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Tag: phenotyping

Seeds to beat the heat in lowland tropics

Written by dmedina on . Posted in Features.

South Asia, a region heavily impacted by climate change, faces rising temperatures, erratic monsoon rains causing intermittent drought and excessive moisture within the season, and frequent episodes of heat waves. These extreme weather events are challenging agrarian practices and affecting millions, especially smallholder farmers dependent upon rainfed cultivations. The halcyon days of consistent environmental conditions are gone, and adaptation and mitigation strategies have become essential in South Asia.

In May 2024, over 20 districts in the Terai region of Nepal and many parts of northern India recorded maximum temperatures between 40°C and 45°C, with several districts also experiencing heat waves during the same period. The temperature rise is not limited to the lowland plains; the effects are also being felt in the mountains, where rapid snowmelt is becoming increasingly common. In the Hindu Kush Himalayas region of Pakistan, farmers have had to shift their cropping cycles by a month to cope with drought stress caused by rising temperatures, which are leading to the early melting of snow in the region.

Partners in South Asia visiting heat stress tolerant hybrids demonstration in Nepal (Photo: CIMMYT-Nepal)

Collaborating to rise above the challenge

Amid the growing climate crisis, the Heat Stress Tolerant Maize for Asia (HTMA) project was launched by CIMMYT in 2012, with support from the United States Agency for International Development (USAID) under the Feed the Future initiative of the U.S. Government. The overarching goal of the HTMA project was to help farm families, particularly maize growers, to adapt to the impacts of soaring heat on maize productivity in South Asia. The project was implemented in partnership with 28 public and private sector stakeholders across the region and beyond to develop a multipronged approach to overcoming these challenges.

“Our aim is to develop and deploy maize hybrids with high yield potential and possess traits resilient to heat and drought stresses,” said P.H. Zaidi, Principal Scientist, and HTMA project lead at CIMMYT. Zaidi noted that during heat stress “high temperatures alone are not the only limiting factor- it is the combination of high temperature with low atmospheric humidity (high vapor pressure deficit), that creates a “killer combination” for maize production in the Asian tropics.”

This was also emphasized in a recently published article that he co-authored.

The development of heat stress-tolerant maize involves the use of cutting-edge breeding tools and methods, including genomics-assisted breeding, double haploidy, field-based precision phenotyping, and trait-based selection. Over 20 such hybrids have been officially released in India, Nepal, Bangladesh, Pakistan, and Bhutan. Between 2023 and 2024, over 2,500 metric tons of seed from these hybrids were distributed to farmers, helping them beat the heat.

Agile partnerships-from discovery to scaling

The first phase of the project (2012-2017) focused on discovering heat-tolerant maize varieties. During this time, pipeline products underwent field evaluations in stress-prone environments, leveraging the project’s product evaluation network of public and private partners, who contributed by managing trials and generating performance data. In the second phase (2018-2023), the focus shifted toward the deployment and scaling of heat-tolerant hybrids and strengthening seed systems in target countries to enable large-scale delivery, benefiting millions of farm families, particularly in South Asia’s rainfed ecologies. For example, the seed produced in 2023-2024 sufficed to cover over 125,000 hectares and benefited nearly 2.5 million people in the region.

HTMA project partners gathered in Nepal for the annual and project closure meeting (Photo-CIMMYT-Nepal)

Hailu Tefera, from USAID, praised the project’s success during the annual review and project closure meeting held in Nepal from August 21-22, 2024. “We have seen great strides in scaling heat stress tolerant hybrids in the region. This initiative aligns with the US Government’s Global Food Security Strategy, where building farmers’ resilience to shocks and climate vulnerability is central,” said Tefera, acknowledging the adaptive and agile partnership demonstrated by the project’s partners throughout HTMA’s discovery and scaling phases.

One of the project’s key achievements was creating a multi-stakeholder platform and leveraging resources across the region. Partners, including national agricultural research systems, seed companies, and higher learning institutes, expanded the project’s impact. “The collaboration we fostered under the HTMA project is a working example of effective partnerships,” said B.M. Prasanna, Director of CIMMYT’s Global Maize Program. He highlighted how synergies with other developmental projects in the region, especially projects supported by the USAID country mission in Nepal helped launch local hybrid seed production, transforming the country from a net importer of hybrid maize seeds to producing locally in just a few years, and such seeds of resilience cover nearly 10,000 hectares in 2023/24 alone. Using heat tolerant (HT) maize seed allows smallholder farmers to harvest nearly one metric ton per hectare additional yield than normal maize under stress conditions.

The value of the seed these new hybrids was validated by adopter farmers who grow maize in stress-vulnerable ecologies by expressing their willingness to pay a premium price for HT hybrid seed as per the study conducted in Nepal and India. “The spillover effect of the project is helping countries like Bhutan to strengthen their seed systems and initiate hybrid seed production for the first time,” added Prasanna, expressing gratitude to USAID and all project partners.

The salient achievements of the project, including technical know-how, outputs, outcomes, and learnings were compiled as an infographic, titled “HTML Tool‘‘ and it was formally released by Narahari Prasad Ghimire, Director General of the Department of Agriculture, Government of Nepal, during the HTMA meeting in Nepal.

Rewarding achievement

Subash Raj Upadhyay, Managing Director of Lumbini Seed Company in Nepal, recalls the early days of producing heat stress-tolerant hybrid maize seed in Nepal, which began in 2018. “Our journey started with just one hectare of seed production in 2018 and 2019, and we expanded to 30 hectares by 2022. This was the first time that we started hybrid maize seed production in Nepal, specifically RH-10, a heat stress tolerant hybrid from CIMMYT, released by the National Maize Research Program of Nepal. The support of USAID’s projects like the Nepal seed and fertilizer project was crucial for our success,” said Upadhyay, who was among the award recipients for setting a potent example in scaling up heat stress-tolerant hybrids.

HTMA TOOL- an infographic launched during the meeting (Photo-CIMMYT Nepal)

In addition to Lumbini Seed Company, Jullundur Seed Private Limited Company in Pakistan was also recognized for its efforts in seed scaling. The National Maize Research Program of Nepal and the University of Agricultural Sciences, Raichur, India, were acknowledged for their rewarding achievement in research and development during the project period.

“The recognition exemplifies the public-private partnership that we demonstrated under the HTMA project, where the public sector mainly focused on strategic research and product development, and seed companies took charge of seed delivery and scaling,” said Zaidi during the project’s phaseout meeting in Nepal, attended by over 60 participants from the project’s target and spillover countries. “Such partnership models need to be strengthened and replicated in other projects. It is important to consolidate the gains and maintain the momentum of the HTMA project in the years to come to benefit millions of smallholder farmers,” echoed Prasanna, who presented certificates of recognition to the partners in the presence of USAID representatives, senior government officials from Nepal and project partners from South Asia and beyond.

Deployment of new tools and technologies into the CGIAR-NARS breeding program increases the rate of genetic gain per dollar invested

Written by dmedina on . Posted in Publications.

Food security in the prevailing uncertain climatic and economic conditions can only be guaranteed by deliberate actions toward maximizing production, especially in stress-prone environments. The main priority of the CGIAR and NARS breeding programs is to enhance genetic gain in crops through the assessment of seed varieties with drought-resilient, nutritional, and yield traits. This is achieved by leveraging data-driven approaches and embracing contemporary tools and methodologies.

Innovative approaches such as molecular tools, doubled haploid technology, and refined breeding schemes have greatly contributed to the strides made in CIMMYT’s endeavor to elevate genetic gain within breeding pipelines. These advancements not only drive improved productivity but also promise cost-effective strategies for navigating the challenges posed by climate variability.

Molecular Tools

In maize breeding, traditionally, at each stage of the pipeline, entries are grown in multi-location trials. Phenotyping in multiple environments helps to select the best entries not only based on their genetic values but also on environmental factors and their interaction with diverse environments. However, this is also a labor-intensive and time-consuming step in the breeding pipeline. Molecular breeding offers a transformative solution by expanding breeding programs while minimizing phenotyping requirements. It is a well-known fact that trait phenotype results from both genetic and non-genetic factors, with genetic factors being contributed by the expression of genes at the DNA level.

Identifying genomic regions close to causative genes for traits of interest, such as high yield, disease resistance, or quality, can help to incorporate desirable genes/alleles into selected elite genotypes. DNA-based markers aid in efficiently tracking the inheritance of genetic traits, thereby facilitating the selection of desired traits in breeding programs. Marker-assisted forward breeding accelerates the selection of plants with desired traits by identifying the genetic markers associated with those traits. With such harnessed genotypic information, breeders can pre-select genetic material before embarking on the resource-intensive phenotyping stages. This strategic utilization of molecular markers, particularly in identifying susceptibility to key diseases like maize streak virus (MSV) and maize lethal necrosis (MLN), enables the judicious allocation of resources for phenotyping.

 

Figure 1. Summary of marker-assisted forward breeding across six breeding pipelines for MLN- and MSV-resistance haplotypes over the past six years.

Since 2018, CIMMYT has been implementing marker-assisted forward breeding for MSV and MLN. Since then, more than 100,000 pure breeding lines have been tested by examining their favorable haplotypes with a small set of 10 genetic markers and discarding the lines carrying unfavorable haplotypes for MSV and MLN resistance. In the last six years, nearly 30,000 lines have been rejected before undergoing field testing. In southern Africa, for instance, a rapid response to seed movement using molecular and serological techniques prevented the spread of MLN and facilitated the incorporation of resistance traits into new plant varieties.

Most hybrids in the final stages of breeding pipelines are passed through forward breeding. While Fall Armyworm, Gray Leaf Spot, common rust, and Turcicum Leaf Blight also cause substantial yield reductions in sub-Saharan Africa, research carried out under the AGG project indicates that the genetic makeup of these traits is oligogenic, governed by both moderate and small effect quantitative trait loci (QTLs), but lacking a single major-effect QTL and not amenable to forward breeding. This means that their resistance is influenced by complex multiple genetic factors, rather than being primarily controlled by a few major genetic regions. Alternatively, these biotic stress traits can be improved effectively through genomic selection.

Genomic selection is used to improve complex traits that are controlled by many small-effect QTLs. This approach does not require prior genetic information about the trait of interest and uses genome-wide marker information to estimate all marker effects and select individuals with high genomic-estimated breeding values (GEBVs). This means it uses data from various genetic markers to predict which individuals are likely to have desirable alleles for MSV and MLN. Genomic selection is being applied for grain yield under drought stress, and efforts are underway to extend its application to address more complex challenges related to plant diseases and pests. Foliar diseases are moderately complex traits.

Proof of concept on applying genomic selection for foliar diseases like gray leaf spot and northern corn leaf blight showed high prediction accuracies, supporting the implementation of genomic selection together with forward breeding for other traits at the early stage of the breeding pipeline. Implementing genomic selection for GY under optimum and drought management proved that maize breeders could obtain the same gain as with conventional breeding, where all entries are phenotyped in the field, but at approximately 35-40% less cost. Many candidate hybrids now entering the advanced stages of the breeding pipeline were developed using genomic selection. Several of our earlier studies (Beyene et al., 2015, 2016, 2019, 2021; Chaikam et al., 2019; Crossa et al., 2017; Prasanna et al., 2022; Vivek et al., 2017) showed that breeding pipelines achieved high genetic gain by adopting new molecular tools, thus confirming the benefit of adopting molecular breeding tools.

Currently, in CIMMYT’s eastern and southern breeding pipelines, all product profiles are using genomic selection at stage I, where the training population is evaluated in multiple locations with a sparse design, estimating the GEBVs for the unphenotyped lines, and using GEBVs and phenotypic BLUPs of test crosses in the selection for stage II. This process allows the handling of a large number of lines at stage I with a fixed budget without losing selection accuracy. Since 2017, we have used the “test half and predict half” strategy (Figure 2), where all the lines were genotyped with mid-density markers, and the selected ~50% of the total stage I lines were testcrossed and evaluated in multiple locations to be used as a training population to estimate the GEBVs for the other 50% of the unphenotyped lines for the traits of interest. High prediction correlations were observed in three selected product profiles for GY under optimum, managed drought, and low soil N conditions (Figure 3).

Genomic selection is also implemented to reduce the breeding cycle. However, our final products are three-way cross hybrids, where genomic selection is applied only to select the best line rather than selecting the best hybrid combinations. Historical data were used to test the possibility of reducing the breeding cycle. However, our results showed that the use of historical data to predict 100% of lines from the current year yielded low to moderate prediction correlations both under optimum and drought conditions for GY, anthesis date, and plant height (Figure 4). Incorporating 10 to 30% of the testing population into the training population leads to high prediction correlations. This concludes that by using historical data, the training population, which needs to be test-crossed and evaluated in multiple locations every year, can be reduced from 50% to 10-30%, which helps breeders allocate the saved resources to evaluate more lines without losing prediction accuracy.

Doubled Haploid Technology

Doubled haploid technology speeds up the creation of inbred lines by producing entirely uniform lines. Pedigree line development is a traditional method in plant breeding aimed at gradually improving and stabilizing the genetic makeup of the new variety over time. It involves multiple generations of controlled crosses between parent plants with known characteristics. Each subsequent generation is carefully selected based on specific traits of interest, such as yield, disease resistance, or quality. Pedigree line development is expensive, particularly when nurseries are in remote locations.

Unlike traditional methods where some genetic variation remains, doubled haploid lines are completely homogeneous. This means that there is increased heritability of desirable traits and improved accuracy of selection. Doubled haploid technology, which is more compatible with the use of molecular markers, simplifies breeding processes and shortens the time needed to develop inbred lines (Chaikam et al., 2019).

The first doubled haploid facility in Africa was established in 2013 and is extensively used by the CGIAR, NARES, and the private sector. Over the past five years, 1,349 populations have been induced and more than 223,144 doubled haploid lines delivered to breeding programs from CGIAR, NARES, and the private sector in sub-Saharan Africa. Shifting from traditional pedigree-based breeding to doubled haploid technology has shown a high impact on key breeding metrics (gain per cycle and gain per year) not only in CIMMYT but also in national partners’ breeding programs, thus increasing genetic gain within the available budget.

Figure 2. Number of lines evaluated with phenotypic selection (PS) and genomic selection (GS) at stage I in EAPP1 product profile from 2017 to 2023. (PS – phenotypic selection, GS – genomic selection)
Figure 3. Prediction correlations for grain yield (GY) under optimum (OPT), drought (MDt) and low soil N (low N) management conditions in EAPP1, EAPP2 and SAPP1 at stage I in 2023

 

Figure 4. Prediction accuracies for grain yield (GY), anthesis date (AD) and plant height (PH) estimated from independent validation schemes using a training population (TRN) consisting of 2017- and 2018-years breeding data and 10%, 30%, 50%, 70% and 90% of 2019 data converted from the testing population (TST) to the training population under optimum and managed drought conditions

 

References

Beyene, Y., Gowda, M., Olsen, M., Robbins, K. R., Pérez-Rodríguez, P., Alvarado, G., Dreher, K., Gao, S. Y., Mugo, S., and Prasanna, B. M. (2019). Empirical comparison of tropical maize hybrids selected through genomic and phenotypic selections. Frontiers in plant science 10, 1502.

Beyene, Y., Gowda, M., Pérez-Rodríguez, P., Olsen, M., Robbins, K. R., Burgueño, J., Prasanna, B. M., and Crossa, J. (2021). Application of genomic selection at the early stage of breeding pipeline in tropical maize. Frontiers in Plant Science 12, 685488.

Beyene, Y., Gowda, M., Suresh, L. M., Mugo, S., Olsen, M., Oikeh, S. O., Juma, C., Tarekegne, A., and Prasanna, B. M. (2017). Genetic analysis of tropical maize inbred lines for resistance to maize lethal necrosis disease. Euphytica 213.

Beyene, Y., Semagn, K., Crossa, J., Mugo, S., Atlin, G. N., Tarekegne, A., et al. (2016). Improving maize grain yield under drought stress and non-stress environments in sub-saharan africa using marker-assisted recurrent selection. Crop Science 56, 344–353. doi: 10.2135/cropsci2015.02.0135

Beyene, Y., Semagn, K., Mugo, S., Tarekegne, A., Babu, R., Meisel, B., Sehabiague, P., Makumbi, D., Magorokosho, C., and Oikeh, S. (2015). Genetic gains in grain yield through genomic selection in eight bi‐parental maize populations under drought stress. Crop Science 55, 154-163.

Chaikam, V., Molenaar, W., Melchinger, A. E., and Prasanna, B. M. (2019). Doubled haploid technology for line development in maize: technical advances and prospects. Theor. Appl. Genet. 132, 3227–3243. doi: 10.1007/s00122-019-03433-x

Crossa, J., Pérez-Rodríguez, P., Cuevas, J., Montesinos-López, O., Jarquín, D., de los Campos, G., et al. (2017). Genomic selection in plant breeding: Methods, models, and perspectives. Trend Plant Sci. 22, 961–975. doi: 10.1016/j.tplants.2017.08.011

Prasanna BM, Burgueño J, Beyene Y, Makumbi D, Asea G, Woyengo V, Tarekegne A, Magorokosho C, Wegary D, Ndhlela T, Zaman-Allah M, Matova PM, Mwansa K, Mashingaidze K, Fato P, Teklewold A, Vivek BS, Zaidi PH, Vinayan MT, Patne N, Rakshit S, Kumar R, Jat SL, Singh SB, Kuchanur PH, Lohithaswa HC, Singh NK, Koirala KB, Ahmed S, San Vicente F, Dhliwayo T, Cairns JE. 2022. Genetic trends in CIMMYT’s tropical maize breeding pipelines. Scientific Reports 12, 20110. https://doi.org/10.1038/s41598-022-24536-4

Vivek, B. S., Krishna, G. K., Vengadessan, V., Babu, R., Zaidi, P. H., Kha, L. Q., et al. (2017). Use of genomic estimated breeding values results in rapid genetic gains for drought tolerance in maize. Plant Genome 10, 1–8. doi: 10.3835/plantgenome2016.07.0070

Building global capacity to combat wheat blast

Written by Julian Bañuelos-Uribe on . Posted in News.

Researchers and experts from 15 countries convened in Zambia, between 4-15 March 2024, for an international training on wheat blast disease screening, surveillance, and management.

Wheat blast, caused by pathogen Magnaporthe oryzae pathotype triticum, is threatening global wheat production especially in warmer and humid regions. The disease was first observed in Parana state of Brazil in 1985 and subsequently spread to Bolivia, Paraguay, and Argentina. Outside of South America, wheat blast incidences were recorded for the first time in Bangladesh in 2016 and in Zambian wheat fields in 2018.

To mitigate the impact of this potential plant pandemic, the Zambia Agriculture Research Institute (ZARI), in collaboration with CIMMYT and other partners, organized a comprehensive training for building research capacity and raising awareness within the local and international community, especially in at-risk countries.

“This collaborative effort, supported by various international partners and funders, underscores the importance of global cooperation in addressing agricultural challenges such as wheat blast. The objective of the training was to empower researchers with knowledge and tools for enhanced wheat production resilience in regions vulnerable to this destructive disease,” said Pawan Kumar Singh, principal scientist and project leader at CIMMYT. Singh collaborated with Batiseba Tembo, wheat breeder at ZARI-Zambia, to coordinate and lead the training program.

Thirty-eight wheat scientists, researchers, professors, policymakers, and extension agents from countries including Bangladesh, Brazil, Ethiopia, India, Kenya, Mexico, Nepal, South Africa, Sweden, Tanzania, United Kingdom, Uruguay, Zambia, and Zimbabwe convened at the Mt. Makulu Central Research Station in Chilanga, Zambia.

“Wheat blast is a devastating disease that requires concerted efforts to effectively manage it and halt further spread. The disease is new to Africa, so developing capacity amongst country partners before the disease spreads more widely is critical,” said Tembo.

Participants at the International Training on Wheat Blast Screening and Surveillance. (Photo: CIMMYT)

Highlights from the training: discussions, lab exercises, and field visits

During the training, participants engaged in lectures, laboratory exercises, and field visits. There were insightful discussions on key topics including the fundamentals of wheat blast epidemiology, disease identification, molecular detection of the wheat blast pathogen, isolation and preservation techniques for the pathogen, disease scoring methods, disease management strategies, and field surveillance and monitoring.

The course also provided practical experience in disease evaluation at the Precision Phenotyping Platform (PPP) screening nursery located in Chilanga research station. This involved characterization of a diverse range of wheat germplasm with the aim of releasing resistant varieties in countries vulnerable to wheat blast. Additionally, participants undertook field visits to farmers’ fields, conducting surveillance of wheat blast-infected areas. They collected samples and recorded survey data using electronic open data kit (ODK) capture tools.

Participants listen to a lecture by B.N. Verma, director of Zambia Seed Co., on the history of wheat production in Zambia. (Photo: CIMMYT)

“The killer disease needs to be understood and managed utilizing multi-faceted approaches to limit the expansion and damages it can cause to global wheat production. The Bangladesh Wheat and Maize Research Institute (BWMRI) is willing to share all the strategies it deployed to mitigate the effect of wheat blast,” said Golam Faruq, BWMRI’s director general.

Participants visited seed farms to gain practical insights into seed production processes and quality assurance measures. These visits provided first-hand knowledge of seed selection, breeding techniques, and management practices crucial for developing resistant wheat varieties. Participants also visited research sites and laboratories to observe advanced research methodologies and technologies related to wheat blast management. These visits exposed them to cutting-edge techniques in disease diagnosis, molecular analysis, and germplasm screening, enhancing their understanding of effective disease surveillance and control strategies.

Field visit. (Photo: CIMMYT)

“The training and knowledge sharing event was a significant first step in developing understanding and capacity to deal with wheat blast for partners from several African countries. It was wonderful to see the efforts made to ensure gender diversity among participants,” said Professor Diane Saunders from the John Innes Centre, UK.

CIMMYT and China join forces to tackle wheat disease in Africa

Written by Julian Bañuelos-Uribe on . Posted in News.

While wheat acreage has been increasing across the whole of Africa, the sub-Saharan countries account for a significant proportion of the total growth and yield, equaling an area of approximately 3.1 million hectares and a production of more than 9 million tons. However, in recent years, Fusarium head blight (FHB) or head scab has become a major disease in the region, causing significant reductions in yield and quality due to the lack of resistant varieties and management tools.

In China, a successful wheat shuttle breeding program by the Chinese Academy of Agricultural Sciences (CAAS) and CIMMYT for improving FHB has existed since the 1980s. Additionally, CIMMYT and the Jiangsu Academy of Agricultural Sciences (JAAS) have provided an FHB screening station in Nanjing since 2019. With a wealth of experience in confronting the disease, this ongoing partnership can help to solve the challenges currently faced by farmers in Africa.

To this end, CAAS, JAAS, and CIMMYT organized a training workshop on FHB management for Africa, which took place with financial support from China Aid in Beijing and Nanjing, China, between 10 and 23 April 2024. Twenty participants, 45% of which were women, attended the workshop, with specialists in wheat breeding, pathology, seed quarantine, and other related fields at public institutions in Ethiopia, Zambia, and Lesotho.

“This is the first time China has worked with an international organization to conduct an agricultural training workshop for sub-Saharan Africa,” said Zhonghu He, CIMMYT distinguished scientist and country liaison officer in China.

A hands-on demonstration at the Jiangsu Academy of Agricultural Sciences (JAAS) and CIMMYT Fusarium head blight (FHB) precision phenotyping platform helps scientists in Africa to better understand and fight the wheat disease. (Photo: Liu Xiyan/CAAS)

Practical tools to target FHB

Experts from China and CIMMYT shared their successful experiences of FHB management, including breeding resistant varieties. The trainees benefitted from hands-on experience of FHB identification, disease screening (including inoculum preparation, inoculation, and scoring), mycotoxin quantification techniques, and wheat breeding.

At the end of the workshop, the participants were extremely pleased to observe the impressive progress made in China on wheat FHB both on breeding and disease control, and they expressed strong willingness to contribute to collaboration between Africa, China, and CIMMYT on more wheat breeding and research. Netsanet Bacha Hei from the Ethiopian Institute of Agricultural Research (EIAR) was impressed with the scientific and technical expertise provided in the training and mentioned that sub-Saharan Africa needs similar practical trainings to mitigate the threat of FHB. Similar opinions were echoed by Doreen Malekano Chomba from the Zambian Plant Quarantine and Phytosanitary Service (PQPS), who discussed the need to have an effective in-country surveillance and monitoring to assess and manage FHB in the region.

Participants gather for the opening ceremony of the workshop at the Chinese Academy of Agricultural Sciences (CAAS) in Beijing. (Photo: Li Simin/CAAS)

Xu Zhang, who heads the FHB research program at JAAS, is very appreciative of the collaborative work that has been going on for several decades between CIMMYT and China, highlighting that the workshop represents another step in understanding and managing FHB in sub-Saharan Africa and beyond, Zhang said, JAAS and CIMMYT has grown together through strong partnership.

“This training lays firm groundwork for future China-Africa-CIMMYT collaboration on mitigating the threat of FHB and improving wheat production and food security in sub-Saharan African countries,” said He.

Heat tolerant maize hybrids: a pursuit to strengthen food security in South Asia

Written by Julian Bañuelos-Uribe on . Posted in Blogs.

After a decade of rigorous effort, CIMMYT, along with public-sector maize research institutes and private-sector seed companies in South Asia, have successfully developed and released 20 high-yielding heat-tolerant (HT) maize hybrids across Bangladesh, Bhutan, India, Nepal, and Pakistan. CIMMYT researchers used a combination of unique breeding tools and methods including genomics-assisted breeding, doubled haploidy (a speed-breeding approach where genotype is developed by chromosome doubling), field-based precision phenotyping, and trait-based selection to develop new maize germplasm that are high-yielding and also tolerant to heat and drought stresses.

While the first batch of five HT maize hybrids were released in 2017, by 2022 another 20 elite HT hybrids were released and eight varieties are deployed over 50,000 ha in the above countries.

In South Asia, maize is mainly grown as a rainfed crop and provides livelihoods for millions of smallholder farmers. Climate change-induced variability in weather conditions is one of the major reasons for year-to-year variation in global crop yields, including maize in Asia. It places at risk the food security and livelihood of farm families living in the stress-vulnerable lowland tropics. “South Asia is highly vulnerable to the detrimental effects of climate change, with its high population density, poverty, and low capacity to adapt. The region has been identified as one of the hotspots for climate change fueled by extreme events such as heat waves and intermittent droughts,” said Pervez H. Zaidi, principal scientist at CIMMYT.

Heat stress impairs the vegetative and reproductive growth of maize, starting from germination to grain filling. Heat stress alone, or in combination with drought, is projected to become a major production constraint for maize in the future. “If current trends persist until 2050, major food yields and food production capacity of South Asia will decrease significantly—by 17 percent for maize—due to climate change-induced heat and water stress,” explained Zaidi.

From breeding to improved seed delivery–the CIMMYT intervention

In the past, breeding for heat stress tolerance in maize was not accorded as high a priority in tropical maize breeding programs as other abiotic stresses such as drought, waterlogging, and low nitrogen in soil. However, in the last 12–15 years, heat stress tolerance has emerged as one of the key traits for CIMMYT’s maize breeding program, especially in the South Asian tropics. The two major factors behind this are increased frequency of weather extremes, including heat waves with prolonged dry period, and increasing demand for growing maize grain year-round.

At CIMMYT, systematic breeding for HT maize was initiated under Heat Stress Tolerant Maize for Asia (HTMA), a project funded by the United States Agency for International Development (USAID) Feed the Future program. The project was launched in 2013 in a public–private alliance mode, in collaboration with public-sector maize research institutions and private seed companies in Bangladesh, Bhutan, India, Nepal, and Pakistan.

The project leveraged the germplasm base and technical expertise of CIMMYT in breeding for abiotic stress tolerance, coupled with the research capacity and expertise of the partners. An array of activities was undertaken, including genetic dissection of traits associated with heat stress tolerance, development of new HT maize germplasm and experimental hybrids, evaluation of the improved hybrids across target populations of environments using a heat stress phenotyping network in South Asia, selection of elite maize hybrids for deployment, and finally scaling via public–private partnerships.

Delivery of HT maize hybrids to smallholder farmers in South Asia

After extensive testing and simultaneous assessment of hybrid seed production and other traits for commercial viability, the selected hybrids were officially released or registered for commercialization. Impact assessment of HT maize hybrid seed was conducted in targeted areas in India and Nepal. Studies showed farmers who adopted the HT varieties experienced significant gains under less-favorable weather conditions compared to farmers who did not.

Under favorable conditions the yield was on par with those of other hybrids. It was also demonstrated that HT hybrids provide guaranteed minimum yield (approx. 1 t ha-1) under hot, dry unfavorable weather conditions. Adoption of new HT hybrids was comparatively high (19.5%) in women-headed households mainly because of the “stay-green” trait that provides green fodder in addition to grain yield, as women in these areas are largely responsible for arranging fodder for their livestock.

“Smallholder farmers who grow maize in stress vulnerable ecologies in the Tarai region of Nepal and Karnataka state in southern India expressed willingness to pay a premium price for HT hybrid seed compared to seed of other available hybrids in their areas,” said Atul Kulkarni, socioeconomist at CIMMYT in India.

Going forward–positioning and promoting the new hybrids are critical

A simulation study suggested that the use of HT varieties could reduce yield loss (relative to current maize varieties) by up to 36% and 93% by 2030 and by 33% and 86% by 2050 under irrigated and rainfed conditions respectively. CIMMYT’s work in South Asia demonstrates that combining high yields and heat-stress tolerance is difficult, but not impossible, if one adopts a systematic and targeted breeding strategy.

The present registration system in many countries does not adequately recognize the relevance of climate-resilience traits and the yield stability of new hybrids. With year-to-year variation in maize productivity due to weather extremes, yield stability is emerging as an important trait. It should become an integral parameter of the registration and release system.

Positioning and promoting new HT maize hybrids in climate-vulnerable agroecologies requires stronger public–private partnerships for increasing awareness, access, and affordability of HT maize seed to smallholder farmers. It is important to educate farming communities in climate-vulnerable regions that compared to normal hybrids the stress-resilient hybrids are superior under unfavorable conditions and at par with or even superior to the best commercial hybrids under favorable conditions.

For farmers to be able to easily access the new promising hybrids, intensive efforts are needed to develop and strengthen local seed production and value chains involving small-and medium-sized enterprises, farmers’ cooperatives, and public-sector seed enterprises. These combined efforts will lead to wider dissemination of climate-resilient crop varieties to smallholder farmers and ensure global food security.

Cream of the crop: Developing the next generation of wheat scientists is key to sustaining wheat production in Pakistan

Written by mcallejas on . Posted in News.

On July 17-18, 2023, 87 wheat scientists gathered to learn about new approaches and methods for wheat improvement in Faisalabad, Pakistan. CIMMYT and the Wheat Research Institute, Faisalabad (WRI-FSD) jointly organized a two-day training. The course covered two topics: high throughput genotyping technologies and high throughput phenotyping platforms. The trainees, who were able to attend in person or remotely and 27% of whom were women, hailed from 17 NARES partners across Pakistan.

Trainees at Faisalabad, Pakistan. (Photo: CIMMYT)

After being welcomed by the Director General of Ayub Agricultural Research Institute (AARI), Akhtar Ali, and CIMMYT’s Country Representative, TP Tiwari, participants received an update on the status of wheat in Pakistan from Muhammad Sohail, national wheat coordinator for the Pakistan Agricultural Research Council (PARC). Subsequently, WRI-FSD Director, Javed Ahmed, discussed wheat research in Punjab, where over 70% wheat is grown in Pakistan. Kevin Pixley, interim director of CIMMYT’s Global Wheat Program, joined the proceedings remotely for a conversation about CIMMYT’s and CGIAR’s collaboration with NARES. Participants discussed the model’s successes, bottlenecks, the role of NARES, and the potential for capacity development. The conversation generated broad interest and suggestions for enhancing the partnership’s effectiveness. Akhtar Ali, Muhammad Sohail, and Javed Ahmed all spoke very highly about CIMMYT’s support in Pakistan.

This event was organized as part of a collaborative project entitled “Rapid development of climate resilient wheat varieties for South Asia using genomic selection” that is jointly managed by Kansas State University and CIMMYT with funding from the USAID Feed the Future program.

“Training emphasized the need for an output-oriented researcher that covered the development of climate-resilient wheat varieties, given the environmental challenges we are experiencing like, drought and heat, and highlighted the importance of innovative methodologies and advanced tools for high throughput phenotyping and genotyping for sustainable and resilient wheat production in Pakistan” said Muhammad Ishaq, a senior research officer and one of the training participants from Kohat Research Station, Khyber Pakhtunkhwa.

At the conclusion of the training, Javed, direct of WRI Faisalabad, commended CIMMYT’s support and suggested continuing the pace of training. Dr. Tiwari stressed the importance of such efforts will help Pakistan’s scientists develop and deploy climate resilient, impactful wheat varieties to boost wheat production and reduce wheat imports in the country.

Harnessing new high-resolution satellite imagery to plant breeding

Written by Julian Bañuelos-Uribe on . Posted in Publications.

In plant breeding, efforts to increase the rate of genetic gains and enhance crop resilience to the effects of climate change are often limited by the inaccessibility and costs of phenotyping methods. The recent rapid development of sensors, image-processing technology and data analysis has provided new opportunities for multiple scales phenotyping methods and systems. Among these, satellite imagery may represent one of the best ways to remotely monitor trials and nurseries planted in multiple locations, while standardizing protocols and reducing costs.

This is because relevant data collected as part of crop phenotyping can be generated from satellite images. For instance, the sensors onboard the SkySat satellite constellation of Planet Labs have four spectral bands—blue, green, red, and infrared—which can be used to calculate the normalized difference vegetation index (NDVI), which is a measure of vegetation and its greenness, and various canopy traits like ground cover, leaf area index and chlorosis. It can also be used to monitor plot establishment and phenological parameters.

High-resolution RGB orthomosaic of wheat experiments, assessing the effect of plot size and spacing in the spectral signature, collected from SkySat satellite images. (Photo: Gilberto Thompson)

The use of satellite-based phenotyping in breeding trials has typically been restricted by low resolution, high cost and long intervals between fly-overs. However, the advent of a new generation of high-resolution satellites—such as the SkySat constellation—now offers multispectral images at a 0.5m resolution with close to daily acquisition attempts on any place on Earth. This could be a game changer in terms of the scale at which yield trials can be conducted, enabling more precise variety placement and thereby increasing genetic diversity across farmer’s fields and reducing the probability of disease epidemics. It could also revolutionize the capacity for research in realistic field conditions, since traits can be measured throughout the cycle in a highly standardized way, over multiple sites at low cost. For example, an image which covers 25 km2 can monitor an entire research station at a cost of about US$300.

To test the suitability of this technology, a team of researchers from CIMMYT set out to evaluate the reliability of SkySat NDVI estimates for maize and wheat breeding plots of different sizes and spacing, as well as testing its capacity for detecting seasonal changes and genotypic differences.

Both their initial findings, recently published in Frontiers in Plant Science, and more recently acquired data, show that the SkySat satellites can be used to monitor plots commonly used in wheat and maize nurseries. While wheat yield plots usually are 1.2m wide, maize plots tend to consist of at least two rows, resulting in a width of 1.5m. Plot length ranges from 2-4m. The authors also discuss on other factors to be considered when extracting and interpreting satellite data from yield trials, such as plot spacing.

Through the successful collection of six satellite images in Central Mexico during the rainy season and parallel monitoring of a maize trial in Zimbabwe, the researchers demonstrate the flexibility of this tool. Beyond the improvement of spatial resolution, the researchers suggest that the next challenge will be the development and fine-tuning of operational procedures that ensure high quality, standardized data, allowing them to harness the benefits of the modern breeding triangle, which calls for the integration of phenomics, enviromics and genomics, to accelerate breeding gains.

Read the full study: Satellite imagery for high-throughput phenotyping in breeding plots

This research was supported by the Foundation for Food and Agriculture Research, the CGIAR Research Program on Maize, the CGIAR Research Program on Wheat, and the One CGIAR Initiatives on Digital Innovation, F2R-CWANA, and Accelerated Breeding.

CIMMYT and BWMRI host international training program on surveillance and management strategies for wheat blast

Written by Julian Bañuelos-Uribe on . Posted in News.

The devastating disease wheat blast is a threat to crop production in many South Asian countries. In Bangladesh, it was first identified in seven southern and southwestern districts in 2016, and later spread to 27 others causing significant damage. The International Maize and Wheat Improvement Center (CIMMYT) is working with the Bangladesh Wheat and Maize Research Institute (BWMRI) and other national partners to conduct research and extension activities to mitigate the ongoing threat.

From March 1-10, 2023, a group of 46 wheat researchers, government extension agents, and policy makers from ten countries — Bangladesh, Brazil, China, Ethiopia, India, Japan, Mexico, Nepal, Sweden, and Zambia — gathered in Jashore, Bangladesh to learn about and exchange experiences regarding various wheat diseases, particularly wheat blast. Following the COVID-19 pandemic, this was the first in-person international wheat blast training held in Bangladesh. It focused on the practical application of key and tricky elements of disease surveillance and management strategies, such as resistance breeding and integrated disease management.

Training participants get hands-on practice using a field microscope, Bangladesh. (Photo: Ridoy/CIMMYT)

“This is an excellent training program,” said Shaikh Mohammad Bokhtiar, executive chairman of the Bangladesh Agriculture Research Council (BARC), during the opening session.  “Participants will learn how to reduce the severity of the blast disease, develop and expand blast resistant varieties to farmers, increase production, and reduce imports.”

This sentiment was echoed by Golam Faruq, director general of BWMRI. “This program helps in the identification of blast-resistant lines from across the globe,” he said. “From this training, participants will learn to manage the devastating blast disease in their own countries and include these learnings into their national programs.”

Hands-on training

The training was divided into three sections: lectures by national and international scientists; laboratory and field experiment visits; and trips to farmers’ fields. Through the lecture series, participants learned about a variety of topics including disease identification, molecular detection, host-pathogen interaction, epidemiology and integrated disease management.

Hands-on activities were linked to working on the Precision Phenotyping Platform (PPP), which involves the characterization of more than 4,000 wheat germplasm and releasing several resistant varieties in countries vulnerable to wheat blast. Participants practiced taking heading notes, identifying field disease symptoms, tagging, and scoring disease. They conducted disease surveillance in farmers’ fields in Meherpur and Faridpur districts — both of which are extremely prone to wheat blast — observing the disease, collecting samples and GPS coordinates, and completing surveillance forms.

Muhammad Rezaul Kabir, senior wheat breeder at BWMRI, explains the Precision Phenotyping Platform, Bangladesh. (Photo: Md. Harun-Or-Rashid/CIMMYT)

Participants learned how to use cutting-edge technology to recognize blast lesions in leaves using field microscopes. They went to a pre-installed spore trapping system in a farmer’s field to learn about the equipment and steps for collecting spore samples, observing them under a compound microscope, and counting spores. They also visited the certified seed production fields of Shawdesh Seed, a local company which has played an important role in promoting wheat blast resistant varieties BARI Gom 33 and BWMRI Gom 3 regionally, and Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) in Gazipur to see current wheat blast research in action.

Blast-resistance in Bangladesh

“I am so happy to see the excellent infrastructure and work ethics of staff that has made possible good science and impactful research come out of the PPP,” said Aakash Chawade, associate professor in Plant Breeding at the Swedish University of Agricultural Sciences. “Rapid development of blast-resistant varieties and their dissemination will help Bangladesh mitigate the effects of wheat blast, not only inside the country but by supporting neighboring ones as well.”

Training participants scout and score disease in a blast-infected wheat field, Bangladesh. (Photo: Md. Harun-Or-Rashid/CIMMYT)

“Besides the biotic and abiotic challenges faced in wheat production, climate change and the Russia-Ukraine crisis are further creating limitations to wheat production and marketing,” said Pawan Kumar Singh, head of Wheat Pathology at CIMMYT and lead organizer of the training. “Due to the development of blast-resistant wheat varieties and its commercial production under integrated disease management practices, the domestic production of wheat in Bangladesh has increased and there is increased interest from farmers in wheat.”

Dave Hodson, a principal scientist at CIMMYT and one of the training’s resource speakers, added: “This is a remarkable success that researchers developed two blast resistant varieties in Bangladesh urgently. It was only achievable because of the correct measures taken by the researchers and support of Government policies.”

However, there are still some barriers to widespread adoption of these varieties. As such, in parallel to other activities, a team from Bangladesh Agricultural University (BAU) joined the field trip to meet local farmers and conduct research into the socio-economic factors influencing the adoption and scaling of relevant wheat varieties.

The Australian High Commission, ACIAR and BARC delegates recognizes the BWMRI-CIMMYT collaborative wheat blast research platform in Bangladesh

Written by Sarah McLaughlin on . Posted in News.

Delegates with other officials in front of the seminar room. (Photo: Biswajit/BWMRI)

Representatives from Australian Centre for International Agricultural Research (ACIAR) and Bangladesh Agricultural Research Council (BARC) paid a visit to Bangladesh to see the valuable work of the Precision Phenotyping Platform (PPP).

PPP was established in response to the devastating wheat blast disease, which was first reported in the country in 2016.

Technical and financial support from the International Maize and Wheat Improvement Center (CIMMYT), the Australian Commission for International Agricultural Research and the Australian Centre for International Agricultural Research, along with other funders, has contributed to the effort to combat the disease.

This is achieved by generating precise data for wheat blast resistance in germplasm in Bangladesh, as well as other wheat growing countries. This PPP has been used to screen elite lines and genetic resources from various countries.

On February 16 and 17, 2023, two groups of national and international delegations visited the BWMRI-CIMMYT collaborative research platform PPP at the BWMRI regional station in Jashore, Bangladesh.

The first group was made up of representatives from both the Australian Commission for International Agricultural Research and the Australian Centre for International Agricultural Research. This included seven commissioners under the direction of Fiona Simson, along with ACIAR senior officials from Australia and India.

The other group was from BARC, which was led by Executive Chairman Shaikh Mohammad Bokhtiar, along with Golam Faruq, Director General of BWMRI, and Andrew Sharpe, Bangabandhu Research Chair, Global Institute of Food Security (GIFS), University of Saskatchewan in Canada.

Both delegations were welcomed by Muhammad Rezaul Kabir, the Senior Wheat Breeder at BWMRI. Kabir gave a brief presentation about the platform and other wheat blast collaborative research programs in the seminar room.

The delegations then went to the PPP field, where BWMRI researchers Kabir and Robiul Islam, as well as CIMMYT researcher Md. Harun-Or-Rashid, explained further information about the BWMRI-CIMMYT collaborative research. Both commissioners and delegates appreciated seeing the work being conducted in person by the national and international collaborations of BWMRI and CIMMYT on wheat blast research.

Visitors observing blast disease symptoms in wheat leaves. (Photo: Muhammad Rezaul Kabir/BWMRI)

“It is important, innovative work, that is affecting not only Bangladesh but many countries around the world that are now starting to be concerned about the impacts of wheat blast,” commissioner Simson said. “This study is very important for Australia and we are pleased to be contributing to it.”

Lindsay Falvey, another commissioner, added, “This is a wonderful experiment, using high-level science and technologies to combat wheat blast in Bangladesh. The experiment is well-planned. Overall, it is an excellent platform.”

ACIAR delegate Eric Huttner added to the praise for the project. “The platform is performing extremely well for the purpose of evaluating lines, resistance to the disease and that’s very useful for Bangladesh and rest of the world,” he said. “This is a gift that Bangladesh is giving to the neighboring countries to protect wheat.”

The delegates pledged to share their expert advice with the Minister of Foreign Affairs in Bangladesh in order to increase investments and improve facilities for agricultural research programs in the country.

Golam Faruq, Director General of BWMRI discussing the PPP with Shaikh Mohammad Bokhtiar, Executive Chairman of BARC (Photo: Md. Harun-Or-Rashid/CIMMYT)

“This is an excellent work,” Executive Chairman of BARC, Bokhtiar said. “We can get more information from screening activities by using bioinformatics tools and training people through the BARC-GIFS program.”

Pawan Kumar Singh, Head of Wheat Pathology at CIMMYT-Mexico and Project Leader, coordinated the visits virtually and expressed his thanks to the delegations for their visit to the platform. This PPP, within a short span of few years, has been highly impactful, characterizing more than 15,000 entries and releasing several resistant varieties in countries vulnerable to wheat blast.

Wheat stalks grow in a in India. (Photo: Saad Akhtar)

CIMMYT, AGG wheat experts share latest discoveries at BGRI Technical Workshop

Written by Marcia MacNeil on . Posted in News.

Dave Hodson, International Maize and Wheat Improvement Center (CIMMYT) senior scientist delivered a large-scale overview of the current global wheat rust situation and the state of disease surveillance systems. He underscored the importance of comprehensive early warning systems and promising new detection tools that help to raise awareness and improve control. A new assessment of the early warning system for rust In Ethiopia showed a real impact on farmers’ interest, awareness, and farming practices to control the disease, as well as high-level policy changes.

Alison Bentley, CIMMYT Global Wheat Program director, described cutting-edge tools and methods by CIMMYT and, in particular, the Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project to increase wheat productivity in the face of changing climates. In addition to the new approaches on the supply side, she argued, we also need increased research on the demand side to better understand why farmers will choose a new variety, the role of markets and gender, and how we can scale up these systems. Bentley emphasized the criticality of supporting public and private sector efforts to get more improved germplasm into farmers’ fields in less time.

Philomin Juliana, CIMMYT Global Wheat Program associate scientist highlighted the pivotal role that data plays in breeding decisions and line advancements in CIMMYT’s wheat breeding program. This has been facilitated by improvements in how data sets, like genomic estimated breeding values (GEBVs), are shared with breeders. “CIMMYT has adopted a holistic, data-driven selection approach” that leverages phenotypic data, genomic-estimated breeding values (GEBVs) and selection indices, Juliana explained.

Breaking Ground: Fatima Camarillo invests in education

Written by Madeline Dahm on . Posted in Features.

It was clear to Fatima Camarillo Castillo from a young age that her future was in agriculture. She grew up on a farm in a small village in Zacatecas, Mexico, and recalls working in the fields alongside her father and siblings, helping with the harvests and milking the cows. And every year, her family ran into the same issue with their crops: droughts.

“Sometimes the harvest was okay, but sometimes we didn’t have any harvest at all,” says Camarillo. “For us that meant that, if we didn’t have enough harvest, then for the whole year my mother and father struggled to send us to school.”

But they did send her to school, and instead of escaping the persistent challenges that agriculture had presented her family in her young life, she was determined to solve them. “After elementary school we had to leave the farm to continue our education,” she explains. “I knew about all the challenges that small farmers face and I wanted to have an impact on them.”

To this day, Camarillo believes in the power of education. Her schooling took her all the way to the International Maize and Wheat Improvement Center (CIMMYT), where she is now not only a researcher, but an educator herself. After her extensive study of plant breeding, genetics and wheat physiology, Camarillo gained a master’s degree from the University of Massachusetts, Amherst, and a PhD from Texas A+M University.

She was a part of CIMMYT’s fellowship program while pursuing her doctorate, and she joined the organization’s wheat breeding team shortly afterward. Camarillo now splits her time between wheat research and organizing the training activities for CIMMYT’s Global Wheat Program (GWP) wheat improvement course.

Fatima Camarillo analyzes durum wheat in the field at CIMMYT’s experimental research station in Ciudad Obregón, Mexico. (Photo: CIMMYT)

A special legacy

CIMMYT’s wheat improvement course is an internationally recognized program where scientists from national agricultural research programs (NARS) from around the world travel to CIMMYT Headquarters in Texcoco, Mexico, and then to Ciudad Obregón, for a 16-week training. Participants observe an entire breeding cycle and learn about the latest technologies and systems for breeding.

“A crucial component of having an impact on farmers is establishing good relationships with national programs, where all the germplasm that CIMMYT develops is going to go,” says Camarillo. “But at the same time, these partners need training. They need to know what is behind these varieties and the process for developing them, and we try to keep them updated with the vision, the current technologies and the breeding pipeline.”

The organization’s university-focused training programs are also special to Camarillo for many reasons, having participated in one of them herself. In fact, her first ever exposure to CIMMYT was through the annual Open Doors day which she attended during her first year of university, watching the breeders and scientists that would eventually become her colleagues give talks on germplasm development and distribution.

The courses also give students a chance to see all how their theoretical education can be applied in the real world. “When you are in graduate school you care a lot about data analysis and the most recent molecular tools,” says Camarillo. “But there is something else out there, the real problems outside. By taking the breeding program course you understand these challenges and situations.”

Camarillo remembers being struck by the thought that something that happens in a research station in Mexico can have an impact on the whole world. “CIMMYT cares about how other countries will adopt new varieties, it’s not just about developing germplasm for the sake of it,” she explains. “We’re interested in how new varieties are going to reach the farmers who need them, and for that, training is essential.”

“At the end of the day, these researchers are the ones who will help us evaluate germplasm. If they’re well trained, the efficiency of the whole process will increase.”

Fatima Camarillo (standing, third from the right) in Ciudad Obregón, Mexico, with participants on the GWP’s 2019 training program. (Photo: CIMMYT)

Keeping an eye on the breeding pipeline

With one foot in education and the other in research, Camarillo has a unique perspective on CIMMYT’s strategy for bringing tools and findings out of the lab, and towards the next step in the impact pathway. A key part of her work involves helping to research physiological traits by developing new tools to increase phenotyping efficiency in the breeding pipeline.

In particular, she is working on a project to develop high-throughput phenotyping tools, which use hyperspectral sensors and cameras to measure several traits in plants. This can help reflect how the plant is responding to different stresses internally, and helps physiologists and breeders understand how the plant behaves within a specific environment, and then quickly integrate these traits into the breeding process.

“Overall it increases the efficiency of selection, so farmers will have better materials, better germplasm, and more reliable yield across environments in a shorter period of time,” says Camarillo.   

Sharing the recipe for success

Camarillo’s role in both breeding and training speaks to CIMMYT’s historic and proven strategy of working with national programs to effectively deliver improved seeds to the farmers who need them. In addition to developing friendships with trainees from around the world, she is helping CIMMYT to expand its global network of research and agriculture professionals.

As a product and purveyor of a great agricultural education, Camarillo is dedicated to it passing on. “I think we have to invest in education,” she says. “It is the only path to solve the current problems we face, not only in agriculture, but in every single discipline.”

“If we don’t invest and take the time for education, our future is very uncertain.”

A view from above

Written by Alison Doody on . Posted in Features.

Scientists at the International Maize and Wheat Improvement Center (CIMMYT) have been harnessing the power of drones and other remote sensing tools to accelerate crop improvement, monitor harmful crop pests and diseases, and automate the detection of land boundaries for farmers.

A crucial step in crop improvement is phenotyping, which traditionally involves breeders walking through plots and visually assessing each plant for desired traits. However, ground-based measurements can be time-consuming and labor-intensive.

This is where remote sensing comes in. By analyzing imagery taken using tools like drones, scientists can quickly and accurately assess small crop plots from large trials, making crop improvement more scalable and cost-effective. These plant traits assessed at plot trials can also be scaled out to farmers’ fields using satellite imagery data and integrated into decision support systems for scientists, farmers and decision-makers.

Here are some of the latest developments from our team of remote sensing experts.

An aerial view of the Global Wheat Program experimental station in Ciudad Obregón, Sonora, Mexico (Photo: Francisco Pinto/CIMMYT)

Measuring plant height with high-powered drones

A recent study, published in Frontiers in Plant Science validated the use of drones to estimate the plant height of wheat crops at different growth stages.

The research team, which included scientists from CIMMYT, the Federal University of Viçosa and KWS Momont Recherche, measured and compared wheat crops at four growth stages using ground-based measurements and drone-based estimates.

The team found that plant height estimates from drones were similar in accuracy to measurements made from the ground. They also found that by using drones with real-time kinematic (RTK) systems onboard, users could eliminate the need for ground control points, increasing the drones’ mapping capability.

Recent work on maize has shown that drone-based plant height assessment is also accurate enough to be used in maize improvement and results are expected to be published next year.

A map shows drone-based plant height estimates from a maize line trial in Muzarabani, Zimbabwe. (Graphic: CIMMYT)

Advancing assessment of pests and diseases

CIMMYT scientists and their research partners have advanced the assessment of Tar Spot Complex — a major maize disease found in Central and South America — and Maize Streak Virus (MSV) disease, found in sub-Saharan Africa, using drone-based imaging approach. By analyzing drone imagery, scientists can make more objective disease severity assessments and accelerate the development of improved, disease-resistant maize varieties. Digital imaging has also shown great potential for evaluating damage to maize cobs by fall armyworm.

Scientists have had similar success with other common foliar wheat diseases, Septoria and Spot Blotch with remote sensing experiments undertaken at experimental stations across Mexico. The results of these experiments will be published later this year. Meanwhile, in collaboration with the Federal University of Technology, based in Parana, Brazil, CIMMYT scientists have been testing deep learning algorithms — computer algorithms that adjust to, or “learn” from new data and perform better over time — to automate the assessment of leaf disease severity. While still in the experimental stages, the technology is showing promising results so far.

CIMMYT researcher Gerald Blasch and EIAR research partners Tamrat Negash, Girma Mamo and Tadesse Anberbir (right to left) conduct field work in Ethiopia. (Photo: Tadesse Anberbir)

Improving forecasts for crop disease early warning systems

CIMMYT scientists, in collaboration with Université catholique de Louvain (UCLouvain), Cambridge University and the Ethiopian Institute of Agricultural Research (EIAR), are currently exploring remote sensing solutions to improve forecast models used in early warning systems for wheat rusts. Wheat rusts are fungal diseases that can destroy healthy wheat plants in just a few weeks, causing devastating losses to farmers.

Early detection is crucial to combatting disease epidemics and CIMMYT researchers and partners have been working to develop a world-leading wheat rust forecasting service for a national early warning system in Ethiopia. The forecasting service predicts the potential occurrence of the airborne disease and the environmental suitability for the disease, however the susceptibility of the host plant to the disease is currently not provided.

CIMMYT remote sensing experts are now testing the use of drones and high-resolution satellite imagery to detect wheat rusts and monitor the progression of the disease in both controlled field trial experiments and in farmers’ fields. The researchers have collaborated with the expert remote sensing lab at UCLouvain, Belgium, to explore the capability of using European Space Agency satellite data for mapping crop type distributions in Ethiopia. The results will be also published later this year.

CIMMYT and EIAR scientists collect field data in Asella, Ethiopia, using an unmanned aerial vehicle (UAV) data acquisition. (Photo: Matt Heaton)

Delivering expert irrigation and sowing advice to farmers phones

Through an initiative funded by the UK Space Agency, CIMMYT scientists and partners have integrated crop models with satellite and in-situ field data to deliver valuable irrigation scheduling information and optimum sowing dates direct to farmers in northern Mexico through a smartphone app called COMPASS — already available to iOS and Android systems. The app also allows farmers to record their own crop management activities and check their fields with weekly NDVI images.

The project has now ended, with the team delivering a webinar to farmers last October to demonstrate the app and its features. Another webinar is planned for October 2021, aiming to engage wheat and maize farmers based in the Yaqui Valley in Mexico.

CIMMYT researcher Francelino Rodrigues collects field data in Malawi using a UAV. (Photo: Francelino Rodrigues/CIMMYT)

Detecting field boundaries using high-resolution satellite imagery

In Bangladesh, CIMMYT scientists have collaborated with the University of Buffalo, USA, to explore how high-resolution satellite imagery can be used to automatically create field boundaries.

Many low and middle-income countries around the world don’t have an official land administration or cadastre system. This makes it difficult for farmers to obtain affordable credit to buy farm supplies because they have no land titles to use as collateral. Another issue is that without knowing the exact size of their fields, farmers may not be applying to the right amount of fertilizer to their land.

Using state of the art machine learning algorithms, researchers from CIMMYT and the University of Buffalo were able to detect the boundaries of agricultural fields based on high-resolution satellite images. The study, published last year, was conducted in the delta region of Bangladesh where the average field size is only about 0.1 hectare.

A CIMMYT scientist conducts an aerial phenotyping exercise in the Global Wheat Program experimental station in Ciudad Obregón, Sonora, Mexico. (Photo: Francisco Pinto/CIMMYT)

Developing climate-resilient wheat

CIMMYT’s wheat physiology team has been evaluating, validating and implementing remote sensing platforms for high-throughput phenotyping of physiological traits ranging from canopy temperature to chlorophyll content (a plant’s greenness) for over a decade. Put simply, high-throughput phenotyping involves phenotyping a large number of genotypes or plots quickly and accurately.

Recently, the team has engaged in the Heat and Drought Wheat Improvement Consortium (HeDWIC) to implement new high-throughput phenotyping approaches that can assist in the identification and evaluation of new adaptive traits in wheat for heat and drought.

The team has also been collaborating with the Accelerating Genetic Gains in Maize and Wheat (AGG) project, providing remote sensing data to improve genomic selection models.

Cover photo: An unmanned aerial vehicle (UAV drone) in flight over CIMMYT’s experimental research station in Ciudad Obregon, Mexico. (Photo: Alfredo Saenz/CIMMYT)

National Wheat Coordinator Ruth Wanyera (third from right) gives a lesson to pathology interns in the field of a fungicide efficiency trial at KALRO Njoro Research Station, Nakuru, Kenya.

“Let there be food to eat”

Written by Madeline Dahm on . Posted in News.

“We want to feed the people, we don’t want them to go hungry. We have to do something to make sure there is food on the table. That is where my motivation is… Let there be food to eat.”

— Ruth Wanyera, 2019

The International Maize and Wheat Improvement Center (CIMMYT) has long attributed its widespread impact and reach to strong collaborations with national agricultural research systems (NARS) around the world. Today, CIMMYT — and especially the Global Wheat Program and the CGIAR Research Program on Wheat — wish to honor one long-term collaborator whose work and dedication to wheat research has had abiding positive effects beyond her home region of sub-Saharan Africa.

Ruth Wanyera, national wheat research program coordinator at the Kenya Agricultural and Livestock Research Organization (KALRO), has spent her more than 30-year career dedicated to plant protection research, fueled by her motivation to “feed the people.” She was one of the first scientists to recognize stem rust in east Africa and has been one of CIMMYT’s strongest allies in fighting the devastating wheat disease, stem rust Ug99.

Wanyera recently won both the Norman Borlaug Lifetime Achievement Award from the Borlaug Global Rust Initiative and the Kenya Agricultural Research (KARA) Award at the High Panel Conference on Agricultural Research in Kenya. Wanyera’s team at KALRO has also been recognized with the prestigious Borlaug Global Rust Initiative (BGRI) Gene Stewardship Award.

National Wheat Coordinator Ruth Wanyera (third from right) gives a lesson to pathology interns in the field of a fungicide efficiency trial at KALRO Njoro Research Station, Nakuru, Kenya.
National Wheat Coordinator Ruth Wanyera (third from right) gives a lesson to pathology interns in the field of a fungicide efficiency trial at KALRO Njoro Research Station, Nakuru, Kenya. (Photo:CIMMYT)

A long-term relationship with CIMMYT

Sridhar Bhavani, senior scientist and head of Rust Pathology and Molecular Genetics at CIMMYT has worked closely with Wanyera and her team since the mid-2000s.

“Ruth is a passionate researcher who has tirelessly dedicated her entire career to cereal pathology, and as a team, we coordinated the stem rust phenotyping platform for over a decade and had great successes on multiple international projects,” he said.

CIMMYT’s relationship with Wanyera’s team strengthened when Nobel Prize Laureate Norman Borlaug visited the Kenyan research facility to observe the emerging threat of stem rust. Upon witnessing how serious the outbreak had become, Borlaug organized an emergency summit in Nairobi in 2005, famously “sounding the alarm” for swift and concerted action on stem rust, and ultimately leading to the establishment of the BGRI.

“Ruth and her team of dedicated scientists from KALRO have not only made Kenya proud but have also made a remarkable contribution to the global wheat community in mitigating the threat of stem rust Ug99,” says Bhavani. “Ruth has mentored master’s and PhD students who are now leading researchers at KALRO. She has elevated the research capacity of KALRO to international repute.”

Two recent wheat breeding projects helped extend the CIMMYT-KALRO partnership beyond Kenya. The Durable Rust Resistance in Wheat (DRRW) and Delivering Genetic Gain in Wheat (DGGW) projects brought in a partnership with the Ethiopia Institute for Agricultural Research (EIAR) to establish and operate stem rust phenotyping platforms that addressed the global threat of Ug99 and other serious stem rust races, and helped provide solutions for the region. Thanks to KALRO’s screening efforts at the CIMMYT-KALRO Stem Rust Screening Platform in Njoro, Kenya, CIMMYT-derived rust-resistant varieties now cover more than 90% of the wheat farming area in Kenya and Ethiopia.

Ruth Wanyera receives the Kenya Agricultural Research Award (KARA), during the High Panel Conference on Agricultural Research in Kenya. (Photo: CIMMYT)
Ruth Wanyera receives the Kenya Agricultural Research Award (KARA), during the High Panel Conference on Agricultural Research in Kenya. (Photo: CIMMYT)

The partnership continues to grow

Continued collaboration with Ruth’s team at KALRO will be essential in the new Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project. AGG — which aims to accelerate the development and delivery of more productive, climate-resilient, gender-responsive, market-demanded, and nutritious wheat varieties in in sub-Saharan Africa and South Asia — has a particular focus on enhanced collaboration with national partners such as KALRO.

Its success is also closely tied to the Njoro Stem Rust Screening Platform — which, since its establishment in 2008, has conducted crucial screening for over 600,000 wheat lines, varieties, varietal candidates, germplasm bank accessions and mapping populations. Wanyera’s leadership in the Platform, alongside that of CIMMYT wheat scientist Mandeep Randhawa,  plays a major role in screening, monitoring, and clearing seed in time for sowing.

As Hans Braun, former director of the CIMMYT Global Wheat Program said, “Without our national agriculture research system partnerships, CIMMYT would become obsolete.”

Indeed, the unparalleled wealth of knowledge, skills, and research facilities of the CGIAR as a whole would not be so uniquely impactful if it weren’t for the 3000+ partnerships with national governments, academic institutions, enthusiastic farmers, private companies and NGOs that help carry out this work.

CIMMYT’s historic and continued impact depends on close international partnerships with scientists and leaders like Ruth Wanyera, and we congratulate her on her numerous awards, thank her for her collaboration, and wish her a pleasant retirement.

Wheat stalks grow in a in India. (Photo: Saad Akhtar)

Progress and opportunities for CIMMYT spring wheat breeding

Written by Alison Doody on . Posted in News.

Wheat stalks grow in a in India. (Photo: Saad Akhtar)
Wheat stalks grow in a field in India. (Photo: Saad Akhtar)

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.

A wheat field is fed by drip irrigation in Obregon, Mexico. (Photo: H. Gomez/CIMMYT)
A wheat field is fed by drip irrigation in Obregon, Mexico. (Photo: H. Gomez/CIMMYT)

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.

Building resistance in wheat: International collaboration fights Septoria tritici blotch disease

Written by Alison Doody on . Posted in News.

Phenotypic selection of resistant lines (Ms. H. Kouki Field technician and consultant A. Yahyaoui) at the Septoria Precision Phenotyping Platform at Kodia/INGC. (Photo: Septoria Precision Phenotyping Platform)

Tunisia has been a major durum wheat producer and consumer since Roman times, a crop used now for couscous, bread and pasta dishes throughout North Africa and the Mediterranean Basin.

However, a persistent disease known as Septoria tritici blotch (STB) has been threatening durum wheat harvests across the country thanks to its increasing resistance to fungicides and adaptability to harsher climatic conditions. The disease, which is caused by the fungus Zymoseptoria tritici, thrives under humid conditions and can cause up to 60% yield loss in farmers’ fields.

To help fight this disease, the International Maize and Wheat Improvement Center (CIMMYT) established the Septoria Precision Phenotyping Platform in collaboration with the Institution of Agricultural Research and Higher Education of Tunisia (IRESA) and the International Center for Agricultural Research in the Dry Areas (ICARDA) in Tunisia in 2015.

The platform aims to accelerate the transfer of STB resistance genes into elite durum wheat lines from national and international breeding programs, particularly CIMMYT and ICARDA breeding programs. Researchers at the platform have tested an impressive diversity of durum wheat lines for resistance to the disease from research institutes across Tunisia, Morocco, Algeria, Mexico, France, Italy, the UK, USA and Canada.

STB field reactions showing typical necrotic symptoms containing pycnidia on an infected adult plant leaf of wheat. (Photo: Septoria Precision Phenotyping Platform)

“New and more virulent strains of the pathogen are constantly emerging, which results in previously resistant wheat varieties becoming more susceptible,” said Sarrah Ben M’Barek, head of the laboratory at the Septoria Precision Phenotyping platform.

Field phenotyping – the use of field-testing to identify desired plant traits — is the heart of the platform. Scientists can test as many as 30,000 plots each year for STB resistance.

Evaluations are conducted at two main field research stations managed by the Regional Field Crop Center (CRRGC) and the National Institute of Field Crops (INGC), based at two major hotspots for the disease in Beja and Kodia. This work is complemented by laboratory research at the National Agronomic Institute of Tunisia (INAT) at Tunis.

“The platform plays a critical role in identifying STB resistant wheat germplasm and characterizing the resistance genes they possess. These resistant sources be can further utilized in hybridization schemes by durum wheat breeders worldwide to develop durable resistant varieties,” explained CIMMYT consultant and platform coordinator Amor Yahyaoui.

With the help of data from the platform, breeders hope to combine multiple resistance genes in an individual variety to create a genetically complex “lock” whose combination the fungus will not easily break.

According to Ben M’Barek, the huge genetic diversity in wheat and its ancestors has helped breeders to develop new varieties for almost a century. However, the adoption of new varieties has typically been slow.

Farmers in Tunisia traditionally rely on fungicides to manage the disease. However, with the pathogen recently becoming more resistant to fungicides and more adaptive to harsher climatic conditions, interest in STB resistant varieties is increasing.

Field disease reactions of a susceptible wheat cultivar. (Photo: Septoria Precision Phenotyping Platform)

A hub for training and collaboration

The platform is also a hub for training and capacity development for national and international scientists, field research and lab. assistants, students and farmers. It brings together research staff and technicians from different institutions within Tunisia including the CRRGC, INGC, the National Institute of Agricultural Research of Tunisia (INRAT), INAT and the University of Jendouba.

Farmer’s organizations and regional extension services, as well as private organizations such as Comptoir Multiservices Agricoles (CMA), seed and chemical companies also collaborate with the platform. The result is a team effort that has generated a tremendous wealth of data, made only possible through the dedication of Yahyaoui, said Ben M’Barek.

“Spending a few days at the platform each year is a like a crash course on STB resistance. All subjects are covered and great experts around the world come together to discuss all details of this host-pathogen interaction,” said Filippo Bassi, senior durum wheat breeder at ICARDA.

“Sending young scientists to spend some time at the platform ensures that they learn all about the mechanisms of resistance and take them back to their home country to deploy them in their own breeding programs. It is like a true university for STB.”

Yet, the platform still has a lot of work to do, according to Ben M’Barek. Scientists at the platform are now working on raising awareness on crop and pest management such as integrated management approaches amongst farming communities, setting up on-farm field trials and developing disease early warning surveillance.

Next year the platform will provide a unique podium for students, academics and researchers to exchange ideas and research findings on cereal leaf blight diseases. The International Symposium on Cereal Leaf Blights will take place on May 19-21, 2021 in Tunisia. Details can be found here.

The Septoria Precision Phenotyping Platform is led by the International Maize and Wheat Improvement Center (CIMMYT), in collaboration with the Institution of Agricultural Research and Higher Education of Tunisia (IRESA) and the International Center for Agricultural Research in the Dry Areas (ICARDA) and is supported by the CGIAR Research Program in Wheat (WHEAT).

Septoria Precision Phenotyping Platform at Oued Béja (CRRGC). (Photo: Gert Kema/Wageningen University)