Publication summary: Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields

A new quantitative genetics study makes a strong case for the yield testing strategies the International Maize and Wheat Improvement Center (CIMMYT) uses in its wheat breeding program.

Wheat fields at CIMMYT’s Campo Experimental Norman E. Borlaug (CENEB) in Ciudad Obregón. Photo: CIMMYT.

The process for breeding for grain yield in bread wheat at the International Maize and Wheat Improvement Center (CIMMYT) involves three-stage testing at an experimental station in the desert environment of Ciudad Obregón, in Mexico’s Yaqui Valley. Because the conditions in Obregón are extremely favorable, CIMMYT wheat breeders are able to replicate growing environments all over the world, and test the yield potential and climate-resilience of wheat varieties for every major global wheat growing area. These replicated test areas in Obregón are known as selection environments (SEs).

This process has its roots in the innovative work of wheat breeder and Nobel Prize winner Norman Borlaug, more than 50 years ago.  Wheat scientists at CIMMYT, led by wheat breeder Philomin Juliana, wanted to see if it remained effective.

The scientists conducted a large quantitative genetics study comparing the grain yield performance of lines in the Obregón SEs with that of lines in target growing sites throughout the world. They based their comparison on data from two major wheat trials: the South Asia Bread Wheat Genomic Prediction Yield Trials in India, Pakistan and Bangladesh initiated by the U.S. Agency for International Development Feed the Future initiative, and the global testing environments of the Elite Spring Wheat Yield Trials.

The findings, published in Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields, in Frontiers in Plant Science, found that the Obregón yield testing process in different SEs is very efficient in developing high-yielding and resilient wheat lines for target sites.

The authors found higher average heritabilities, or trait variations due to genetic differences, for grain yield in the Obregón SEs than in the target sites (44.2 and 92.3% higher for the South Asia and global trials, respectively), indicating greater precision in the SE trials than those in the target sites.   They also observed significant genetic correlations between one or more SEs in Obregón and all five South Asian sites, as well as with the majority (65.1%) of the Elite Spring Wheat Yield Trial sites. Lastly, they found a high ratio of selection response by selecting for grain yield in the SEs of Obregón than directly in the target sites.

“The results of this study make it evident that the rigorous multi-year yield testing in Obregón environments has helped to develop wheat lines that have wide-adaptability across diverse geographical locations and resilience to environmental variations,” said Philomin Juliana, CIMMYT associate scientist and lead author of the article.

“This is particularly important for smallholder farmers in developing countries growing wheat on less than 2 hectares who cannot afford crop losses due to year-to-year environmental changes.”

In addition to these comparisons, the scientists conducted genomic prediction for grain yield in the target sites, based on the performance of the same lines in the SEs of Obregón. They found high year-to-year variations in grain yield predictabilities, highlighting the importance of multi-environment testing across time and space to stave off the environment-induced uncertainties in wheat yields.

“While our results demonstrate the challenges involved in genomic prediction of grain yield in future unknown environments, it also opens up new horizons for further exciting research on designing genomic selection-driven breeding for wheat grain yield,” said Juliana. 

This type of quantitative genetics analysis using multi-year and multi-site grain yield data is one of the first steps to assessing the effectiveness of CIMMYT’s current grain yield testing and making recommendations for improvement—a key objective of the new Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project, which aims to accelerate the breeding progress by optimizing current breeding schemes.

This work was made possible by the generous support of the Delivering Genetic Gain in Wheat (DGGW) project funded by the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth & Development Office (FCDO) and managed by Cornell University; the U.S. Agency for International Development’s Feed the Future initiative; and several collaborating national partners who generated the grain yield data.

Read the full article here: https://doi.org/10.3389/fpls.2020.580136

Excellence in Agronomy 2030 initiative launched at African Green Revolution Forum

New research platform focuses on helping smallholder farmers sustainably increase production and adapt to climate change, reducing yield and efficiency gaps in major crops

Nine CGIAR centers, supported by the Big Data Platform, launched the Excellence in Agronomy 2030 initiative today at the African Green Revolution Forum (AGRF) online summit.

The Excellence in Agronomy 2030 (EiA 2030) initiative will assist millions of smallholder farmers to intensify their production systems while preserving key ecosystem services under the threat of climate change. This initiative, co-created with various scaling partners, represents the collective resolve of CGIAR’s agronomy programs to transform the world’s food systems through demand- and data-driven agronomy research for development.

EiA 2030 will combine big data analytics, new sensing technologies, geospatial decision tools and farming systems research to improve spatially explicit agronomic recommendations in response to demand from scaling partners. Our science will integrate the principles of Sustainable Intensification and be informed by climate change considerations, behavioral economics, and scaling pathways at the national and regional levels.

A two-year Incubation Phase of EiA 2030 is funded by the Bill & Melinda Gates Foundation. The project will demonstrate the added value of demand-driven R&D, supported by novel data and analytics and increased cooperation among centers, in support of a One CGIAR agronomy initiative aiming at the sustainable intensification of farming systems.

Speaking on the upcoming launch, the IITA R4D Director for Natural Resource Management, Bernard Vanlauwe, who facilitates the implementation of the Incubation Phase, said that “EiA 2030 is premised on demand-driven agronomic solutions to develop recommendations that match the needs and objectives of the end users.”

Christian Witt, Senior Program Officer from the Bill & Melinda Gates Foundation, lauded the initiative as a cornerstone for One CGIAR. “It is ingenious to have a platform like EiA 2030 that looks at solutions that have worked in different settings on other crops and whether they can be applied in a different setting and on different crops,” Witt said.

Martin Kropff, Director General of the International Maize and Wheat Improvement Center (CIMMYT), spoke about the initiative’s goals of becoming the leading platform for next-generation agronomy in the Global South, not only responding to the demand of the public and private sectors, but also increasing efficiencies in the development and delivery of solutions through increased collaboration, cooperation and cross-learning between CGIAR centers and within the broader agronomy R&D ecosystem, including agroecological approaches.

CGIAR centers that are involved in EiA include AfricaRice, the International Center for Tropical Agriculture (CIAT), the International Maize and Wheat Improvement Center (CIMMYT), the International Potato Center (CIP), the International Center for Agricultural Research in the Dry Areas (ICARDA), World Agroforestry Center (ICRAF), the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the International Institute of Tropical Agriculture (IITA), and the International Rice Research Institute (IRRI)

BGRI launches virtual global wheat conference Oct. 7-9

This press release was originally posted on the website of the Borlaug Global Rust Initiative (BGRI).

As the world grapples with a disastrous human health crisis, scientists will gather virtually October 7-9 to discuss strategies to safeguard the health of one of the planet’s most important food sources — wheat.

The Borlaug Global Rust Initiative’s (BGRI) virtual technical workshop will bring together scientists at the forefront of wheat science for cutting-edge training and knowledge sharing. Experts from global institutions such as Cornell University, the International Maize and Wheat Improvement Center (CIMMYT), the International Center for Agricultural Research in the Dry Areas (ICARDA), and the John Innes Centre, with presenters from Ethiopia, Kenya, India, Australia, Finland, Mexico, the United Kingdom and United States, will lead in-depth talks and discussions on the most pressing challenges facing global wheat security.

Event registration is now open.

“Right now we are witnessing the devastation that the global spread of disease can cause, and it underscores the continual threat that diseases pose to our most important food crops,” said Ronnie Coffman, vice-chair of the BGRI and an international professor in Cornell’s Department of Global Development and School of Integrative Plant Science. “Devastating wheat epidemics would be catastrophic to human health and wellbeing. October’s workshop is an opportunity for wheat scientists to converge virtually for the practical training and knowledge-sharing we need to fight numerous challenges.”

The three-day workshop in October will be broken up into sessions with keynotes from leading experts and presentations focused on key areas of wheat research:

  • Breeding technologies
  • Disease surveillance
  • Molecular host-pathogen interaction
  • Disease resistance
  • Gene stewardship

The BGRI is a strong proponent of responsible gene deployment to ensure the efficacy of disease resistant genes available to breeders. Since 2012, the BGRI has bestowed the Gene Stewardship Award in recognition of excellence in the development, multiplication and/or release of rust resistant wheat varieties that encourage diversity and complexity of resistance. The winners of the 2020 BGRI Gene Stewardship award will be announced at the workshop.

Maricelis Acevedo, associate director for science for the Delivering Genetic Gain in Wheat (DGGW) project and researcher in Cornell’s Department of Global Development, said: “The BGRI has been at the forefront of developing the next generation of wheat warriors, especially in strengthening the technical and professional skills of women and men scientists from developing countries. We are taking a global approach to help reduce the threat of diseases that can overwhelm farmers’ wheat fields. Issues related to improving world food security, especially in the face of climate change, can only be addressed by a diverse and united global community.”

She added: “The BGRI’s technical workshop has long been the premiere meeting ground for wheat scientists around the world. It’s more important than ever that we come together to address the challenges before us.”

The BGRI 2020 Technical Workshop originally planned for June 1-4 in Norwich, United Kingdom was postponed due to COVID-19.

Wheat is one of the world’s largest primary commodity, with global production of over 700 million tons, grown on over 215 million hectares. Eaten by over 2.5 billion people in 89 countries, wheat provides 19% of the world’s total available calories and 20% of all protein.

Over the past 20 years, the global area under wheat production has not increased. To produce the required amount of wheat needed to feed the world’s growing population, researchers predict wheat yields must increase at least 1.4% per acre through 2030.

Wheat faces pressure from the changing environment and diseases, especially rust diseases increasingly prevalent in wheat-growing regions everywhere. The BGRI was formed in 2005 in response to a novel strain of rust discovered in East Africa known as Ug99 that posed risks of epidemic proportions to global wheat production. Norman Borlaug galvanized global scientists and donors in a bid to combat Ug99 and other disease pressures.

“The world averted disaster thanks to the commitment of researchers and farmers from all over the world who participated in the BGRI’s coordinated global response,” said Coffman. “With the backing of far-sighted donors, the BGRI focused on delivering rust-resilient varieties of wheat to farmers around the world, and dedicating our efforts to small-holder farmers in wheat-producing countries in Africa and Asia — men and women who do not always have access to new technologies and improved seed.” 

Registration page is now live.

The BGRI is a community of hunger fighters dedicated to protecting the world’s wheat. The initiative receives funding through the DGGW project, supported by the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth & Development Office.

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Alison Bentley to be new CIMMYT Global Wheat Program and WHEAT director

The new director of the CGIAR Research Program on Wheat brings many years of experience in wheat genetics, wheat genetic resources and wheat pre-breeding.

This story by Marta Millere was originally published on the CIMMYT website.

Alison Bentley (right) and Martin Jones of the University of Cambridge inspect wheat in a glasshouse. (Photo: Toby Smith/Gloknos)

In November 2020, Alison Bentley will be joining the International Maize and Wheat Improvement Center (CIMMYT) as the new director of the Global Wheat Program and the CGIAR Research Program on Wheat (WHEAT). She will be succeeding Hans Braun, who has steered CIMMYT’s Global Wheat Program for the last 16 years, and has led the CGIAR Research Program on Wheat since its establishment in 2014.

Bentley expressed that she is thrilled to join CIMMYT and excited about the opportunity to harness science and breeding to improve livelihoods. She believes in a collective vision for equitable food supply and in science-led solutions to deliver impact.

“It really is an exciting time for wheat research: the international community has worked together to produce sequence and genomic resources, new biological and physiological insights, a wealth of germplasm and tools for accelerating breeding. This provides an unparalleled foundation for accelerating genetic gains and connecting ideas to determine how we can practically apply these tools and technologies with partners to deliver value-added outputs,” she said.

Bentley has worked on wheat — wheat genetics, wheat genetic resources and wheat pre-breeding — her entire career. She is the UK’s representative on the International Wheat Initiative Scientific Committee, and is a committee member for the Genetics Society, the UK Plant Sciences Federation, the Society of Experimental Botany, and the Editorial Board of Heredity.

Bentley obtained her PhD from the University of Sydney, Australia, in 2007. She then joined the National Institute of Agricultural Botany (NIAB) in the UK, where she progressed from Senior Research Scientist (2007) to Program Leader for Trait Genetics (2013), and Director of Genetics and Breeding (since 2016).

Currently, Bentley is involved in international research projects in Ethiopia, The Gambia, Ghana, India and Pakistan. She leads a number of UK-India projects with partners including Punjab Agricultural University, the Indian National Institute of Plant Genome Research and the University of Cambridge, studying variation and developing wheat and other cereal germplasm with enhanced resource use efficiency.

Multi-disciplinary approaches to crop improvement for faster climate change adaptation

This article by Sakshi Saini was originally published on the CCAFS website

A high throughput crop phenotyping platform, the ‘Leasyscan’ located at ICRISAT’s HQ Patancheru, India. Photo: A. Whitbread (ICRISAT)
A high throughput crop phenotyping platform, the ‘Leasyscan’ located at ICRISAT’s HQ Patancheru, India. Photo: A. Whitbread (ICRISAT)

Ever-increasing emissions of greenhouse gases (GHG) is a global concern due to the association of high atmospheric GHG concentrations with global warming and climate change. A large and growing body of evidence predicts that this would further have a multifaceted impact on the human population, especially the poor and vulnerable groups, further exacerbating their vulnerabilities.

But what about crops? Plants use carbon dioxide (CO2)—one of the most abundant GHGs, for photosynthesis. So shouldn’t an increase in atmospheric carbon dioxide aid crops to flourish? A counter-argument to this would be that at the same time there would be changes in other factors such as a change in precipitation rate, frequency and intensity of rains, among others, which might negatively impact crop production. So, how exactly would climatic variations impact the yield and productivity of crops? These are some of the questions that have been a global concern. Many studies have researched this, employing varied approaches such as systems biology, physiology and crop modelling. However, unprecedented changes in climatic conditions still pose uncertainties on the impacts on crops.

Recent research by an interdisciplinary team of scientists from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the CGIAR Research Program on Climate Chanage, Agriculture and Food Security (CCAFS)-Africa and CCAFS-Asia aspires to answer some of these questions. As part of this research, they have compiled recent progress made in the physiological and molecular attributes in plants, with special emphasis on legumes under elevated CO2 conditions in a climate change scenario. The study proposes a strategic research framework for crop improvement that integrates genomics, systems biology, physiology and crop modelling approaches to cope with the changing climate. Some of the prime results of the study are as follows:

1. Major physiological and biochemical alterations in legumes triggered by elevated CO2

A range of physiological and biochemical alterations take place in plants exposed to elevated CO2. In the case of legumes, elevated atmospheric COconcentrations also affect the nutritional quality and nodulation, causes changes in rhizosphere and Biological Nitrogen Fixation (BNF), among others. Studies have shown that elevated CO2 would stimulate plant growth under nitrogen-sufficient conditions, but under nitrogen-limited conditions, it may have the detrimental effect of reducing plant growth by altering its primary metabolism. The anatomical differences between C3 and C4 plants (plants with C3 and C4 photosynthetic pathways) and their different ways of sequestering carbon (removing carbon dioxide from the atmosphere), have been an area of interest for climate scientists. Elevated COcombined with limited nitrogen may also promote biological ageing (senescence) rates as observed in flag leaves of rice and wheat. Studies also show that a higher level of carbon dioxide increases senescence rate in legumes.

2. Impact of elevated carbon-dioxide interaction with other abiotic stresses

As mentioned earlier, CO2 is not the only factor that is impacting plant growth, it is dependent on other environmental factors such as water deficit stress and temperature, among others. Thus, these factors also need to be considered in combination with the atmospheric concentration. Studies have reported that elevated CO2 induced a decrease (of 10%) in evaporation rates in both C3 and C4 plants. This caused an increase in canopy temperature (0.7 °C) coupled with a 19% yield increase in C3 crops. There is evidence that an increase in CO2 has also phased down the effect of oxidative stress. Though, there is limited literature available about the impact of elevated carbon dioxide keeping into consideration the drought and heat responses of various crops.

3. Elevated carbon dioxide and its interaction with biotic stress-altered pathogen aggravation and virulence

The changing climate has affected pest-crop dynamics with more frequent outbreaks and changed the geographical distribution of pests, posing an economic threat to crops. Sometimes, other abiotic stresses like drought could increase fungal virulence as reported in drought-tolerant peanut and Aspergillus interaction. However, a combined interaction is not always additive as both unique and common responses have been observed. Increased COcauses greater photosynthate availability, but reduced foliage quality along with an increased concentration of plant defensive compounds after a pest infestation. This, in turn, affects insect feeding and increases disease incidence and predator parasitism interactions.

4. Molecular interventions for crop improvement under elevated carbon-dioxide

While elevated CO2 may cause greater photosynthate availability, the interaction of elevated CO2 with mentioned biotic and abiotic stresses calls for the development of climate change ready crop varieties. Thus, genomics assisted breeding along with other modern approaches can be very powerful tools to develop superior varieties, to de-risk the existing food system. This transformative approach towards the production of plants and crops would be instrumental in sustainably ensuring food security.

An integrated research framework for the future

The discussion and evidence presented illustrate that the effect of elevated CO2 under a changing climate scenario is multifaceted and aggravated by the overlapping interaction of stressors. The notion that CO2 has beneficial effects in terms of increased productivity is now being questioned since the photosynthetic fertilization effect is short term and often not time-tested for major crop species. The IPCC 2018 special report highlights several policy-level approaches that are aimed at limiting greenhouse gas emission. The scientific community needs to be prepared with suitable research outcomes to cope with the effects of elevated atmospheric CO2 levels. In this regard, an integrated framework combining different biological disciplines has been proposed by the team (Fig. 1).

Figure 1: A representation of a multifaceted strategy that could be employed to harness cutting edge technologies and greater precision to cope with elevated CO2, and generally with a changing climate.
Figure 1: A representation of a multifaceted strategy that could be employed to harness cutting edge technologies and greater precision to cope with elevated CO2, and generally with a changing climate.

While significant advances have been made in crop genomics, systems biology and genomics-assisted breeding, the success of trait dissection and trait deployment is very much dependent on the quality and precision of phenotyping. Recent advances in plant phenotyping using high throughput phenotyping tools have revolutionized the uptake of phenotype and allelic information in a more precise and robust way and complemented high throughput genomic resources

In the opinion of the authors of the publication, an integrated research framework that includes genomics/ systems biology and phenomics together with crop modelling would result in faster data-driven advances for understanding the optimal GxExM (genotype x environment x management) scenarios for current and projected climates. Interdisciplinary approaches as has been done through the Climate-Smart Village approach, are key to graduating from a descriptive level to an improved quantitative and process-level understanding of sustainable crop productivity.

Read more:

A view from Afghanistan

Rajiv Kumar Sharma on insecurity, rural isolation and challenge of supporting crop production in a conflict zone.

by Emma Orchardson

Farmers inspect wheat in Balkh, Afghanistan. Credit: USAID Afghanistan

In September 2002, looters raided the storage facilities housing Afghanistan’s largest collection of crop genetic material. In the towns of Ghazni and Jalalabad, hundreds of samples of the country’s rich agricultural heritage were lost as wheat, barley, pistachio and pomegranate seeds were ripped from the plastic containers designed to preserve them. The incident was described as a tragic loss, with representatives from the United Nations lamenting the fact that these lost varieties were essential genetic resources for sustaining future food production in a country where farmers struggle to withstand harsh climatic conditions such as recurrent drought.

Nearly two decades later, these climatic challenges have been further compounded by demographic ones, as rising population and income levels fuel consumption of some of the country’s most important cereal crops, including wheat – which makes up around 60% of the nation’s daily caloric intake – and maize. Failure to meet domestic demand could have devasting consequences in a country whose growth and economy are dominated by agriculture.

Some of Afghanistan’s obstacles to crop production are not unique. Poor market support, limited mechanization and inadequate storage stifle growing and processing activities from Latin America to South Asia. Others – such as rain dependent wheat and grossly deficient extension services – are more specific to a country in the midst of ongoing and widespread conflict. As anti-government forces continue to target transport infrastructure and police road travel between provinces, links between the nation’s pockets of relative urban security and the 70% of Afghans who live and work in rural areas are drastically reduced.

Farmers beyond reach

“Insecurity is by far the biggest hurdle in communication with and reaching out to farmers,” says Rajiv Kumar Sharma, the International Maize and Wheat Improvement Center’s (CIMMYT) Country Representative for Afghanistan.

The organization has been operating in the country since 2002, supporting national agricultural research systems through the provision of germplasm, support for data collection and analysis, and working to release high-yielding, disease resistant crop varieties into the Afghan seed system and farmers’ fields. While capacity development for local research partners has been extremely successful, connecting directly with farmers remains practically impossible in many areas.

Sharma points to the results of a 2016 survey on the adoption of new improved maize and wheat varieties and crop management practices under local conditions, which found much higher adoption rates among farmers who had received some form of training or who had access to markets and a main road. “However, because even the most basic transport facilities are missing in most places, during our field visits or meetings it was not unusual to hear from farmers that it was the first time they had ever met their extension workers.”

“It’s a very complicated situation,” he explains. “We cannot look at any one factor in isolation because everything is interconnected – insecurity, governance, infrastructure, logistics, access to roads, transport and markets.”

Even the country’s seed market, he adds, seems to be an artificial one. “I used to say that the seed market was donor-driven because they would give money to the government, who would purchase all the seed produced and distribute among farmers. But once that system dwindled around 2014/15, seed production came down. If production is not remunerative, farmers simply aren’t going to invest.”

In the face of limited resources and capacity, non-available irrigation services, collapsed industry and a fragile economy, Sharma highlights the lack of infrastructure as the main limiting factor in developing the country’s seed sector. “It matters because it really impacts the extent to which we can reach people.”

“Did you know, for example, that Afghanistan did not have a postal system until few years ago and the one present today is not fully functioning. Can you imagine how much effort it takes for us just to move our seed packets and data sheets from one province to another?”

With no functioning courier services and limited public transport between cities, trial data dispatches are sent across the country using private taxi services. There are obvious and imaginable challenges involved in working in a conflict zone, he explains, but realities on the ground are often more challenging than what you’d expect.

Successes with seed

It’s not all doom and gloom in Kabul though, and Sharma remains optimistic about the progress of CIMMYT’s work in Afghanistan despite the numerous challenges. “It’s not easy working here, but still we can do something.”

Recent successes include the release of four new high yielding and disease resistant wheat varieties in early 2020 and the successful culmination of the “Improving food security by enhancing wheat production and its resilience to climate change through maintaining the diversity of currently grown landraces” project in December 2019. Funded by the International Treaty on Plant Genetic Resources for Food and Agriculture, the project supported the collection, characterization and evaluation of the country’s landraces and relied heavily on dedicated local staff and their ability to navigate the territory as safely as possible. “They know where they can and can’t go, as well as the dynamics and how to protect themselves,” Sharma explains.

In the northwestern provinces of Balkh and Herat, staff were able to collect landraces from farmer fields for testing against modern improved varieties at research stations. The team were then able to remove those susceptible to disease, purify the superior ones and improve them with regards to variability and uniformity. They found that, on average, Afghan wheat landraces yielded highest under rainfed conditions when compared with those from Iran and Turkey, as well as against winter wheat trials carried out in 2018.

These landraces have since been used in breeding improvement and crossing programs, as well as being multiplied and given back to local communities. “This has really enriched regional variability and made these landraces more useful for those communities who grow them and thus contribute to conserving useful variability on farm.”

Historic wheat research station poised to host cutting-edge research

This story by Alison Doody was originally published on the CIMMYT website.

Early photo of Toluca station. (Photo: Fernando Delgado/CIMMYT)

It was the site where International Maize and Wheat Improvement Center (CIMMYT) scientist Norman Borlaug famously received news of his 1970 Nobel Peace Prize win. Now, Toluca station will become CIMMYT’s new testing site for rapid generation advancement and speed breeding in wheat – a method that accelerates generation advancement of crops and shortens the breeding cycle using tools like continuous lighting and temperature control.

The Toluca wheat experimental station is one of CIMMYT’s five experimental stations in Mexico, located in a picturesque town on the outskirts of Mexico’s fifth largest city, Toluca, about 60 kilometers southwest of Mexico City. The station was strategically chosen for its cool, humid conditions in summer. These conditions have made it an ideal location for studying wheat resistance to deadly diseases including yellow rust and Septoria tritici blotch.

Since its formal establishment in 1970, Toluca has played a key role in CIMMYT’s wheat breeding program. The site is also of significant historical importance due to its origins as a testing ground for Borlaug’s shuttle breeding concept in the 1940s, along with Ciudad Obregón in the Sonora state of northern Mexico. The breeding method allowed breeders to plant at two locations to advance generations and half the breeding cycle of crops.

Applying this unorthodox breeding method, Borlaug was able to advance wheat generations twice as fast as standard breeding programs. Planting in contrasting environments and day lengths — from the cool temperatures and high rainfall of Toluca to the desert heat of Ciudad Obregón — also allowed Borlaug and his colleagues to develop varieties that were more broadly adaptable to a variety of conditions. His shuttle breeding program was so successful that it provided the foundations of the Green Revolution.

Toluca was also the site where the first sexual propagation of the destructive plant pathogen Phytophtora infestans was reported. The deadly pathogen is best known for causing the potato late blight disease that triggered the Irish potato famine.

Recent progress of the rapid generation advancement screenhouse under construction at Toluca station. (Photo: Suchismita Modal/CIMMYT)

New life for the historic station

More than 50 years since its establishment, the station will once again host cutting-edge innovation in wheat research, as the testing ground for a new speed breeding program led by wheat scientists and breeders from Accelerating Genetic Gains in Maize and Wheat (AGG).

Funded by the Bill & Melinda Gates Foundation, the UK Department for International Development (DFID), the U.S. Agency for International Development (USAID) and the Foundation for Food and Agriculture Research (FFAR), AGG aims to accelerate the development and delivery of more productive, climate-resilient, gender-responsive, market-demanded, and nutritious maize and wheat varieties.

While most breeding programs typically take between 7-8 years before plants are ready for yield testing, shuttle breeding has allowed CIMMYT to cut the length of its breeding programs in half, to just 4 years to yield testing. Now, AGG wheat breeders are looking to shorten the breeding cycle further, through rapid generation advancement and speed breeding.

Speed breeding room at Toluca station. The Heliospectra lights support the faster growth of plants. (Photo: Suchismita Mondal/CIMMYT)

“The AGG team will use a low-cost operation, in-field screenhouse, spanning 2 hectares, to grow up to 4 generations of wheat per year and develop new germplasm ready for yield testing within just 2 years,” said Ravi Singh, CIMMYT distinguished scientist and head of wheat improvement. “This should not only save on cost but also help accelerate the genetic gain due to a significant reduction in time required to recycle best parents.”

Construction of the new rapid generation advancement and speed breeding facilities is made possible by support from the Bill and Melinda Gates Foundation and DFID through Delivering Genetic Gain in Wheat (DGGW), a 4-year project led by Cornell University, which ends this year. It is expected to be complete by September.

The concept of speed breeding is not new. Inspired by NASA’s efforts to grow crops in space, scientists at the University of Sydney, the University of Queensland (UQ) and the John Innes Centre developed the technique to accelerate the development of crops and improve their quality. The breeding method has been successfully used for crops like spring wheat, barley, pea, chickpea, radish and canola.

CIMMYT Global Wheat Program Director Hans Braun highlighted the importance of testing the new breeding scheme. “Before completely adopting the new breeding scheme, we need to learn, optimize and analyze the performance results to make necessary changes,” he said.

If all goes well, Toluca could once again be on the vanguard of wheat research in the near future.

“We plan to use the speed breeding facility for rapid integration of traits, such as multiple genes for resistance, to newly-released or soon to be released varieties and elite breeding lines,” said CIMMYT Wheat Breeder Suchismita Mondal, who will lead the work in these facilities. We are excited to initiate using the new facilities.”

Rapid generation advancement screenhouse under construction at Toluca station in October 2019. (Photo: Alison Doody/CIMMYT)

“Better, faster, equitable, sustainable” – wheat research community partners join to kick off new breeding project

This story by Marcia MacNeil was originally published on the CIMMYT website.

More than 100 scientists, crop breeders, researchers, and representatives from funding and national government agencies gathered virtually to initiate the wheat component of a groundbreaking and ambitious collaborative new crop breeding project led by the International Maize and Wheat Improvement Center (CIMMYT).

The new project, Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods, or AGG, 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 U.K. Department for International Development (DFID) and the U.S. Agency for International Development (USAID), the project specifically focuses on supporting smallholder farmers in low- and middle-income countries. The international team uses innovative methods — such as rapid cycling and molecular breeding approaches — that improve breeding efficiency and precision to produce varieties that are climate-resilient, pest and disease resistant and highly nutritious, targeted to farmers’ specific needs.

The wheat component of AGG builds on breeding and variety adoption work that has its roots with Norman Borlaug’s Nobel Prize winning work developing high yielding and disease resistance dwarf wheat more than 50 years ago. Most recently, AGG builds on Delivering Genetic Gain in Wheat (DGGW), a 4-year project led by Cornell University, which ends this year.

“AGG challenges us to build on this foundation and make it better, faster, equitable and sustainable,” said CIMMYT Interim Deputy Director for Research Kevin Pixley.

At the virtual gathering on July 17, donors and partner representatives from target countries in South Asia joined CIMMYT scientists to describe both the technical objectives of the project and its overall significance.

“This program is probably the world’s single most impactful plant breeding program. Its products are used throughout the world on many millions of hectares,” said Gary Atlin from the Bill & Melinda Gates Foundation. “The AGG project moves this work even farther, with an emphasis on constant technological improvement and an explicit focus on improved capacity and poverty alleviation.”

Alan Tollervey from DFID spoke about the significance of the project in demonstrating the relevance and impact of wheat research.

“The AGG project helps build a case for funding wheat research based on wheat’s future,” he said.

Nora Lapitan from the USAID Bureau for Resilience and Food Security listed the high expectations AGG brings: increased genetic gains, variety replacement, optimal breeding approaches, and strong collaboration with national agricultural research systems in partner countries.

Reconnecting with trusted partners

The virtual meeting allowed agricultural scientists and wheat breeding experts from AGG target countries in South Asia, many of whom have been working collaboratively with CIMMYT for years, to reconnect and learn how the AGG project both challenges them to a new level of collaboration and supports their national wheat production ambitions.

“With wheat blast and wheat rust problems evolving in Bangladesh, we welcome the partnership with international partners, especially CIMMYT and the funders to help us overcome these challenges,” said Director General of the Bangladesh Wheat and Maize Research Institute Md. Israil Hossain.

Director of the Indian Institute for Wheat and Barley Research Gyanendra P. Singh praised CIMMYT’s role in developing better wheat varieties for farmers in India.

“Most of the recent varieties which have been developed and released by India are recommended for cultivation on over 20 million hectares. They are not only stress tolerant and high yielding but also fortified with nutritional qualities. I appreciate CIMMYT’s support on this,” he said.

Executive Director of the National Agricultural Research Council of Nepal Deepak K. Bhandari said he was impressed with the variety of activities of the project, which would be integral to the development of Nepal’s wheat program.

“Nepal envisions increased wheat productivity from 2.84 to 3.5 tons per hectare within five years. I hope this project will help us to achieve this goal. Fast tracking the replacement of seed to more recent varieties will certainly improve productivity and resilience of the wheat sector,” he said.

The National Wheat Coordinator at the National Agricultural Research Center of Pakistan, Atiq Ur-Rehman, told attendees that his government had recently launched a “mega project” to reduce poverty and hunger and to respond to climate change through sustainable intensification. He noted that the support of AGG would help the country increase its capacity in “vertical production” of wheat through speed breeding. “AGG will help us save 3 to 4 years” in breeding time,” he said.

For CIMMYT Global Wheat Program Director Hans Braun, the gathering was personal as well as professional.

“I have met many of you over the last decades,” he told attendees, mentioning his first CIMMYT trip to see wheat programs in India in 1985. “Together we have achieved a lot — wheat self-sufficiency for South Asia has been secured now for 50 years. This would not be possible without your close collaboration, your trust and your willingness to share germplasm and information, and I hope this will stay. “

Braun pointed out that in this project, many national partners will gain the tools and capacity to implement their own state of the art breeding strategies such as genomic selection.

“We are at the beginning of a new era in breeding,” Braun noted. “We are also initiating a new era of collaboration.”

The wheat component of AGG serves more than 30 million wheat farming households in Bangladesh, Ethiopia, India, Kenya, Nepal and Pakistan. A separate inception meeting for stakeholders in sub-Saharan Africa is planned for next month.

New infographic highlights an early warning system for wheat blast in Bangladesh

Wheat blast is a devastating fungal disease threatening agricultural productivity and food security in the Americas and South Asia. First identified in Brazil in 1984, it spread to Bangladesh in 2016, prompting the government to request scientists for an early warning system.

A new infographic, developed by researchers at the Cereal Systems Initiative for Asia (CSISA) explains how wheat blast is spread and how an early warning system can help extension agents and farmers get ahead of the disease.

Harnessing the potential of state-of-the-art genomic technologies for accelerating the rate of genetic gain in wheat

This blog by Philomin Juliana was originally published on the Borlaug Global Rust Initiative website.

Genomic breeding technologies offer exciting opportunities for wheat improvement amidst escalating challenges like changing climates, unpredictable temperatures, reduced precipitation and biotic stresses. Recognizing the need for accelerating the rate of genetic gain in wheat, the Delivering Genetic Gain in Wheat and the USAID Feed the Future projects have contributed extensively to the phenotyping and genotyping of an impressive number of 74,403 CIMMYT wheat breeding lines, generating more than a million phenotyping datapoints and 3 billion marker datapoints. These big datasets have been leveraged for evaluating state-of-the-art genomic technologies like genomic selection, genome-wide association mapping, and genomic fingerprinting that have empowered the CIMMYT wheat breeding program to efficiently deliver high-yielding, climate resilient and disease resistant varieties.

Genomic selection, a genomics-based selection strategy where genomic-estimated breeding values obtained from genome-wide molecular markers are used for the selection of individuals has gained burgeoning interest in recent years and is advocated as an approach that can dramatically accelerate genetic gains and change the role of phenotyping in breeding. Since it can be beneficial for CIMMYT and other wheat breeding programs, particularly in developing countries that are constrained in their ability to evaluate a large number of breeding lines due to limited resources, we have done a comprehensive evaluation of genomic selection for 35 key traits in wheat evaluated by CIMMYT and national partners.

Our results have provided strong evidence that genomic selection will be a very powerful tool for end-use quality related traits like alveograph, mixing time, grain protein, flour yield, flour sedimentation, loaf volume etc. and some diseases, that were well predicted using historic training populations. Hence, genomic estimated breeding values for these traits have been routinely integrated into selection decisions and selections have been scaled up to un-phenotyped early-generations using predicted values. This has led to a paradigm shift in integrating genomic breeding tools into CIMMYT’s wheat breeding pipeline and has resulted in better selection efficiency and high phenotyping cost-savings to the program.

We have also explored several genomic selection implementation scenarios for grain yield and determined the prospects of using genomic selection for minimizing the number of lines, years and sites tested by borrowing information from relatives, correlated years and sites. For this, we leveraged a large dataset of 61,064 grain yield observations from 1,974 yield trials evaluated by CIMMYT and national partners at 100 locations in 34 countries including Afghanistan, Algeria, Angola, Argentina, Bangladesh, Canada, Chile, China, Egypt, Ethiopia, Greece, India, Iran, Iraq, Libya, Mexico, Morocco, Myanmar, Nepal, Nigeria, Pakistan, Paraguay, Portugal, South Africa, Spain, Sudan, Taiwan, Tanzania, Tunisia, Turkey, Ukraine, Venezuela, Zambia and Zimbabwe. We also applied a quantitative genetics framework to explore the relationships between grain yield predictabilities and estimated heritabilities, variance components, phenotypic and genetic correlations for grain yield evaluated in different environments, all of which provided substantial insights into the challenges of predicting grain yield and the prospects for designing future genomic selection schemes.

We also performed a large genome-wide association study that led to a significant breakthrough in understanding the genetic-architecture of key traits like phenology, plant height, lodging, resistance to rusts and other foliar diseases, grain color, kernel weight, dough strength, bread-making quality, protein content and grain yield in wheat. We have identified hundreds of significant marker-trait associations and delineated 142 unique linkage-based QTLs, among which 55.6% were novel. One of the extremely intriguing and novel co-locations identified in our study was the association of the 2NS translocation from Aegilops ventricosa with grain yield in 10 different environments, stem rust seedling resistance to many races, stripe rust in Mexico, wheat blast, and lodging, demonstrating its remarkable value for wheat breeding. We also anchored about 542 significant trait-associated markers and 118 previously reported genes in proximity to the significant markers onto a powerful reference phenotype-genotype map aligned to the refence genome of bread wheat, which is a valuable resource providing new opportunities for accelerating genomics-assisted wheat breeding through a targeted selection of desired regions.

We have fingerprinted 44,624 wheat lines for 195 traits-associated markers, generating over 7.6 million data-points, which is a phenomenal resource to the global wheat community for enhancing productivity and stress-resilience in wheat. The fingerprinted panel comprises several key varieties cultivated worldwide, parents from CIMMYT’s crossing blocks 2009-2018 and is a quantum leap in understanding the genetic basis of traits in superior varieties. For example, a benchmark high-yielding CIMMYT-derived Mexican variety, BORLAUG100 F2014 was found to be rich in grain yield favorable alleles and a key stem rust QTL against the Ug99 lineage was traced back to old Kenyan (Kenya Fahari, Kenya Swara) and Ethiopian (FH6-1-7) varieties.

Furthermore, we also examined the marker allele frequency dynamics for key traits over 15 years to characterize the role of selection at CIMMYT in shaping patterns of allelic variation over time. While there was a spectacular increase in favorable allele frequencies for many traits over years due to selection, the results also emphasized the need for a continued effort to introduce novel sources of favorable alleles and the importance of integrating genomic tools in achieving accelerated enrichment of favorable alleles. Overall, our research has facilitated extending the frontiers of genomics-assisted breeding in wheat and will be very beneficial for future diagnostic marker development, gene discovery, marker-assisted selection and genomic selection in wheat.

Philomin Juliana’s 5 May 2020 seminar is here.