly, giving consumers what they like is one of the essential steps in enhancing a variety’s commercial success in the market, argues Ludovicus Okitoi, Director of Kenya Agricultural and Livestock Organization’s (KALRO) Kakamega Center.

“Despite continuously breeding and releasing varieties every year, some farmers still buy some older varieties, possibly because they have a preference for a particular taste in some of the varieties they keep buying,” Okitoi said. “It is a good thing that socioeconomists and breeders are talking more and more with the farmers.”

Advancements in breeding techniques may help accelerate the integration of multiple traits, which could eventually contribute to quicker varietal turnover.

“Previously, we did not conduct this type of varietal evaluations at the consumer level. A breeder would, for instance, just breed on-station and conduct national performance trials at specific sites. The relevant authorities would then grant their approval and a variety would be released. Things are different now, as you have to go back to the farmer as an essential part of incorporating end-user feedback in a variety’s breeding process,” explained Hugo de Groote, Agricultural Economist at CIMMYT.

Breaking Ground: Aparna Das leads efficient and demand-driven maize research

Getting a good maize harvest, or just enough to feed the family, has always been a challenge for maize small farmers in developing countries. Faced with variable rainfall, heat waves, insect attacks or diseases, they rarely yield more than two tons of maize per hectare, and sometimes lose their crops altogether. Climate change, invasive pests like fall armyworm or new diseases like maize lethal necrosis could jeopardize even further the livelihoods of maize farmers and trigger severe food crises.

In this scenario, the lives and income of maize farmers rely on good seeds: seeds that are climate-resilient, pest- and disease-resistant, and that grow and yield well under local conditions, often with minimum inputs.

“That is where the maize improvement research at the International Maize and Wheat Improvement Center (CIMMYT) plays a crucial role in this challenge of food security. You need to develop the right location-specific varieties that farmers want, that partner seed companies are willing to produce, in a cost- and time-efficient way,” says Aparna Das. She joined CIMMYT’s Global Maize research program in August 2018 as Technical Program Manager.

“My role is to work  with and guide the Breeding and Seed Systems team, so that our research is more client- and product-oriented, efficient, and so that there is a better coordination and monitoring, aligned with the available resources and skills within CIMMYT, and with our numerous public and private partners,” she explains.

Value-for-money farmer impact

An important activity Das coordinated recently is a series of collaborative product profiling workshops with CIMMYT’s partners. Integrating the priorities of the national agricultural research systems and partner seed companies, this exercise reviewed and redefined what maize traits and attributes research should focus on in years to come. After this consultation, partners not only pick up CIMMYT germplasm based on trial data, but they can also verify if it fits with their own profile, to make sure that the traits they want are there. It makes breeding much more targeted and efficient.

“Product profiling has already influenced our research. For instance, all partners mentioned husk cover as a ‘must-have’ trait, because you have less insect attacks and grain spoilage,” Das explains. “Although it was considered a base trait, the breeders did not consider it systematically during their maize line selection and product advancement. Now it is integrated,” she notes.

“Our impact should not be limited to the number of varieties released or the number of papers published, but also how many varieties are picked up by partners, adopted by farmers and scaled up,” Das points out.

Breeders and seed systems specialists have worked together to estimate and track the costs of delivering products. Teams responsible for product profiles can now, through simulation, test different solutions and see what costs could be reduced or adjusted to develop the hybrid.

Das enjoys this type of collaboration. “Managing behavioral change is a key part of my role, being able to work with different teams and cultures, which makes my job so interesting,” she says.

Plates of boiled and roasted maize are displayed for tasting during a farmer participatory varietal selection exercise in Embu, Kenya, in August 2019. Flavors of varieties are very distinct and could explain why some old varieties are still preferably grown by farmers. (Photo: S. Palmas/CIMMYT)
Plates of boiled and roasted maize are displayed for tasting during a farmer participatory varietal selection exercise in Embu, Kenya, in August 2019. Flavors of varieties are very distinct and could explain why some old varieties are still preferably grown by farmers. (Photo: S. Palmas/CIMMYT)

An out-of-the-book thinker in a men’s world

Plant breeding is a male-dominated world but Das is used to fitting in as a minority. Originally from West Bengal, she grew up in Ludhiana, another Indian state and a different culture. She learned genetics and plant breeding at Punjab Agricultural University (PAU) in Ludhiana. Discovering the new field of molecular breeding, at its infancy twenty-five years ago, was an exciting challenge.

At PAU, Das pursued crop improvement research, first in wheat and potato, and later in rice genetics. She received an award from India’s Department of Science and Technology under the Young Scientist Program for her work on jumping genes in basmati rice, aimed at creating shorter and more productive basmati varieties while maintaining the basmati aroma.

Later she joined the International Rice Research Institute (IRRI) to work on the development of Golden Rice, a provitamin A-rich variety, through genetic engineering.

“Being a woman in plant breeding, especially as a breeder, is not that common. Women are not expected to do plant breeding fieldwork, away from the lab and offices. But I did not back off. I did my rice fieldwork in the paddy fields, at 40 degrees, all on my own. I believe that women bring a level of precision that is very important in breeding.”

Bridging public and private sectors

After ten years of public research, she moved to the private seed sector, to learn how seed companies integrate farmers’ needs to their research pipeline, and then channel this research to deliver to millions of farmers. “A big lesson from corporations is the value for money at each stage of their research, and that market research is instrumental to really understand farmers’ needs and guide breeding,” she notes.

After a decade in the private sector, Das was keen to move on and use her experience in the nonprofit sector. Then she joined CIMMYT. “This opportunity of technical program manager was timely. I knew the strengths of CGIAR, having highly educated scientists and the great potential outreach of the research. I knew where crop research could be improved, in converting basic research into demand-driven research.”

“Since my time at IRRI a decade ago, I realized things had moved on in the CGIAR system. Seed systems, product profiling and value chain research are now fully integrated in the Global Maize program. It is a crucial time to be here at CIMMYT. With the CGIAR reform, with the climate emergency, and emerging pests and diseases, we have to be even more inventive and reactive to continue to deliver greater impact,” she concludes.

New publications: Breeders can benefit much more from phenotyping tools

In crop research fields, it is now a common sight to see drones or other high-tech sensing tools collecting high-resolution data on a wide range of traits — from simple measurement of canopy temperature to complex 3D reconstruction of photosynthetic canopies.

This technological approach to collecting precise plant trait information, known as phenotyping, is becoming ubiquitous, but according to experts at the International Maize and Wheat Improvement Center (CIMMYT) and other research institutions, breeders can profit much more from these tools, when used judiciously.

In a new article in the journal Plant Science, CIMMYT researchers outline the different ways in which phenotyping can assist breeding — from large-scale screening to detailed physiological characterization of key traits — and why this methodology is crucial for crop improvement.

“While having been the subject of debate in the past, extra investment for phenotyping is becoming more accepted to capitalize on recent developments in crop genomics and prediction models,” explain the authors.

Their review considers different contexts for phenotyping, including breeding, exploration of genetic resources, parent building and translations research to deliver other new breeding resources, and how these different categories of phenotyping apply to each. Some of the same tools and rules of thumb apply equally well to phenotyping for genetic analysis of complex traits and gene discovery.

The authors make the case for breeders to invest in phenotyping, particularly in light of the imperative to breed crops for warmer and harsher climates. However, wide scale adoption of sophisticated phenotyping methods will only occur if new techniques add efficiency and effectiveness.

In this sense, “breeder-friendly” phenotyping should complement existing breeding approaches by cost-effectively increasing throughput during segregant selection and adding new sources of validated complex traits to crossing blocks. With this in mind, stringent criteria need to be applied before new traits or phenotyping protocols are incorporated into mainstream breeding pipelines.

Read the full article in Plant Science:
Breeder friendly phenotyping.

A researcher flies a UAV to collect field data at CIMMYT’s experiment station in Ciudad Obregón, Mexico. (Photo: Alfonso Cortés/CIMMYT)
A researcher flies a UAV to collect field data at CIMMYT’s experiment station in Ciudad Obregón, Mexico. (Photo: Alfonso Cortés/CIMMYT)

See more recent publications from CIMMYT researchers:

  1. Genome-wide association study to identify genomic regions influencing spontaneous fertility in maize haploids. 2019. Chaikam, V., Gowda, M., Nair, S.K., Melchinger, A.E., Prasanna, B.M. In: Euphytica v. 215, no. 8, art. 138.
  2. Adapting irrigated and rainfed wheat to climate change in semi-arid environments: management, breeding options and land use change. 2019. Hernandez-Ochoa, I.M., Pequeno, D.N.L., Reynolds, M.P., Md Ali Babar, Sonder, K., Molero, A., Hoogenboom, G., Robertson, R., Gerber, S., Rowland, D.L., Fraisse, C.W., Asseng, S. In: European Journal of Agronomy.
  3. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. 2019. Gardiner, L.J., Brabbs, T., Akhunova, A., Jordan, K., Budak, H., Richmond, T., Sukhwinder-Singh, Catchpole, L., Akhunov, E., Hall, A.J.W. In: GigaScience v. 8, no. 4, art. giz018.
  4. Rethinking technological change in smallholder agriculture. 2019. Glover, D., Sumberg, J., Ton, G., Andersson, J.A., Badstue, L.B. In: Outlook on Agriculture v. 48, no. 3, p. 169-180.
  5. Food security and agriculture in the Western Highlands of Guatemala. 2019. Lopez-Ridaura, S., Barba‐Escoto, L., Reyna, C., Hellin, J. J., Gerard, B., Wijk, M.T. van. In: Food Security v. 11, no. 4, p. 817-833.
  6. Agronomic, economic, and environmental performance of nitrogen rates and source in Bangladesh’s coastal rice agroecosystems. 2019. Shah-Al Emran, Krupnik, T.J., Kumar, V., Ali, M.Y., Pittelkow, C. M. In: Field Crops Research v. 241, art. 107567.
  7. Highlights of special issue on “Wheat Genetics and Breeding”. 2019. He Zhonghu, Zhendong Zhao, Cheng Shun-He In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 207-209.
  8. Progress in breeding for resistance to Ug99 and other races of the stem rust fungus in CIMMYT wheat germplasm. 2019. Bhavani, S., Hodson, D.P., Huerta-Espino, J., Randhawa, M.S., Singh, R.P. In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 210-224.
  9. China-CIMMYT collaboration enhances wheat improvement in China. 2019. He Zhonghu, Xianchun Xia, Yong Zhang, Zhang Yan, Yonggui Xiao, Xinmin Chen, Li Simin, Yuanfeng Hao, Rasheed, A, Zhiyong Xin, Zhuang Qiaosheng, Ennian Yang, Zheru Fan, Yan Jun, Singh, R.P., Braun, H.J. In: Frontiers of Agricultural Science and Engineering v. 6. No. 3, p. 233-239.
  10. International Winter Wheat Improvement Program: history, activities, impact and future. 2019. Morgounov, A.I., Ozdemir, F., Keser, M., Akin, B., Payne, T.S., Braun, H.J. In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 240-250.
  11. Genetic improvement of wheat grain quality at CIMMYT. 2019. Guzman, C., Ammar, K., Velu, G., Singh, R.P. In: Frontiers of Agricultural Science and Engineering v. 6, no. 3, p. 265-272.
  12. Comments on special issue on “Wheat Genetics and Breeding”. 2019. He Zhonghu, Liu Xu In: Frontiers of Agricultural Science and Engineering, v. 6. No. 3, p. 309.
  13. Spectral reflectance indices as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait associations. 2019. Caiyun Liu, Pinto Espinosa, F., Cossani, C.M., Sukumaran, S., Reynolds, M.P. In: Frontiers of Agricultural Science and Engineering, v. 6, no. 3, p. 296-308.
  14. Beetle and maize yield response to plant residue application and manual weeding under two tillage systems in northern Zimbabwe. 2019. Mashavakure, N., Mashingaidze, A.B., Musundire, R., Gandiwa, E., Thierfelder, C., Muposhi, V.K. In: Applied Soil Ecology v. 144, p. 139-146.
  15. Optimizing dry-matter partitioning for increased spike growth, grain number and harvest index in spring wheat. 2019. Rivera Amado, A.C., Trujillo, E., Molero, G., Reynolds, M.P., Sylvester Bradley, R., Foulkes, M.J. In: Field Crops Research v. 240, p. 154-167.
  16. Small businesses, potentially large impacts: the role of fertilizer traders as agricultural extension agents in Bangladesh. 2019. Mottaleb, K.A., Rahut, D.B., Erenstein, O. In: Journal of Agribusiness in Developing and Emerging Economies v. 9, no. 2, p. 109-124.
  17. Heterogeneous seed access and information exposure: implications for the adoption of drought-tolerant maize varieties in Uganda. 2019. Simtowe, F.P., Marenya, P. P., Amondo, E., Regasa, M.W., Rahut, D.B., Erenstein, O. In: Agricultural and Food Economics v. 7. No. 1, art. 15.
  18. Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. 2019. Krause, M., Gonzalez-Perez, L., Crossa, J., Perez-Rodriguez, P., Montesinos-Lopez, O.A., Singh, R.P., Dreisigacker, S., Poland, J.A., Rutkoski, J., Sorrells, M.E., Gore, M.A., Mondal, S. In: G3: Genes, Genomes, Genetics v.9, no. 4, p. 1231-1247.
  19. Unravelling the complex genetics of karnal bunt (Tilletia indica) resistance in common wheat (Triticum aestivum) by genetic linkage and genome-wide association analyses. 2019. Emebiri, L.C., Sukhwinder-Singh, Tan, M.K., Singh, P.K., Fuentes Dávila, G., Ogbonnaya, F.C. In: G3: Genes, Genomes, Genetics v. 9, no. 5, p. 1437-1447.
  20. Healthy foods as proxy for functional foods: consumers’ awareness, perception, and demand for natural functional foods in Pakistan. 2019. Ali, A., Rahut, D.B. In: International Journal of Food Science v. 2019, art. 6390650.
  21. Northern Himalayan region of Pakistan with cold and wet climate favors a high prevalence of wheat powdery mildew. 2019. Khan, M.R., Imtiaz, M., Farhatullah, Ahmad, S., Sajid Ali.In: Sarhad Journal of Agriculture v. 35, no. 1, p. 187-193.
  22. Resistance to insect pests in wheat—rye and Aegilops speltoides Tausch translocation and substitution lines. 2019. Crespo-Herrera, L.A., Singh, R.P., Sabraoui, A., Moustapha El Bouhssini In: Euphytica v. 215, no. 7, art.123.
  23. Productivity and production risk effects of adopting drought-tolerant maize varieties in Zambia. 2019. Amondo, E., Simtowe, F.P., Rahut, D.B., Erenstein, O. In: International Journal of Climate Change Strategies and Management v. 11, no. 4, p. 570-591.
  24. Review: new sensors and data-driven approaches—A path to next generation phenomics. 2019. Roitsch, T., Cabrera-Bosquet, L., Fournier, A., Ghamkhar, K., Jiménez-Berni, J., Pinto Espinosa, F., Ober, E.S. In: Plant Science v. 282 p. 2-10.
  25. Accountability mechanisms in international climate change financing. 2019. Basak, R., van der Werf, E. In: International Environmental Agreements: Politics, Law and Economics v. 19, no. 3, p. 297-313.
  26. Enhancing the rate of genetic gain in public-sector plant breeding programs: lessons from the breeder’s equation. 2019. Cobb, J.N., Juma, R.U., Biswas, P.S., Arbelaez, J.D., Rutkoski, J., Atlin, G.N., Hagen, T., Quinn, M., Eng Hwa Ng. In: Theoretical and Applied Genetics v. 132, no. 3, p. 627-645.

One-minute science: Suchismita Mondal on breeding resilient wheat

Reduced water availability for irrigation and increasing temperatures are of great concern. These two factors can considerably affect wheat production and reduce grain yields.

Watch CIMMYT Wheat Breeder Suchismita Mondal explain — in just one minute — how breeders are developing wheat varieties that have stable grain yield under low water availability and high temperatures.

Breeder friendly phenotyping

In crop research fields, drones and other high-tech sensing tools are now a common sight. They collect high-resolution data on a wide range of traits — from simple measurement of canopy temperature to complex 3D reconstruction of photosynthetic canopies.

This technological approach to collecting precise plant trait information, known as phenotyping, is becoming ubiquitous. According to experts at the International Maize and Wheat Improvement Center (CIMMYT) and other research institutions, breeders can profit much more from these tools, when used judiciously.

Examples of different classes and applications of breeder friendly phenotyping. (Image: M. Reynolds et al.)
Examples of different classes and applications of breeder friendly phenotyping. (Image: M. Reynolds et al.)

In a new article in the journal Plant Science, CIMMYT Wheat Physiologist Matthew Reynolds and colleagues explain the different ways that phenotyping can assist breeding — from simple to use, “handy” approaches for large scale screening, to detailed physiological characterization of key traits to identify new parental sources — and why this methodology is crucial for crop improvement. The authors make the case for breeders to invest in phenotyping, particularly in light of the imperative to breed crops for warmer and harsher climates.

Read the full article: 
Breeder friendly phenotyping.

This article was originally published on WHEAT.

Cover photo: Remote sensing specialist Francisco Pinto operates a UAV at CIMMYT’s research station in Ciudad Obregón, in Mexico’s Sonora state.

Development of the Enterprise Breeding System well underway

Members of the Enterprise Breeding System advisory committee listen to a presentation from Tom Hagen. (Photo: Alfonso Cortés/CIMMYT)
Members of the Enterprise Breeding System advisory committee listen to a presentation from Tom Hagen. (Photo: Alfonso Cortés/CIMMYT)

Members of the Enterprise Breeding System (EBS) advisory committee met on January 17-18, 2019, to review progress on the development of a full-spectrum breeding data management software.

CGIAR plant breeders currently rely on a suite of different software projects to make use of the data that is crucial to developing better varieties. Developed under the CGIAR Excellence in Breeding Platform (EiB), the EBS aims to provide a single solution that links data across new and existing applications so that the entire breeding data workflow — from experiment creation to analytics — can be accessed from a single user-friendly dashboard.

Development of the system is well underway, with the goal of providing a “minimum viable implementation” to pilot users at the International Maize and Wheat Improvement Center (CIMMYT) and the International Rice Research Institute (IRRI) in 2020. More advanced functions, institutions and crops will be added to the EBS over the next three years.

Working between breeders and developers to ensure needs are translated into software functions, the EBS team has trained CIMMYT staff and consultants as requirements analysts, five of whom presented to members of the EBS advisory committee the meeting on progress in the five “domains” of breeding software functions.

Sharing bits and bytes

Rosemary Shresthra introduced experiment creation, where users can quickly select the type of experiment they wish to run and automatically set up all the steps needed to complete it in the EBS.

Kate Dreher took the attendees through field implementation, where it is possible to map fields in the system and connect them to a range of plot data collection tools developed by external projects.

Ricardo León outlined the germplasm management component of the system, where the seed inventory is kept, and new entries made after trials are harvested to go on to the next stage.

Pedro Medeiros explained how an analytics request manager will allow EBS users to push their data to different analytics tools that support decision-making and, ultimately, their ability to deliver better varieties that meet farmers’ needs.

Finally, Star Gao, a breeding informatics specialist for the Genomic and Open-Source Breeding Informatics Initiative (GOBii), showed how users will be able to request phytosanitary, genotypic and quality analysis of samples from their trials through the EBS system. The system will provide an overview of the status of all samples submitted for analysis with different service providers, in addition to the ability to connect with various databases.

“We can do all this because all information in the EBS is treated the same way, from experiment creation through implementation,” said EBS coordinator Tom Hagen in summary.

The EBS advisory group, which includes user representatives from CIMMYT and IRRI breeding teams alongside EiB staff, ended the day by discussing and prioritizing new functions that could be added to the EBS over the next three years.

One-minute science: Carolina Rivera explains wheat physiology

Wheat provides, on average, 20% of the calories and protein for more than 4.5 billion people in 94 developing countries. To feed a growing population, we need both better agronomic practices and to grow wheat varieties that can withstand the effects of climate change and resist various pests and diseases.

Watch CIMMYT Wheat Physiologist Carolina Rivera discuss — in just one minute — choosing and breeding desirable wheat traits with higher tolerance to stresses.

First steps taken to unify breeding software

Participants of the EBS DevOps Hackathon stand for a group photo at CIMMYT's global headquarters in Texcoco, Mexico. (Photo: Eleusis Llanderal Arango/CIMMYT)
Participants of the EBS DevOps Hackathon stand for a group photo at CIMMYT’s global headquarters in Texcoco, Mexico. (Photo: Eleusis Llanderal Arango/CIMMYT)

From October 21 to November 1, 2019, software developers and administrators from several breeding software projects met at the global headquarters of the International Maize and Wheat Improvement Center (CIMMYT) in Mexico to work on delivering an integrated solution to crop breeders.

Efforts to improve crop breeding for lower- and middle-income countries involves delivering better varieties to farmers faster and for less cost. These efforts rely on a mastery of data and technology throughout the breeding process.

To realize this potential, the CGIAR Excellence in Breeding Platform (EiB) is developing an Enterprise Breeding System (EBS) as a single solution for breeders. EBS will integrate the disparate software projects developed by different institutions over the years. This will free breeders from the onerous task of managing their data through different apps and allow them to rapidly optimize their breeding schemes based on sound data and advanced analytics.

“None of us can do everything,” said Tom Hagen, CIMMYT-EiB breeding software product manager, “so what breeding programs are experiencing is in fact fragmented IT. How do we come together as IT experts to create a system through our collective efforts?”

For the EBS to succeed, it is essential that the system is both low-cost and easy to deploy. “The cost of the operating environment is absolutely key,” said Jens Riis-Jacobson, international systems and IT director at CIMMYT. “We are trying to serve developing country institutions that have very little hard currency to pay for breeding program operations.”

Stacked software

During the hackathon, twelve experts from software projects across CGIAR and public sector institutions used a technology called Docker to automatically stack the latest versions of their applications into a single configuration file. This file can be loaded into any operating environment in less than four minutes — whether it be a laptop, local server or in the cloud. Quickly loading the complete system into a cloud environment means EBS can eventually be available as a one-click, Software-as-a-Service solution. This means that institutions will not need sophisticated IT infrastructure or support staff to maintain the software.

Behind the scenes, different applications are replicated in a single software solution, the Enterprise Breeding System. (Photo: CIMMYT)
Behind the scenes, different applications are replicated in a single software solution, the Enterprise Breeding System. (Photo: CIMMYT)

“If everything goes as planned, the end users won’t know that we exist,” said Peter Selby, coordinator of the Breeding API (BrAPI) project, an online collective working on a common language for breeding applications to communicate with each other. Updates to individual apps will be automatically loaded, tested and pushed out to users.

As well as the benefits to breeders, this automated deployment pipeline should also result in better software. “We have too little time for development because we spend too much time in deployment and testing,” said Riis-Jacobson.

A cross-institution DevOps culture

Though important technical obstacles were overcome, the cultural aspect was perhaps the most significant outcome of the hackathon. The participants found that they shared the same goals, language and were able to define the common operating environment for their apps to work together in.

“It’s really important to keep the collaboration open,” said Roy Petrie, DevOps engineer at the Genomic and Open-Source Breeding Informatics Initiative (GOBii) based at the Boyce Thompson Institute, Cornell University. “Having a communications platform was the first thing.”

In the future, this could mean that teams synchronize their development timeline to consistently release updates with new versions of the EBS, suggested Franjel Consolacion, systems admin at CIMMYT.

“They are the next generation,” remarked Hagen. “This is the first time that this has happened in CGIAR informatics and it validated a key aspect of our strategy: that we can work together to assemble parts of a system and then deploy it as needed to different institutions.”

By early 2020, selected CIMMYT and International Rice Research Institute (IRRI) breeding teams will have access to a “minimal viable implementation” of the EBS, in which they can conduct all basic breeding tasks through a simple user interface. More functionality, breeding programs and crops from other institutions including national agricultural research programs will be added in phases over three years.

New publications: Special collection on wheat genetics and breeding

Global wheat production is currently facing great challenges, from increasing climate variation to occurrence of various pests and diseases. These factors continue to limit wheat production in a number of countries, including China, where in 2018 unseasonably cold temperatures resulted in yield reduction of more than 10% in major wheat growing regions. Around the same time, Fusarium head blight spread from the Yangtze region to the Yellow and Huai Valleys, and northern China experienced a shortage of irrigated water.

In light of these ongoing challenges, international collaboration, as well as the development of new technologies and their integration with existing ones, has a key role to play in supporting sustainable wheat improvement, especially in developing countries. The International Maize and Wheat Improvement Center (CIMMYT) has been collaborating with China on wheat improvement for over 40 years, driving significant progress in a number of areas.

Notably, a standardized protocol for testing Chinese noodle quality has been established, as has a methodology for breeding adult-plant resistance to yellow rust, leaf rust and powdery mildew. More than 330 cultivars derived from CIMMYT germplasm have been released in the country and are currently grown over 9% of the Chinese wheat production area, while physiological approaches have been used to characterize yield potential and develop high-efficiency phenotyping platforms. The development of climate-resilient cultivars using new technology will be a priority area for future collaboration.

In a special issue of Frontiers of Agricultural Science and Engineering focused on wheat genetics and breeding, CIMMYT researchers present highlights from global progress in wheat genomics, breeding for disease resistance, as well as quality improvement, in a collection of nine review articles and one research article. They emphasize the significance of using new technology for genotyping and phenotyping when developing new cultivars, as well as the importance of global collaboration in responding to ongoing challenges.

In a paper on wheat stem rust, CIMMYT scientists Sridhar Bhavani, David Hodson, Julio Huerta-Espino, Mandeep Randawa and Ravi Singh discuss progress in breeding for resistance to Ug99 and other races of stem rust fungus, complex virulence combinations of which continue to pose a significant threat to global wheat production. The authors detail how effective gene stewardship and new generation breeding materials, complemented by active surveillance and monitoring, have helped to limit major epidemics and increase grain yield potential in key target environments.

In the same issue, an article by Caiyun Lui et al. discusses the application of spectral reflectance indices (SRIs) as proxies to screen for yield potential and heat stress, which is emerging in crop breeding programs. The results of a recent study, which evaluated 287 elite lines, highlight the utility of SRIs as proxies for grain yield. High heritability estimates and the identification of marker-trait associations indicate that SRIs are useful tools for understanding the genetic basis of agronomic and physiological traits.

Other papers by CIMMYT researchers discuss the history, activities and impact of the International Winter Wheat Improvement Program, as well as the ongoing work on the genetic improvement of wheat grain quality at CIMMYT.

Find the full collection of articles in Frontiers of Agricultural Science and Engineering, Volume 6, Issue 3, September 2019.

See more recent publications by CIMMYT researchers:

  1. Genetic diversity among tropical provitamin A maize inbred lines and implications for a biofortification program. 2019. Julius Pyton Sserumaga, Makumbi, D., Warburton, M.L., Opiyo, S.O., Asea, G., Muwonge, A., Kasozi, C.L. In: Cereal Research Communications v. 47, no. 1, p. 134-144.
  2. Diversity and conservation priorities of crop wild relatives in Mexico. 2019. Contreras-Toledo, A. R., Cortes-Cruz, M. A., Costich, D.E., Rico-Arce, M. de L., Magos Brehm, J., Maxted, N. In: Plant Genetic Resources: Characterisation and Utilisation v. 17, no. 2, p. 140-150.
  3. Global wheat production with 1.5 and 2.0°C above pre-industrial warming. 2019. Bing Liu, Martre, P., Ewert, F., Porter, J.R., Challinor, A.J., Muller, C., Ruane, A.C., Waha, K., Thorburn, P.J., Aggarwal, P.K., Mukhtar Ahmed, Balkovic, J., Basso, B., Biernath, C., Bindi, M., Cammarano, D., De Sanctis, G., Dumont, B., Espadafor, M., Eyshi Rezaei, E., Ferrise, R., Garcia-Vila, M., Gayler, S., Yujing Gao, Horan, H., Hoogenboom, G., Izaurralde, R.C., Jones, C.D., Kassie, B.T., Kersebaum, K.C., Klein, C., Koehler, A.K., Maiorano, A., Minoli, S., Montesino San Martin, M., Soora Naresh Kumar, Nendel, C., O’Leary, G.J., Palosuo, T., Priesack, E., Ripoche, D.,Rotter, R., Semenov, M.A., Stockle, C., Streck, T., Supit, I., Fulu Tao, Van der Velde, M., Wallach, D., Wang, E. |Webber, H., Wolf, J., Liujun Xiao, Zhao Zhang, Zhigan Zhao, Yan Zhu, Asseng, S. In: Global Change Biology v. 25, no. 4, p. 1428-1444.
  4. Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas. 2019. Sandhu, N., Dixit, S., Mallikarjuna Swamy, B.P., Raman, A.K., Kumar, S., Singh, S.P., Yadaw, R.B., Singh, O.N., Reddy, J.N., Anandan, A., Yadav, S., Venkataeshwarllu, C., Henry, A., Verulkar, S., Mandal, N.P., Ram, T., Badri, J., Vikram, P., Arvind Kumar In: Rice v. 12, no. 1, art. 8.
  5. Modeling Genotype × Environment Interaction Using a Factor Analytic Model of On-Farm Wheat Trials in the Yaqui Valley of Mexico. 2019. Vargas-Hernández, M., Ortiz-Monasterio, I., Perez-Rodriguez, P., Montesinos-Lopez, O.A., Montesinos-Lopez, A., Burgueño, J., Crossa, J. In: Agronomy Journal v. 111, no. 1, p. 1-11.
  6. Does Size Matter? A Critical Review of Meta-analysis in Agronomy. 2019. Krupnik, T.J., Andersson, J.A., Rusinamhodzi, L., Corbeels, M., Shennan, C., Gerard, B. In: Experimental Agriculture v. 55 no. Special issue 2, p. 200-229.
  7. Effects of tillage, crop establishment and diversification on soil organic carbon, aggregation, aggregate associated carbon and productivity in cereal systems of semi-arid Northwest India. 2019. Jat, H.S., Datta, A., Choudhary, M., Yadav, A.K., Choudhary, V., Sharma, P.C., Gathala, M.K., Jat, M.L., McDonald, A. In: Soil and Tillage Research v. 190, p. 128-138.
  8. Transgenic solutions to increase yield and stability in wheat: shining hope or flash in the pan? 2019. Araus, J.L., Serret, M.D., Lopes, M.S. In: Journal of Experimental Botany v. 70, no. 5, p. 1419-1424.
  9. Model-Driven Multidisciplinary Global Research to Meet Future Needs: The Case for “Improving Radiation Use Efficiency to Increase Yield.” 2019. Asseng, S., Martre, P., Ewert, F., Dreccer, M.F., Beres, B.L., Reynolds, M.P., Braun, H.J., Langridge, P., Gouis, J. Le., Salse, J., Baenziger, P.S. In: Crop Science v. 59, p. 1-7.
  10. Proteome analysis of biofilm produced by a Fusarium falciforme keratitis infectious agent. 2019. Calvillo-Medina, R.P., Reyes‐Grajeda, J.P., Barba‐Escoto, L., Bautista-Hernandez, L.A., Campos‐Guillen, J., Jones, G.H., Bautista‐de Lucio, V.M. In: Microbial Pathogenesis v. 130, p. 232-241.