Jared Crain, a research assistant professor of plant pathology, collaborates with CIMMYT on wheat genomics. Leading the Feed the Future Innovation Lab for Applied Wheat Genomics at K-State, Crain and his team annually analyze DNA from 19,000 plants.
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In 2023, India reached a record wheat harvest of over 110 million tons. A partnership between CIMMYT and the Indian Institute of Wheat and Barley Research (IIWBR) now allows farmers to pre-order advanced wheat varieties, transforming the nation’s agriculture.
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Agriculture is central to South Asian economies, lives and livelihoods. However, the challenges of an increasing population and brisk economic growth are straining the agriculture sector as it struggles to meet the present and future demand for food, nutritional security, and economic development. Not only this, the three Cs – COVID, climate change and conflict – are fueling the growing fragility in food systems across the world.
To address these issues and find potential solutions, the Borlaug Institute for South Asia (BISA) organized a high-level meeting with top agriculture ministry officials from its neighboring countries – Sri Lanka, Nepal, Bangladesh, Bhutan, India and Pakistan – to collaborate and learn from each other.
BISA’s outreach to India’s neighbors in South Asia has already produced results. Data from the BISA farm in Ludhiana, India, on resistance to yellow rust that affects wheat crop has been used in Nepal, Afghanistan, and Pakistan. Genomic prediction evaluation for grain yield and other traits worked on at BISA through the help of the Global Wheat Program of the International Maize and Wheat Improvement Center (CIMMYT) has been extended to Pakistan, Bangladesh, and Nepal since 2020. Regular training is organized for students, scientists and farmers in India on breeding and climate resistant technologies, and BISA scientists organize courses in Nepal on climate-smart technologies.
Read more in Amar Ujala (published in Hindi): Can agriculture bring South Asian countries together?
Cover photo: Tara Miah (50) is a farmer from Rajguru in Rahamanbari union, Barisal, Bangladesh. He used seeder fertilizer drills to plant wheat on his fields. Previously, this was done manually. SFD has resulted in a better harvest for Miah. (Credit: Ranak Martin)
For thousands of years, farmers in Afghanistan, Turkey and other countries in the region, have been breeding wheat, working closely with the environment to develop traditional wheat varieties known as landraces. Untouched by scientific breeding, landraces were uniquely adapted to their environment and highly nutritious.
As agriculture became more modernised and intensified, it threatened to push these traditional landraces into extinction, resulting in the loss of valuable genetic diversity. Institutions around the world decided to act, forming germplasm collections known as genebanks to safely house these landraces.
In 2009, a team of wheat scientists from the International Maize and Wheat Improvement Center (CIMMYT), the International Center for Agricultural Research in the Dry Areas (ICARDA), the UN Food and Agriculture Organization (FAO), and national partners set off on a five-year expedition across Central Asia to collect as many landraces as they could find. The project, led by FAO Cereal Breeder and former CIMMYT Principal Scientist Alexey Morgunov, was made possible by the International Treaty on Plant Genetic Resources for Food and Agriculture Benefit-Sharing Fund.
The project had two main missions. The first is to preserve landrace cultivation in three countries, Afghanistan, Turkey and other countries in the region by selecting, purifying, and multiplying the landraces and giving them back to farmers. The second is to scientifically evaluate, characterize and use these landrace varieties in ongoing breeding programmes, exchange the information between the countries, and to deposit the seeds in genebanks to safely preserve them for future generations.
The latest results from the project were published in July in the journal Crops. The study, authored by a team of experts from CIMMYT, ICARDA, FAO, and research institutes in Afghanistan, Turkey and other countries in the region, compared the diversity, performance, and adaptation of the collected wheat landraces with modern varieties grown in the regions using a series of field experiments and cutting-edge genomic tools.
“Landraces are very useful from a breeding perspective because they have been cultivated by farmers over thousands of years and are well adapted to climate change, have strong resistance to abiotic stresses and have very good nutritional quality,” said Rajiv Sharma, a CIMMYT senior scientist and co-author of the paper.
“We were interested in seeing how well landraces adapt to certain environments, how they perform agronomically, and whether they are more diverse than modern varieties grown in these regions – as well as give their improved versions back to farmers before they are lost.”
The experiments, which were carried out in 2018 and 2019 in Turkey, and 2019 in Afghanistan, and other countries in the region revealed several physical characteristics in landraces which are no longer present in modern varieties. For example, the team found striking differences in spike and grain colors with landraces more likely to have red spikes and white grains, and modern varieties tending to have white spikes and red grains. This may have adaptive values for high altitudes and dry conditions.
A surprising finding from the study, however, was that landraces were not more genetically diverse than modern landraces.
“Many people thought that when we went from cultivating landraces to modern varieties, we lost a lot of diversity but genetically speaking, that’s not true. When you look at the genomic profile, modern varieties are just as diverse as landraces, maybe even a little bit more so,” said Sharma.
When the team compared landraces and modern varieties on crop performance, the results were mixed with modern wheat varieties outyielding landraces in half of the environments tested. However, they found that the highest yielding landraces were just as good as the best modern varieties – a reassuring finding for farmers concerned about the productivity of their crops.
A new breeding paradigm
The results of the study have important implications for landrace conservation efforts in farmers’ fields and in future breeding strategies. While crossing wheat landraces with modern varieties to develop improved modern varieties is not new, the authors proposed a novel alternative breeding strategy to encourage the continued cultivation of landraces: improving landraces by crossing them with other landraces.
“In order to maintain landraces, we have to make them competitive and satisfy farmers’ needs and requirements. One option is that we breed landraces,” said Sharma.
“For example, you might have a landrace that is very-high yielding but susceptible to disease. By crossing this variety with another landrace with disease-resistant traits you can develop a new landrace better suited to the farmer and the environment. This approach maintains all the features of landraces – we are simply accelerating the evolution process for farmers to replace the very fast disappearance of these traditional varieties.”
This approach has already been used by crop scientists at the University of California, Davis who has successfully developed and registered “heirloom-like varieties” of dry beans. The varieties trace about 98% of their ancestry to landraces but are resistant to the common mosaic virus.
Heirloom food products are becoming increasingly popular with health-conscious consumers who are willing to pay a higher price for the products, garnering even more interest in conserving traditional landraces.
One of the overarching aims of the project was to give wheat landraces back to farmers and let nature take its course. Throughout the mission, the team multiplied and returned landrace seed to over 1500 farmers in communities across Afghanistan, Turkey and other countries in the region. The team also supplied over 500 farmers with improved landrace seed between 2018 and 2019.
Despite the political turmoil facing these countries, particularly Afghanistan, farmers are still growing wheat and the project’s contribution to food security will continue.
These landraces will take their place once more in the farming landscape, ensuring on-farm wheat diversity and food security for future generations.
This research was conducted with the financial assistance of the European Union within the framework of the Benefit-Sharing Fund project “W2B-PR-41-TURKEY” of the FAO’s International Treaty on Plant Genetic Resources for Food and Agriculture.
Spot blotch, caused by the fungus Biopolaris sorokiniana poses a serious threat to bread wheat production in warm and humid wheat-growing regions globally, affecting more than 25 million hectares and resulting in huge yield losses.
Chemical control approaches, including seed treatment and fungicides, have provided acceptable spot blotch control. However, their use is unaffordable to resource-poor farmers and poses a hazard to health and the environment. In addition, “abiotic stresses like heat and drought that are widely prevalent in South Asia compound the problem, making varietal genetic resistance the last resort of farmers to combat this disease,” according to Pawan Singh, Head of Wheat Pathology at the International Maize and Wheat Improvement Center (CIMMYT). Therefore, one of CIMMYT’s wheat research focus areas is developing wheat varieties that carry genetic resistance to the disease.
Previously, only four spot blotch resistance genes in bread wheat had been identified. Through a new study, CIMMYT scientists have identified novel genomic regions associated with spot blotch resistance using the genome-wide association mapping approach with 6,736 advanced breeding lines from different years (2013 to 2020), evaluated at CIMMYT’s spot blotch screening platform in Agua Fría, in Mexico’s state of Morelos.
The study’s results are positive and confirmed that:
“Considering the persistent threat of spot blotch to resource-poor farmers in South Asia, further research and breeding efforts to improve genetic resistance to the disease, identify novel sources of resistance by screening different germplasm, and selecting for genomic regions with minor effects using selection tools like genomic selection is essential,” explained Philomin Juliana, Molecular Breeder and Quantitative Geneticist at CIMMYT.
Read the full study:
Genome-Wide Association Mapping Indicates Quantitative Genetic Control of Spot Blotch Resistance in Bread Wheat and the Favorable Effects of Some Spot Blotch Loci on Grain Yield
Cover photo: Researchers evaluate wheat for spot blotch at CIMMYT’s experimental station in Agua Fría, Jiutepec, Morelos state, Mexico. (Photo: Xinyao He and Pawan Singh/CIMMYT)
Five international wheat research teams have been awarded grants for their proposals to boost climate resilience in wheat through discovery and development of new breeding technologies, screening tools and novel traits.
Wheat is one of the world’s most important staple crops, accounting for about 20% of all human calories and protein and is increasingly threatened by the impacts of climate change. Experts around the world are working on ways to strengthen the crop in the face of increasing heat and drought conditions.
The proposals were submitted in response to a call by the Heat and Drought Wheat Improvement Consortium (HeDWIC), led by the International Maize and Wheat Improvement Center (CIMMYT) and global partners, made in 2021.
The grants were made possible by co-funding from the Foundation for Food & Agriculture Research (FFAR) and in-kind contributions from awardees as part of a project which brings together the latest research from scientists across the globe to deliver climate resilient wheat to farmers as quickly as possible.
Cutting-edge wheat research
Owen Atkin, from the Centre for Entrepreneurial Agri-Technology at the Australian National University, leads the awarded project “Discovering thermally stable wheat through exploration of leaf respiration in combination with photosystem II capacity and heat tolerance.”
“The ratio of dark respiration to light and CO2 saturated photosynthesis is a clear indicator of the respiratory efficiency of a plant,” Atkin said. “We will measure and couple this indicator of respiratory efficiency to the leaf hyperspectral signature of field grown wheat exposed to heat and drought. The outcome could be a powerful tool which is capable of screening for wheat lines that are more productive when challenged with drought and heatwave.”
Hannah M. Schneider, of Wageningen University & Research, leads the awarded project examining the use of a novel root trait called Multiseriate Cortical Sclerenchyma to increase drought-tolerance in wheat.
“Drought is a primary limitation to global crop production worldwide. The presence of small outer cortical cells with thick, lignified cell walls (MCS: Multiseriate Cortical Sclerenchyma) is a novel root trait that has utility in drought environments,” Schneider said. “The overall objective of this project is to evaluate and develop this trait as a tool to improve drought resistance in wheat and in other crops.”
John Foulkes, of the University of Nottingham, leads an awarded project titled “Identifying spike hormone traits and molecular markers for improved heat and drought tolerance in wheat.”
“The project aims to boost climate-resilience of grain set in wheat by identifying hormone signals to the spike that buffer grain set against extreme weather, with a focus on cytokinin, ABA and ethylene responses,” Foulkes said. “This will provide novel phenotyping screens and germplasm to breeders, and lay the ground-work for genetic analysis and marker development.”
Erik Murchie, from the University of Nottingham, leads an awarded project to explore new ways of determining genetic variation in heat-induced growth inhibition in wheat.
“High temperature events as part of climate change increasingly limit crop growth and yield by disrupting metabolic and developmental processes. This project will develop rapid methods for screening growth and physiological processes during heat waves, generating new genetic resources for wheat,” Murchie said.
Eric Ober of the National Institute of Agricultural Botany in the UK, leads the awarded project “Targeted selection for thermotolerant isoforms of starch synthase.”
“Wheat remains a predominant source of calories and is fundamental to regional food security around the world. It is urgent that breeders are equipped to produce new varieties with increased tolerance to heat and drought, two stresses that commonly occur together, limiting grain production. The formation and filling of grain depends on the synthesis of starch, but a key enzyme in the pathway, starch synthase, is particularly sensitive to temperatures over 25°C. However, there exist forms of this enzyme that exhibit greater thermotolerance than that found in most current wheat varieties,” Ober said. “This project aims to develop a simple assay to screen diverse germplasm for sources of more heat-resistant forms of starch synthase that could be bred into new wheat varieties in the future.”
Breakthroughs from these projects are expected to benefit other crops, not just wheat. Other benefits of the projects include closer interaction between scientists and breeders and capacity building of younger scientists.
A recent publication in the journal Frontiers of Plant Science provides results of the first-ever study to test genomic selection in breeding for resistance to wheat blast, a deadly disease caused by the fungus Magnaporthe oryzae that is spreading from its origin in Brazil to threaten wheat crops in South Asia and sub-Saharan Africa.
Genomic selection identifies individual plants based on the information from molecular markers, DNA signposts for genes of interest, that are distributed densely throughout the wheat genome. For wheat blast, the results can help predict which wheat lines hold promise as providers of blast resistance for future crosses and those that can be advanced to the next generation after selection.
In this study, scientists from the International Maize and Wheat Improvement Center (CIMMYT) and partners evaluated genomic selection by combining genotypic data with extensive and precise field data on wheat blast responses for three sets of genetically diverse wheat lines and varieties, more than 700 in all, grown by partners at locations in Bangladesh and Bolivia over several crop cycles.
The study also compared the use of a small number of molecular markers linked to the 2NS translocation, a chromosome segment from the grass species Aegilops ventricosa that was introduced into wheat in the 1980s and is a strong and stable source of blast resistance, with predictions using thousands of genome-wide markers. The outcome confirms that, in environments where wheat blast resistance is determined by the 2NS translocation, genotyping using one-to-few markers tagging the translocation is enough to predict the blast response of wheat lines.
Finally, the authors found that selection based on a few wheat blast-associated molecular markers retained 89% of lines that were also selected using field performance data, and discarded 92% of those that were discarded based on field performance data. Thus, both marker-assisted selection and genomic selection offer viable alternatives to the slower and more expensive field screening of many thousands of wheat lines in hot-spot locations for the disease, particularly at early stages of breeding, and can speed the development of blast-resistant wheat varieties.
Read the full study:
Genomic Selection for Wheat Blast in a Diversity Panel, Breeding Panel and Full-Sibs Panel
The research was conducted by scientists from the International Maize and Wheat Improvement Center (CIMMYT), the Bangladesh Wheat and Maize Research Institute (BWMRI), the Instituto Nacional de Innovación Agropecuaria y Forestal (INIAF) of Bolivia, the Borlaug Institute for South Asia (BISA) and the Indian Council of Agricultural Research (ICAR) in India, the Swedish University of Agricultural Sciences (Alnarp), and Kansas State University in the USA. Funding for the study was provided by the Bill & Melinda Gates Foundation, the Foreign and Commonwealth Development Office of the United Kingdom, the U.S. Agency for International Development (USAID), the CGIAR Research Program on Wheat (WHEAT), the Indian Council of Agricultural Research (ICAR), the Swedish Research Council, and the Australian Centre for International Agricultural Research (ACIAR).
Cover photo: A researcher from Bangladesh shows blast infected wheat spikes and explains how the disease directly attacks the grain. (Photo: Chris Knight/Cornell University)
A five-year partnership being launched by the Innovative Genomics Institute (IGI)—a non-profit founded by Nobel Laureate Jennifer Doudna—and CGIAR, the world’s largest publicly-funded agricultural research partnership, will harness the power of science to help millions of people overcome poverty, hunger and malnutrition.
One in four people globally, and rising, are unable to afford a healthy diet. COVID-19 has exacerbated this trend by disrupting food production and distribution, driving up by 20 percent the number of people threatened by hunger in 2020. The pandemic is unfolding amidst an environmental and climate crisis which is undermining food production and our ability to nourish the world.
But global consensus is building for urgent action. At the COP26 meetings in November, 45 nations committed to shifting to more sustainable ways of farming and accelerate the deployment of green innovations. Similarly, in late September, many government representatives at the United Nations Food Systems Summit committed to accelerating the transformation of how we grow, transport, process, and consume food. Recognizing the centrality of science and innovation for driving that transformation, United Nations Secretary-General António Guterres called on the world to scale public and private investment in research for food.
According to Barbara Wells, Global Director for Genetic Innovation at CGIAR: “World-class science is vital for facilitating farmer adaptation and mitigating our food system’s contribution to climate change. Plant-breeding innovations can help ramp up food production while making farms more climate resilient, profitable and environmentally friendly”.
“Technologies such as gene editing, which enable scientists to make targeted changes to a crop’s DNA, can accelerate the development of more disease-resistant, water-efficient varieties that can improve food production and nutrition in areas that are especially vulnerable to climate change,” Dr. Wells explained.
CGIAR has produced and promoted innovations that are boosting the sustainable production of nutritious food in Africa, Asia and Latin America. Over the past five decades, CGIAR scientists and national partners have developed and disseminated robust and highly productive crop varieties and livestock breeds tailored to the needs of local men and women. Those innovations have helped hundreds of millions of people across the Global South overcome hunger and poverty.
The IGI is a collaboration of the University of California, Berkeley and the University of California, San Francisco with a mission to develop revolutionary genome-editing tools that enable affordable and accessible solutions in human health, climate, and agriculture. The IGI’s Climate & Sustainable Agriculture program focuses on developing crops that are resistant to pests and diseases, resilient to a changing climate, and less dependent on farmer inputs. Whereas the IGI is a pioneer in applied genomic research, CGIAR focuses on translating discoveries into improved crop varieties and cropping systems. This partnership provides an accelerated pipeline from upstream innovation to real-world impact.
“The IGI is testing technologies with great potential to benefit people in the countries where CGIAR is active, such as a way of removing the cyanide found in cassava—a staple upon which nearly a billion people depend—and fighting diseases in economically important crops like wheat, rice and bananas,” said Brian Staskawicz, the IGI Director of Sustainable Agriculture.
“The IGI is also pioneering new ways to reduce methane emissions from rice farming, which accounts for 2.5 percent of humanity’s contribution to global warming, by using genomic approaches to reduce methane production by soil microbes,” he added.
“By partnering with CGIAR, the IGI can ensure that the products of its research will benefit farmers and consumers in some of the world’s poorest countries, where CGIAR has been working for 50 years and has extensive partner networks,” said Dr. Melinda Kliegman, Director of Public Impact at the IGI. “Together we can accelerate the development and delivery of more climate-resilient, productive and nutritious crops for resource-poor farmers and consumers.”
Over the next five years, the IGI and CGIAR will use the latest breakthroughs in genomic science to enhance the resilience and productivity of farmers in low- and middle-income countries and improve the wellbeing and livelihoods of women and men in some of the world’s poorest communities.
Authored by CGIAR and the Innovative Genomics Institute (IGI)
Cover photo: Researchers at work at CGIAR’s International Institute of Tropical Agriculture campus in Ibadan, Nigeria. (Credit: Chris de Bode/CGIAR)
To help feed a growing world population, wheat scientists have turned to innovative technologies like genomic selection to hasten selection for positive traits — such as high grain yield performance and good grain quality — in varieties that are still undergoing testing. Instead of being shackled by the long duration of traditional breeding cycles, genomic selection allows scientists to make predictions regarding which traits will present when crossing two varieties; allowing breeders greater guidance and lessening potential time lost when crossing varieties that do not display potential for genetic gain. To reap the benefits of genomic selection, it is vital that the predictive models employed are as accurate as possible.
Currently, wheat breeders select characteristics like grain yield performance early in the breeding process, while selecting traits like good grain quality at a later stage in the breeding process.
In an article in the journal G3 Genes, researchers from the International Maize and Wheat Improvement Center (CIMMYT), and partners, led by CIMMYT scientist José Crossa along with Leonardo A. Crespo, Maria Itria Ibba and Alison R. Bentley, endeavored to determine if genomic prediction models could select for both characteristics simultaneously in the breeding process. This would improve selection accuracy in both early and later breeding stages, resulting a reduction in time and expense in delivering improved wheat varieties. They also tested the accuracy of a set of specific mathematical corrections applied to genomic predictions. These correction models identify correlations between genomic predictions and observed breeding values, such as increased yield or grain quality.
Considering two or more traits, like grain yield and good grain quality, is an example of a multi-trait model. The team examined this multi-trait model against a single trait model that improves one specific trait. Overall, the researchers found that prediction performance was highest using the multi-trait model.
However, the team also demonstrated that when breeding programs arrive at their genetic predictions, applying a specific correction method will account for differences between the predicted breeding value and the actual observed breeding value. Current correction models tend to underestimate that difference, which results in breeding programs not running as efficiently as possible.
By partnering selections from different stages in the breeding process and examining the resulting genetic predictions through a more appropriate correction model, the team has shown that breeding programs can use this to their benefit in developing and ultimately releasing improved wheat varieties that meet growing yield needs worldwide and respond to abiotic and biotic stressors.
The ultimate challenge for crop breeders is to increase genetic gain of a crop: literally, to increase the crop’s yield on farmers’ fields. Wheat and maize breeders from the International Maize and Wheat Improvement Center (CIMMYT) and partner institutions are working to achieve this in record time, developing new varieties tailored for farmers’ needs that are also pest- and disease-resistant, climate-resilient, and nutritious.
This work is part of the Accelerating Genetic Gain in Maize and Wheat for Improved Livelihoods (AGG) project. Among other methods, breeders are using state-of-the-art novel tools such as genomic selection to achieve this ambitious goal.
In genomic selection, breeders use information about a plant’s genetic makeup along with data on its visible and measurable traits, known as phenotypic data, to “train” a model to predict how a cross will turn out — information known as “genomic estimated breeding values (GEBV)” — without having to plant seeds, wait for them to grow, and physically measure their traits. In this way, they save time and costs by reducing the number of selection cycles.
However, research is still ongoing about the best way to use genomic selection that results in the most accurate predictions and ultimately reduces selection cycle time. A recent publication by CIMMYT scientist Sikiru Atanda and colleagues has identified an optimal genomic selection strategy that maximizes the efficiency of this novel technology. Although this research studied CIMMYT’s maize breeding programs, AGG scientists working on wheat genetic gain and zinc nutritional content see cross-crop impacts.
Shortening a lengthy process
In the typical breeding stages, breeders evaluate parental lines to create new crosses, and advance these lines through preliminary and elite yield trials. In the process, thousands of lines are sown, grown and analyzed, requiring considerable resources. In the traditional CIMMYT maize breeding scheme, for example, breeders conduct five stages of testing to identify parental lines for the next breeding cycle and develop high yielding hybrids that meet farmers’ needs.
In the current scheme using genomic selection, breeders phenotype 50% of a bi-parental population to predict the GEBVs of the remaining un-tested 50%. Though this reduces the cost of phenotyping, Atanda and his co-authors suggest it is not optimal because the breeder has to wait three to four months for the plant to grow before collecting the phenotypic data needed to calibrate the predictive model for the un-tested 50%.
Atanda and his colleagues’ findings specify how to calibrate a model based on existing historical phenotypic and genotypic data. They also offer a method for creating “experimental” sets to generate phenotypic information when the models don’t work due to low genetic connectedness between the new population and historical data.
This presents a way forward for breeders to accelerate the early yield testing stage based on genomic information, reduce the breeding cycle time and budget, and ultimately increase genetic gain.
Regional maize breeding coordinator for Africa Yoseph Beyene explained the leap forward this approach represents for CIMMYT’s maize breeding in Africa.
“For the last 5 years, CIMMYT’s African maize breeding program has applied genomic selection using the ‘test-half-and-predict-half’ strategy,” he said. “This has already reduced operational costs by 32% compared to the traditional phenotypic selection.”
“The prediction approach shown in this paper — using historical data alone to predict untested lines that go directly to stage-two trials — could reduce the breeding cycle by a year and save the cost of testcross formation and multi-location evaluation of stage-one testing. This research contributes to our efforts in the AGG project to mainstream genomic selection in all the product profiles.”
Effective for maize and wheat
Atanda, who now works on the use of novel breeding methods to enhance grain zinc content in CIMMYT’s wheat breeding program, believes these findings apply to wheat breeding as well.
“The implications of the research in maize are the same in wheat: accelerating early testing stage and reducing the breeding budget, which ultimately results in increasing genetic gain,” he said.
CIMMYT Global Wheat Program director Alison Bentley is optimistic about the crossover potential. “It is fantastic to welcome Atanda to the global wheat program, bringing skills in the use of quantitative genetic approaches,” she said. “The use of new breeding methods such as genomic selection is part of a portfolio of approaches we are using to accelerate breeding.”
CIMMYT’s wheat breeding relies heavily on a time-tested and validated method using managed environments to test lines for a range of growing environments — from drought to full irrigation, heat tolerance and more — in CIMMYT’s wheat experimental station in Ciudad Obregón, in Mexico’s state of Sonora.
According to CIMMYT senior scientist and wheat breeder Velu Govindan, using the approaches tested by Sikiru can make this even more efficient. As a specialist in biofortification — using traditional breeding techniques to develop crops with high levels of micronutrients — Govindan is taking the lead mainstreaming high zinc into all CIMMYT improved wheat varieties.
“This process could help us identify best lines to share with partners one year earlier — and it can be done for zinc content as easily as for grain yield.”
If this study seems like an excellent fit for the AGG project’s joint focus on accelerating genetic gain for both maize and wheat, that is no accident.
“The goal of the AGG project was the focus of my research,” Atanda said. “My study has shown that this goal is doable and achievable.”
Read the study:
Maximizing efficiency of genomic selection in CIMMYT’s tropical maize breeding program
As scientists study and learn more about the complicated genetic makeup of the wheat genome, one chromosomal segment has stood out, particularly in efforts to breed high-yielding wheat varieties resistant to devastating and quickly spreading wheat diseases.
Known as the 2NvS translocation, this segment on the wheat genome has been associated with grain yield, tolerance to wheat stems bending over or lodging, and multiple-disease resistance.
Now, thanks to a new multi-institution study led by wheat scientist Liangliang Gao of Kansas State University, we have a clearer picture of the yield advantage and disease resistance conferred by this chromosomal segment for wheat farmers — and more opportunities to capitalize on these benefits for future breeding efforts.
The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding, published in Theoretical and Applied Genetics, summarizes the collaborative effort by scientists from several scientific institutions — including International Maize and Wheat Improvement Center (CIMMYT) head of global wheat improvement Ravi Singh and wheat scientist Philomin Juliana — to conduct the first complete cytological characterization of the 2NvS translocation.
A rich background
The 2NvS translocation segment has been very valuable in disease-resistance wheat breeding since the early 1990s. Originally introduced into wheat cultivar VPM1 by the French cytogeneticist Gerard Doussinault in 1983 by crossing with a wild wheat relative called Aegilops ventricosa, the segment has been conferring resistance to diseases like eye spot (Pch1 gene), leaf rust (Lr37 gene), stem rust (Sr38 gene), stripe rust (Yr17 gene), cereal cyst (Cre5 gene), root knot (Rkn3 gene) and wheat blast.
The high-yielding blast-resistant CIMMYT-derived varieties BARI Gom 33 and WMRI#3 (equivalent to Borlaug100),released in Bangladesh to combat a devastating outbreak of wheat blast in the region, carry the 2NvS translocation segment for blast resistance.
Earlier research by Juliana and others found that the proportion of lines with the 2NvS translocation had increased by 113.8% over seven years in CIMMYT’s international bread wheat screening nurseries: from 44% in 2012 to 94.1% in 2019. It had also increased by 524.3% in the semi-arid wheat screening nurseries: from 15% in 2012 to 93.7% in 2019. This study validates these findings, further demonstrating an increasing frequency of the 2NvS translocation in spring and winter wheat breeding programs over the past two decades.
New discoveries
The authors of this study completed a novel assembly and functional annotation of the genes in the 2NvS translocation using the winter bread wheat cultivar Jagger. They validated it using the spring wheat cultivar CDC Stanley and estimated the actual size of the segment to be approximately 33 mega base pairs.
Their findings substantiate that the 2NvS region is rich in disease resistance genes, with more than 10% of the 535 high-confidence genes annotated in this region belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families known to be associated with disease resistance. This was a higher number of NLRs compared to the wheat segment of the Chinese Spring reference genome that was replaced by this segment, adding further evidence to its multiple-disease resistant nature.
In addition to being an invaluable region for disease resistance, the study makes a strong case that the 2NvS region also confers a yield advantage. The authors performed yield association analyses using yield data on lines from the Kansas State University wheat breeding program, the USDA Regional Performance Nursery —comprising lines from central US winter wheat breeding programs — and the CIMMYT spring bread wheat breeding program, and found a strong association between the presence of the segment and higher yield.
Global benefits
The yield and disease resistance associations of the 2NvS genetic segment have been helping farmers for years, as seen in the high proportion of the segment present in the improved wheat germplasm distributed globally through CIMMYT’s nurseries.
“The high frequency of the valuable 2NvS translocation in CIMMYT’s internationally distributed germplasm demonstrates well how CIMMYT has served as a key disseminator of lines with this translocation globally that would have likely contributed to a large impact on global wheat production,” said study co-author Juliana.
Through CIMMYT’s distribution efforts, it is likely that national breeding programs have also effectively used this translocation, in addition to releasing many 2NvS-carrying varieties selected directly from CIMMYT distributed nurseries.
With this study, we now know more about why the segment is so ubiquitous and have more tools at our disposal to use it more deliberately to raise yield and combat disease for wheat farmers into the future.
Wheat constitutes 20% of all calories and protein consumed, making it a cornerstone of the human diet, according to the United Nations. However, hotter and drier weather, driven by a changing climate, threatens the global wheat supply. To address this threat, the Foundation for Food and Agriculture Research (FFAR) awarded a $5 million grant to the International Maize and Wheat Improvement Center (CIMMYT) to develop climate-resilient wheat. CIMMYT leads global research programs on maize and wheat, sustainable cropping systems and policies to improve farmers’ livelihoods. These activities have driven major gains in wheat variety improvement across the globe for decades; in the US alone, for example, over 50% of the wheat acreage is sown with CIMMYT-related varieties.
Wheat is among the most widely grown cereal crops in the world and the third-largest crop grown in the US by acre. Nearly all US wheat crops are improved and supported by public agriculture research. As most wheat in the US is dependent on rainfall and has no access to irrigation, this research is critical for helping the plants — and producers — weather climatic changes including extreme heat and drought. Additionally, the demand for wheat is expected to rise in the coming years — as much as 60% by 2050. Without public research, wheat production could decrease by nearly 30% over the same period due to extreme climate conditions.
“FFAR leverages public agriculture research funding through public-private partnerships to pioneer actionable research. With temperatures on the rise and water becoming scarcer, we are committed to supporting wheat farmers and providing new wheat varieties designed with future environmental challenges in mind,” said FFAR’s Executive Director Sally Rockey.
Using the FFAR grant, CIMMYT researchers are pioneering wheat breeding technologies to produce heat-tolerant, drought-resistant and climate-resilient wheat.
CIMMYT researchers and collaborators are applying cutting-edge approaches in genomics, remote sensing and big data analysis to develop new breeding technologies. A key intervention will explore the vast and underutilized reserve of wheat genetic resources to fortify the crop against current and future climate-related stresses.
“This project will help bridge a longstanding gap between state-of-the-art technological findings and crop improvement to deliver climate resilient wheat to farmers as quickly as possible,” said Matthew Reynolds, head of Wheat Physiology at CIMMYT and principal investigator of the project.
Breakthroughs from the FFAR funded project will achieve impact for growers via the International Wheat Improvement Network (IWIN) that supplies new wheat lines to public and private breeding programs worldwide, and has boosted productivity and livelihoods for wheat farmers for over half a century, especially in the Global South.
The research and breeding supported by FFAR will be conducted under the Heat and Drought Wheat Improvement Consortium (HeDWIC), a project led by CIMMYT in partnership with experts across the globe, designed to ensure wheat’s long-term climate resilience. Under the umbrella of the Wheat Initiative’s AHEAD unit, the most relevant advances in academia will be channeled to HeDWIC to help further boost impacts.
“‘Heat,’ ‘drought’ and ‘wheat’ are three of the most important words for billions of people,” said CIMMYT Interim Deputy Director for Research Kevin Pixley. “This partnership between CIMMYT and FFAR will help ensure that the best agricultural science is applied to sustainably raise production of one of the world’s most important staple crops, despite unprecedented challenges.”
CIMMYT Director General Martin Kropff said, “This project represents not only a breakthrough to develop wheat for the future, but also an emerging partnership between CIMMYT and FFAR. I look forward to a productive collaboration that will move us all closer to our mission of maize and wheat science for improved livelihoods.”
FFAR’s investment was matched by co-investments from the CGIAR Research Program on Wheat (WHEAT) and Accelerating Genetic Gains for Maize and Wheat (AGG), a project which is jointly funded by the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth, and Development Office (FCDO).
FOR MORE INFORMATION, OR TO ARRANGE INTERVIEWS, CONTACT:
Marcia MacNeil, Communications Officer, CGIAR Research Program on Wheat, CIMMYT. +52 5951148943, m.macneil@cgiar.org
Brian Oakes, FFAR. +1 202-604-5756, boakes@foundationfar.org
About the Foundation for Food & Agriculture Research
The Foundation for Food & Agriculture Research (FFAR) builds public-private partnerships to fund bold research addressing big food and agriculture challenges. FFAR was established in the 2014 Farm Bill to increase public agriculture research investments, fill knowledge gaps and complement USDA’s research agenda. FFAR’s model matches federal funding from Congress with private funding, delivering a powerful return on taxpayer investment. Through collaboration and partnerships, FFAR advances actionable science benefiting farmers, consumers and the environment.
Connect: @FoundationFAR | @RockTalking
About CIMMYT
The International Maize and Wheat 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 Research 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
To adequately confront rapidly changing plant pests and diseases and safeguard food security for a growing population, breeders — in collaboration with their partners — have to keep testing and applying new breeding methods to deliver resilient seed varieties at a much faster rate using minimal resources. Molecular markers are essential in this regard and are helping to accelerate genetic gains and deliver better seed to smallholders across sub-Saharan Africa in a much shorter timeframe.
Progress made so far in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a deeper understanding on the role of molecular markers and greatly complemented breeding strategies. However, phenotyping remains the single most costly process in plant breeding, thus limiting options to increase the size of breeding programs.
Application of molecular markers increases the ability to predict and select the best performing lines and hybrids, prior to selection in the field. “This enables breeders to expand the size of a breeding program or the populations they work on using the same amount of resources,” says Manje Gowda, a maize molecular breeder at the International Maize and Wheat Improvement Center (CIMMYT).
“There are three stages in the use of molecular markers: discovery, validation and deployment,” he explains. “At the discovery phase, the objective is to find molecular markers associated or tightly linked with the trait of interest, while also assessing whether the trait is more complex or easier to handle with few markers for selection.”
The molecular markers identified at the discovery stage are validated in independent bi-parental or backcross populations, and the marker trait associations — which are consistent across different genetic backgrounds and diverse environments — are then moved to the deployment stage. Here, they are considered for use in breeding either as part of marker assisted selection or forward breeding, marker assisted back crossing and marker assisted recurrent selection.
Screening for resistance markers
CIMMYT scientists have discovered several marker trait associations for crop diseases including maize lethal necrosis (MLN), maize streak virus (MSV), corn rust and turcicum leaf blight. All these trait-associated markers have been validated in biparental populations.
For MLN, after screening several thousands of lines, researchers identified a few with resistance against the viral disease, namely KS23-5 and KS23-6. These lines were obtained from synthetic populations developed by Kasetsart University in Thailand and serve as trait donors. Researchers were able to use these as part of forward breeding, producing doubled haploid (DH) lines by using KS23-6 as one parent and screening for the presence of MLN resistance genes.
“This screening helps eliminate the lines that may carry susceptible genes, without having to phenotype them under artificial inoculation,” says Gowda. “These markers are also available to all partners to screen for MLN resistance, thereby saving on costs related to phenotyping.”
Scientists also used these MLN resistance markers to introgress the MLN resistance into several elite lines that are highly susceptible to the disease but have other desirable traits such as high grain yield and drought tolerance. The marker-assisted backcrossing technique was used to obtain MLN resistance from the KS23-5 and KS23-6 donor lines. This process involves crossing an elite, commercial line — as a recurrent parent in the case of CIMMYT elite lines — with a donor parent line (KS23) with MLN resistance. These were then backcrossed over two to three cycles to improve the elite line carrying MLN resistance genes. In the past three years, more than 50 lines have been introgressed with the MLN resistance gene from KS23-6 donor line.
An impetus to breeding programs
“The work Manje Gowda has been carrying out is particularly important in that it has successfully moved from discovery of valuable markers and proof-of-concept experiments to scalable breeding methods which are being used effectively,” says CIMMYT Trait Pipeline and Upstream Research Coordinator Mike Olsen. “Enabling routine implementation of molecular markers to increase selection efficiency of breeding programs in the context of African maize improvement is quite impactful.”
At CIMMYT, Gowda’s team applied genomic selection at the early stage of testing the breeding pipeline for different product profiles. “The objective was to testcross and phenotype 50% of the Stage One hybrids and predict the performance of remaining 50% of the hybrids using molecular markers,” Gowda explains.
The team have applied this strategy successfully each year since 2017, and the results of this experiment show that selection efficiency is the same as when using phenotypic selection, but using only 32% of the resources. From 2021 onwards, the aim is to use the previous year’s Stage One phenotypic and genotypic data to predict 100% of the lines. This will not only save the time but improve efficiency and resource use. The previous three-year Stage One historical data is helping to reduce the phenotyping of lines from 50% to 15%, with an increase in saving resources of up to 50%.
For the commercial seed sector, integrating molecular marker-based quality control measures can help deploy high-quality seeds, an important factor for increasing crop yields. In sub-Saharan Africa, awareness on marker-based quality has improved due to increased scientist and breeder trainings at national agricultural research systems (NARS), seed companies and national plant protection organizations, as well as regulators and policymakers.
Currently, many NARS and private sector partners are making it mandatory to apply marker-based quality control to maintain high-quality seeds. Since NARS and small- and medium-sized seed companies’ breeding programs are smaller, CIMMYT is coordinating the collection of samples from different partners for submission to service providers for quality control purposes. CIMMYT staff are also helping to analyze quality control data and interpret results to sharing with partners for decision-making. For the sustainability of this process, CIMMYT is training NARS partners on quality control, from sample collection to data analyses and interpretation, and this will support them to work independently and produce high-quality seed.
Such breeding improvements have become indispensable in supporting maize breeding programs in the public and private sectors to develop and deliver improved maize varieties to smallholder farmers across sub-Saharan Africa.
In a landmark discovery for global wheat production, an international team led by the University of Saskatchewan and including scientists from the International Maize and Wheat Improvement Center (CIMMYT) has sequenced the genomes for 15 wheat varieties representing breeding programs around the world, enabling scientists and breeders to much more quickly identify influential genes for improved yield, pest resistance and other important crop traits.
The research results, just published in Nature, provide the most comprehensive atlas of wheat genome sequences ever reported. The 10+ Genome Project collaboration involved more than 95 scientists from universities and institutes in Australia, Canada, Germany, Israel, Japan, Mexico, Saudi Arabia, Switzerland, the UK and the US.
“It’s like finding the missing pieces for your favorite puzzle that you have been working on for decades,” said project leader Curtis Pozniak, wheat breeder and director of the USask Crop Development Centre (CDC). “By having many complete gene assemblies available, we can now help solve the huge puzzle that is the massive wheat pan-genome and usher in a new era for wheat discovery and breeding.”
“These discoveries pave the way to identifying genes responsible for traits wheat farmers in our partner countries are demanding, such as high yield, tolerance to heat and drought, and resistance to insect pests,” said Ravi Singh, head of global wheat improvement at CIMMYT and a study co-author.
One of the world’s most cultivated cereal crops, wheat plays an important role in global food security, providing about 20 per cent of human caloric intake globally. It’s estimated that wheat production must increase by more than 50% by 2050 to meet an increasing global demand.
The study findings build on the first complete wheat genome reference map published by the International Wheat Genome Sequencing Consortium in 2018, increasing the number of wheat genome sequences almost 10-fold, and allowing scientists to identify genetic differences between wheat varieties.
The research team was also able to track the unique DNA signatures of genetic material incorporated into modern cultivars from wild wheat relatives over years of breeding.
“With partners at Kansas State University, our CIMMYT team found that a DNA segment in modern wheat derived from a wild wheat relative can improve yields by as much as 10%,” said Philomin Juliana, CIMMYT wheat breeder and study co-author. “We can now work to ensure this gene is included in the next generation of modern wheat cultivars.”
The team also used the genome sequences to isolate an insect-resistant gene called Sm1, that enables wheat plants to withstand the orange wheat blossom midge, a pest which can cause more than $60 million in annual losses to Western Canadian producers.
“Understanding a causal gene like this is a game-changer for breeding because you can select for pest resistance more efficiently by using a simple DNA test than by manual field testing,” explained Pozniak.
The 10+ Genome Project was sanctioned as a top priority by the Wheat Initiative, a coordinating body of international wheat researchers.
“This project is an excellent example of coordination across leading research groups around the globe. Essentially every group working in wheat gene discovery, gene analysis and deployment of molecular breeding technologies will use the resource,” said Wheat Initiative Scientific Coordinator Peter Langridge.
Read the full press release from the University of Saskatchewan.
RELATED PUBLICATIONS:
Multiple Wheat Genomes Reveal Global Variation in Modern Breeding
FOR MORE INFORMATION, OR TO ARRANGE INTERVIEWS, CONTACT THE MEDIA TEAM:
Marcia MacNeil, Communications Officer, CGIAR Research Program on Wheat, CIMMYT. M.macneil@cgiar.org
Victoria Dinh, Media Relations, Univeristy of Saskatchewan, Victoria.dinh@usask.ca
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
ABOUT CDC:
The Crop Development Centre (CDC) in the USask College of Agriculture and Bioresources is known for research excellence in developing high-performing crop varieties and developing genomic resources and tools to support breeding programs. Its program is unique in that basic research is fully integrated into applied breeding to improve existing crops, create new uses for traditional crops, and develop new crops. The CDC has developed more than 400 commercialized crop varieties.
Wheat scientists in the Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project, led by the International Maize and Wheat Improvement Center (CIMMYT), presented a range of new research at the 2020 Borlaug Global Rust Initiative (BGRI) Technical Workshop in October, highlighting progress in spring wheat breeding, disease screening and surveillance and the use of novel genomic, physiological tools to support genetic gains.
Sridhar Bhavani, CIMMYT senior scientist and head of Rust Pathology and Molecular Genetics, delivered a keynote presentation on a “Decade of Stem Rust Phenotyping Network: Opportunities, Challenges and Way Forward,” highlighting the importance of the international stem rust phenotyping platforms established with national partners in Ethiopia and Kenya at the Ethiopian Institute for Agricultural Research station in Debre Zeit, and the Kenya Agricultural and Livestock Research Organization station in Njoro, respectively. These platforms support global wheat breeding, genetic characterization and pre-breeding, surveillance and varietal release, and will continue to be an important mechanism for delivering high performing material into farmers’ fields.
CIMMYT wheat breeder Suchismita Mondal chaired a session on breeding technologies, drawing on her expertise leading the trait delivery pipeline in AGG (including rapid generation cycling and speed breeding). She led a lively Q&A on the potential for genomics and data-driven approaches to support breeding.
In the session, CIMMYT Associate Scientist and wheat breeder Philomin Juliana presented a “Retrospective analysis of CIMMYT’s strategies to achieve genetic gain and perspectives on integrating genomic selection for grain yield in bread wheat,” demonstrating that phenotypic selection — making breeding selections based on physically identifiable traits — has helped increase the proportion of genes associated with grain yield in CIMMYT’s globally distributed spring wheat varieties. Her work demonstrates the efficiency of indirect selection for yield in CIMMYT’s Obregon research station, and the potential of genomic selection, particularly when incorporating environmental effects.
The use of Obregon as a selection environment was further explored by CIMMYT wheat breeder Leo Crespo presenting “Definition of target population of environments in India and their prediction with CIMMYT’s international nurseries.” This work confirms Obregon’s relevance as an effective testing site, allowing the selection of superior germplasm under distinct management conditions that correlate with large agroecological zones for wheat production in India. Similar analyses will be conducted in AGG with the support of the CGIAR Excellence in Breeding Platform to optimize selection conditions for eastern Africa.
Supporting future genetic gains
CIMMYT’s Head of Global Wheat Improvement Ravi Singh presented “Genetic gain for grain yield and key traits in CIMMYT spring wheat germplasm — progress, challenges and prospects,” highlighting the International Wheat Improvement Network as an important source of new wheat varieties globally. He described progress on the implementation of genomic selection and the use of state of the art tools to collect precise plant trait information, known as high-throughput phenotyping (HTP), in CIMMYT wheat breeding.
With partners, he is now conducting both genotyping (measuring the genetic traits of a plant) and phenotyping for all entries in the earliest stages of yield trials in Mexico. In addition, his team has succeeded in phenotyping a large set of elite lines at multiple field sites across South Asia. Looking forward, they aim to shorten generation advancement time, improve the parental selection for “recycling” (re-using parents in breeding), and adding new desirable traits into the pipeline for breeding improved varieties.
Following on from Ravi’s presentation, CIMMYT scientist Margaret Krause highlighted progress in HTP in her talk on “High-Throughput Phenotyping for Indirect Selection on Wheat Grain Yield at the Early-generation Seed-limited Stage in Breeding Programs.” This work highlights the potential of drones to capture highly detailed and accurate trait data, known as aerial phenotyping, to improve selection at the early-generation, seed-limited stages of wheat breeding programs.
This kind of physiological understanding will support future phenotyping and selection accuracy, as seen in the work that CIMMYT scientist Carolina Rivera shared on “Estimating organ contribution to grain-filling and potential for source up-regulation in wheat cultivars with contrasting source-sink balance.” Her research shows that a plant’s production of biomass is highly associated with yield under heat stress and that it is possible to achieve greater physiological resolution of the interaction between traits and environment to deliver new selection targets for breeding.
Overall, the talks by AGG scientists demonstrated tremendous progress in spring wheat breeding at CIMMYT and highlighted the importance of new tools and technologies to support future genetic gains.
All presentations can be found on the BGRI Workshop 2020 website.
The Borlaug Global Rust Initiative is an international community of hunger fighters committed to sharing knowledge, training the next generation of scientists, and engaging with farmers for a prosperous and wheat-secure world. The BGRI is funded in part through the Delivering Genetic Gain in Wheat (DGGW) project from the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth & Development Office.