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Retrospective quantitative genetic analysis and genomic prediction of global wheat yields

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

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

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

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

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

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

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

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

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

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

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

Read the full article: Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields

This story was originally posted on the website of the CGIAR Research Program on Wheat (wheat.org).

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

Wheat researchers to gather for October virtual event

A global wheat conference originally scheduled to be held in June in Norwich, United Kingdom, now will take place virtually on Oct. 7-9.

The Borlaug Global Rust Initiative’s (BGRI) virtual technical workshop was postponed earlier this year due to the coronavirus (COVID-19) pandemic.

Read more here: https://www.world-grain.com/articles/14150-wheat-researchers-to-gather-for-october-virtual-event

Supporting smallholder farmers to better combat drought

A farmer in Banke district during monsoon season drought in 2017. (Photo: Anton Urfels/CIMMYT)
A farmer in Banke district during monsoon season drought in 2017. (Photo: Anton Urfels/CIMMYT)

Researchers from the Cereal Systems Initiative for South Asia (CSISA) project have been exploring the drivers of smallholder farmers’ underuse of groundwater wells to combat in-season drought during the monsoon rice season in Nepal’s breadbasket — the Terai region.

Their study, published in Water International, finds that several barriers inhibit full use of groundwater irrigation infrastructure.

Inconsistent rainfall has repeatedly damaged paddy crops in Nepal over the last years, even though most agricultural lands are equipped with groundwater wells. This has contributed to missed national policy targets of food self-sufficiency and slow growth in cereal productivity.

A key issue is farmers’ tendency to schedule irrigation very late in an effort to save their crops when in-season drought occurs. By this time, rice crops have already been damaged by lack of water and yields will be decreased. High irrigation costs, especially due to pumping equipment rental rates, are a major factor of this aversion to investment. Private irrigation is also a relatively new technology for many farmers making water use decisions.

After farmers decide to irrigate, queuing for pumpsets, tubewells, and repairs and maintenance further increases irrigation delays. Some villages have only a handful of pumpsets or tubewells shared between all households, so it can take up to two weeks for everybody to irrigate.

To address these issues, CSISA provides suggestions for three support pathways to support farmers in combatting monsoon season drought:

1. Raise awareness of the importance of timely irrigation

To avoid yield penalties and improve operational efficiency through better-matched pumpsets, CSISA has raised awareness through agricultural FM radio broadcasts on the strong relationship between water stress and yield penalties. Messages highlight the role of the plough pan in keeping infiltration rates low and encouraging farmers to improve irrigation scheduling. Anecdotal evidence suggests that improved pump selection may decrease irrigation costs by up to 50%, and CSISA has initiated follow-up studies to develop recommendations for farmers.

Social interaction is necessary for purchasing fuel, transporting and installing pumps, or sharing irrigation equipment. These activities pose risks of COVID-19 exposure and transmission and therefore require farmers to follow increased safety and hygiene practices, which may cause further delays to irrigation. Raising awareness about the importance of timely irrigation therefore needs to go hand in hand with the promotion of safe and hygienic irrigation practices. This information has been streamlined into CSISA’s ongoing partnerships and FM broadcasts.

2. Improve community-level water markets through increased focus on drought preparedness and overcoming financial constraints

Farmers can save time by taking an anticipatory approach to the terms and conditions of rentals, instead of negotiating them when cracks in the soil are already large. Many farmers reported that pump owners are reluctant to rent out pumpsets if renters cannot pay up front. Given the seasonality of cash flows in agriculture, pro-poor and low interest credit provisions are likely to further smoothen community-level water markets.

Quantified ethnographic-decision tree based on households’ surveys of smallholder decision to use groundwater irrigation in Nepal’s Terai. (Graphic: Urfels et al. (2020))
Quantified ethnographic-decision tree based on households’ surveys of smallholder decision to use groundwater irrigation in Nepal’s Terai. (Graphic: Urfels et al., 2020)

3. Prioritize regional investment

The study shows that delay factors differ across districts and that selectively targeted interventions will be most useful to provide high returns to investments. For example, farmers in Kailali reported that land access issues — due to use of large bullock carts to transport pumpsets — and fuel shortages constitute a barrier for 10% and 39% of the farmers, while in Rupandehi, maintenance and tubewell availability were reported to be of greater importance.

As drought is increasingly threatening paddy production in Nepal’s Terai region, CSISA’s research shows that several support pathways exist to support farmers in combatting droughts. Sustainable water use can only be brought up to a scale where it benefits most farmers if all available tools including electrification, solar pumps and improved water level monitoring are deployed to provide benefits to a wide range of farmers.

Read the study:
Drivers of groundwater utilization in water-limited rice production systems in Nepal

Conservation agriculture key to better income, environment protection: Study

Resorting to conservation agriculture would not only increase crop yield, income and reduce the use of natural resources, but would also confer climate change benefits, according to a study by Indian agricultural scientists and others published in an international journal on Thursday.

The study, published in the journal Nature Sustainability, also showed that conservation agriculture was key to meeting many of the UN’s Sustainable Development Goals (SDGs) such as no poverty, zero hunger, good health and well-being, climate action and clean water. Conservation agriculture can offer positive contributions to several SDGs, said M. L. Jat, a Principal Scientist at the International Maize and Wheat Improvement Center (CIMMYT) and first author of the study.

Read more here: https://www.thehindubusinessline.com/economy/agri-business/conservation-agriculture-key-to-better-income-environment-protection-study/article31364196.ece#

Conservation agriculture key in meeting UN Sustainable Development Goals

During a conservation agriculture course, a young trainee operates a Happy Seeder mounted on a two-wheel tractor, for direct seeding of wheat in smallholder systems. (Photo: CIMMYT)
During a conservation agriculture course, a young trainee operates a Happy Seeder mounted on a two-wheel tractor, for direct seeding of wheat in smallholder systems. (Photo: CIMMYT)

An international team of scientists has provided a sweeping new analysis of the benefits of conservation agriculture for crop performance, water use efficiency, farmers’ incomes and climate action across a variety of cropping systems and environments in South Asia.

The analysis, published today in Nature Sustainability, is the first of its kind to synthesize existing studies on conservation agriculture in South Asia and allows policy makers to prioritize where and which cropping systems to deploy conservation agriculture techniques. The study uses data from over 9,500 site-year comparisons across South Asia.

According to M.L. Jat, a principal scientist at the International Maize and Wheat Improvement Center (CIMMYT) and first author of the study, conservation agriculture also offers positive contributions to the Sustainable Development Goals of no poverty, zero hunger, good health and wellbeing, climate action and clean water.

“Conservation agriculture is going to be key to meet the United Nations Sustainable Development Goals,” echoed JK Ladha, adjunct professor at the University of California, Davis, and co-author of the study.

Scientists from CIMMYT, the Indian Council of Agricultural Research (ICAR), the University of California, Davis, the International Rice Research Institute (IRRI) and Cornell University looked at a variety of agricultural, economic and environmental performance indicators — including crop yields, water use efficiency, economic return, greenhouse gas emissions and global warming potential — and compared how they correlated with conservation agriculture conditions in smallholder farms and field stations across South Asia.

A combine harvester equipped with the Super SMS (left) harvests rice while a tractor equipped with the Happy Seeder is used for direct seeding of wheat. (Photo: Sonalika Tractors)
A combine harvester equipped with the Super SMS (left) harvests rice while a tractor equipped with the Happy Seeder is used for direct seeding of wheat. (Photo: Sonalika Tractors)

Results and impact on policy

Researchers found that many conservation agriculture practices had significant benefits for agricultural, economic and environmental performance indicators, whether implemented separately or together. Zero tillage with residue retention, for example, had a mean yield advantage of around 6%, provided farmers almost 25% more income, and increased water use efficiency by about 13% compared to conventional agricultural practices. This combination of practices also was shown to cut global warming potential by up to 33%.

This comes as good news for national governments in South Asia, which have been actively promoting conservation agriculture to increase crop productivity while conserving natural resources. South Asian agriculture is known as a global “hotspot” for climate vulnerability.

“Smallholder farmers in South Asia will be impacted most by climate change and natural resource degradation,” said Trilochan Mohapatra, Director General of ICAR and Secretary of India’s Department of Agricultural Research and Education (DARE). “Protecting our natural resources for future generations while producing enough quality food to feed everyone is our top priority.”

“ICAR, in collaboration with CIMMYT and other stakeholders, has been working intensively over the past decades to develop and deploy conservation agriculture in India. The country has been very successful in addressing residue burning and air pollution issues using conservation agriculture principles,” he added.

With the region’s population expected to rise to 2.4 billion, demand for cereals is expected to grow by about 43% between 2010 and 2050. This presents a major challenge for food producers who need to produce more while minimizing greenhouse gas emissions and damage to the environment and other natural resources.

“The collaborative effort behind this study epitomizes how researchers, policy-makers, and development practitioners can and should work together to find solutions to the many challenges facing agricultural development, not only in South Asia but worldwide,” said Jon Hellin, leader of the Sustainable Impact Platform at IRRI.


Related publications:

Conservation agriculture for sustainable intensification in South Asia.

Interview opportunities:

M.L. Jat, Principal Scientist and Cropping Systems Agronomist, International Maize and Wheat Improvement Center (CIMMYT)

For more information, or to arrange interviews, contact:

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

Acknowledgements:

Funders of this work include the Indian Council of Agricultural Research (ICAR), the Government of India and the CGIAR Research Programs on Wheat Agri-Food Systems (CRP WHEAT) and Climate Change, Agriculture and Food Security (CCAFS).

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.

Crossing boundaries

Disclaimer: The views and opinions expressed in this article are those of the authors and do not necessarily reflect the official views or position of the International Maize and Wheat Improvement Center (CIMMYT).

Daily life as we know it has grinded to a halt and crop scientists are pondering next steps in face of the global COVID-19 crisis. Hans Braun, Director of the Global Wheat Program at the International Maize and Wheat Improvement Center (CIMMYT) and the CGIAR Research Program on Wheat, joins us for a virtual chat to discuss the need for increased investment in crop disease research as the world risks a food security crisis.

What have you learned from your work on contagious wheat diseases that we can take away during this time?

Wheat epidemics go back to biblical times. Wheat scientists now believe Egypt’s “seven bad years” of harvest referenced in the Bible were due to a stem rust outbreak.

So, we know what happens when we have a crop epidemic: diseases can completely wipe out a harvest. I have seen subsistence farmers stand in front of their swaying, golden wheat fields, but there is not a single grain inside the spikes. All because of wheat blast.

There are a lot of parallel issues that I see with COVID-19.

The epidemiology models for humans which we see now have a lot in common with plant epidemiology. For example, if you take a wheat field sown with a variety which is rust-resistant and then you get a spore which mutates and overcomes the resistance — like COVID-19 overcomes the human immune system — it then takes about two weeks for it to sporulate again and produce millions of these mutated spores. They sporulate once more and then you have billions and trillions of spores — then the wheat fields at the local, national and, in the worst case, regional level are severely damaged and in worst case are going to die.

The problem is that since we cannot quarantine wheat, if the weather is favorable these spores will fly everywhere and — just like with COVID-19 — they don’t need a passport to travel.

Could you elaborate on that? How can wheat diseases go global?

Usually it takes around 5 years, sometimes less, until a mutation in a rust spore can overcome the resistance of a wheat variety. Every so often, we see rust epidemics which cover an entire region. To monitor this movement, the Borlaug Global Rust Initiative of Cornell University and CIMMYT, funded by the Bill & Melinda Gates Foundation and DFID, established a global rust monitoring system that provides live data on spore movements.

For example, if you have a new race of stem rust in Yemen — and in Yemen wheat matures early — and then farmers burn the straw, their action “pushes” the spores up into the air, thus allowing them to enter the jet stream and cover 2,000 to 5,000 kilometers in a short period of time. Spores can also be carried on clothes or shoes by people who walked into an infected wheat field. Take Australia, for example, which has very strict quarantine laws. It is surrounded by sea and still eventually they get the new rust races which fly around or come with travelers. One just cannot prevent it.

Stem rust resistant (left) and susceptible (right) wheat plants at the stem rust phenotyping facility in Njoro, Nakuru County in Kenya. (Photo: Joshua Masinde/CIMMYT)
Stem rust resistant (left) and susceptible (right) wheat plants at the stem rust phenotyping facility in Njoro, Nakuru County in Kenya. (Photo: Joshua Masinde/CIMMYT)

Could climate change exacerbate the spreading of crop diseases?

Yes, the climate and its variability have a lot to do with it. For example, in the case of yellow rust, what’s extremely important is the time it takes from sporulation to sporulation. Take a rust spore. It germinates, then it grows, it multiplies and then once it is ready it will disperse and infect wheat plants. From one dispersal to the next it takes about two weeks.

In the last decades, in particular for yellow rust, new races are better adapted to high temperature and are multiplying faster. In a Nature paper, we showed that 30 years ago yellow rust was not present in the Great Plains in the US. Today, it is the most important wheat disease there. So there really is something going on and changing and that’s why we are so concerned about new wheat disease races when they come up.

What could an epidemiologist specialized in human viruses take from this?

Well, I think human epidemiologists know very well what happens in a case like COVID-19. Ordinary citizens now also start to understand what a pandemic is and what its related exponential growth means.

Maybe you should ask what policymakers can learn from COVID-19 in order to prevent plant epidemics. When it comes to epidemics, what applies to humans applies to plants. If there is a new race of a given crop disease, in that moment, the plant does not have a defense mechanism, like humans in the case of COVID-19, because we haven’t developed any immunity. While in developed countries farmers can use chemicals to control plant diseases, resource-poor farmers do not have this option, due to lack to access or if the plant protective has not been registered in their country.

In addition to this, our lines of work share a sense of urgency. If “doomsday” happens, it will be too late to react. At present, with a human pandemic, people are worried about the supply chain from food processing to the supermarket. But if we have an epidemic in plants, then we do not have the supply chain from the field to the food processing industry. And if people have nothing to eat, they will go to the streets and we will see violence. We simply cannot put this aside.

What other lessons can policymakers and other stakeholders take away from the current crisis?

The world needs to learn that we cannot use economics as the basis for disease research. We need to better foresee what could happen.

Let’s take the example of wheat blast, a devastating disease that can destroy the wheat spike and was initially confined to South America. The disease arrived in Bangladesh in 2016 and caused small economic damage, maybe 30,000 tons loss in a small geographic area — a small fraction of the national production but a disaster for the smallholder farmer, who thus would have lost her entire wheat harvest. The disease is now controlled with chemicals. But what if chemical resistance is developed and the disease spreads to the 10 million hectares in the Indo-Gangetic Plains of India and the south of Pakistan. Unlikely? But what if it happens?

Agriculture accounts for 30% of the global GDP and the research money [going to agriculture] in comparison to other areas is small. Globally only 5% of R&D is invested in research for development related to agriculture. Such a discrepancy! A million U.S. dollars invested in wheat blast research goes a long way and if you don’t do it, you risk a disaster.

If there is any flip side to the COVID-19 disaster, it is that hopefully our governments realize that they have to play a much more serious role in many areas, in particular public health and disease control in humans but also in plants.

A Lloyd’s report concluded that a global food crisis could be caused by governments taking isolating actions to protect their own countries in response to a breadbasket failure elsewhere. I’m concerned that as the COVID-19 crisis continues, governments will stop exports as some did during the 2008 food price crisis, and then, even if there is enough food around, the 2008 scenario might happen again and food prices will go through the roof, with disastrous impact on the lives of the poorest.

This article was originally published by the CGIAR Research Program on Wheat (WHEAT):
Crossing boundaries: looking at wheat diseases in times of the COVID-19 crisis.

Cover photo: Hans Braun, Director of the Global Wheat Program at the International Maize and Wheat Improvement Center (CIMMYT), inspects wheat plants in the greenhouses. (Photo: Alfonso Cortés/CIMMYT)

Agricultural solutions to tackle humanity’s climate crisis

More than 11,000 scientists signed on to a recent report showing that planet Earth is facing a climate emergency and the United Nations warned that the world is on course for a 3.2 degree spike by 2100, even if 2015 Paris Agreement commitments are met.

Agriculture, forestry, and land-use change are implicated in roughly a quarter of global greenhouse gas emissions.

Agriculture also offers opportunities to mitigate climate change and to help farmers — particularly smallholders in developing and emerging economies who have been hardest hit by hot weather and reduced, more erratic rainfall.

Most of CIMMYT’s work relates to climate change, helping farmers adapt to shocks while meeting the rising demand for food and, where possible, reducing emissions.

Family farmer Geofrey Kurgat (center) with his mother Elice Tole (left) and his nephew Ronny Kiprotich in their 1-acre field of Korongo wheat near Belbur, Nukuru, Kenya. (Photo: Peter Lowe/CIMMYT)
Family farmer Geofrey Kurgat (center) with his mother Elice Tole (left) and his nephew Ronny Kiprotich in their 1-acre field of Korongo wheat near Belbur, Nukuru, Kenya. (Photo: Peter Lowe/CIMMYT)

Climate-resilient crops and farming practices

53 million people are benefiting from drought-tolerant maize. Drought-tolerant maize varieties developed using conventional breeding provide at least 25% more grain than other varieties in dry conditions in sub-Saharan Africa — this represents as much as 1 ton per hectare more grain on average. These varieties are now grown on nearly 2.5 million hectares, benefiting an estimated 6 million households or 53 million people in the continent. One study shows that drought-tolerant maize can provide farming families in Zimbabwe an extra 9 months of food at no additional cost. The greatest productivity results when these varieties are used with reduced or zero tillage and keeping crop residues on the soil, as was demonstrated in southern Africa during the 2015-16 El Niño drought. Finally, tolerance in maize to high temperatures in combination with drought tolerance has a benefit at least twice that of either trait alone.

Wheat yields rise in difficult environments. Nearly two decades of data from 740 locations in more than 60 countries shows that CIMMYT breeding is pushing up wheat yields by almost 2% each year — that’s some 38 kilograms per hectare more annually over almost 20 years — under dry or otherwise challenging conditions. This is partly through use of drought-tolerant lines and crosses with wild grasses that boost wheat’s resilience. An international consortium is applying cutting-edge science to develop climate-resilient wheat. Three widely-adopted heat and drought-tolerant wheat lines from this work are helping farmers in Pakistan, a wheat powerhouse facing rising temperatures and drier conditions; the most popular was grown on an estimated 40,000 hectares in 2018.

Climate-smart soil and fertilizer management. Rice-wheat rotations are the predominant farming system on more than 13 million hectares in the Indo-Gangetic Plains of South Asia, providing food and livelihoods for hundreds of millions. If farmers in India alone fine-tuned crop fertilizer dosages using available technologies such as cellphones and photosynthesis sensors, each year they could produce nearly 14 million tons more grain, save 1.4 million tons of fertilizer, and cut CO2-equivalent greenhouse gas emissions by 5.3 million tons. Scientists have been studying and widely promoting such practices, as well as the use of direct seeding without tillage and keeping crop residues on the soil, farming methods that help capture and hold carbon and can save up to a ton of CO2 emissions per hectare, each crop cycle. Informed by CIMMYT researchers, India state officials seeking to reduce seasonal pollution in New Delhi and other cities have implemented policy measures to curb the burning of rice straw in northern India through widespread use of zero tillage.

Farmers going home for breakfast in Motoko district, Zimbabwe. (Photo: Peter Lowe/CIMMYT)
Farmers going home for breakfast in Motoko district, Zimbabwe. (Photo: Peter Lowe/CIMMYT)

Measuring climate change impacts and savings

In a landmark study involving CIMMYT wheat physiologists and underlining nutritional impacts of climate change, it was found that increased atmospheric CO2 reduces wheat grain protein content. Given wheat’s role as a key source of protein in the diets of millions of the poor, the results show the need for breeding and other measures to address this effect.

CIMMYT scientists are devising approaches to gauge organic carbon stocks in soils. The stored carbon improves soil resilience and fertility and reduces its emissions of greenhouse gases. Their research also provides the basis for a new global soil information system and to assess the effectiveness of resource-conserving crop management practices.

CIMMYT scientist Francisco Pinto operates a drone over wheat plots at CIMMYT's experimental station in Ciudad Obregon, Mexico. (Photo: Alfonso Cortés/CIMMYT)
CIMMYT scientist Francisco Pinto operates a drone over wheat plots at CIMMYT’s experimental station in Ciudad Obregon, Mexico. (Photo: Alfonso Cortés/CIMMYT)

Managing pests and diseases

Rising temperatures and shifting precipitation are causing the emergence and spread of deadly new crop diseases and insect pests. Research partners worldwide are helping farmers to gain an upper hand by monitoring and sharing information about pathogen and pest movements, by spreading control measures and fostering timely access to fungicides and pesticides, and by developing maize and wheat varieties that feature genetic resistance to these organisms.

Viruses and moth larvae assail maize. Rapid and coordinated action among public and private institutions across sub-Saharan Africa has averted a food security disaster by containing the spread of maize lethal necrosis, a viral disease which appeared in Kenya in 2011 and quickly moved to maize fields regionwide. Measures have included capacity development with seed companies, extension workers, and farmers the development of new disease-resilient maize hybrids.

The insect known as fall armyworm hit Africa in 2016, quickly ranged across nearly all the continent’s maize lands and is now spreading in Asia. Regional and international consortia are combating the pest with guidance on integrated pest management, organized trainings and videos to support smallholder farmers, and breeding maize varieties that can at least partly resist fall armyworm.

New fungal diseases threaten world wheat harvests. The Ug99 race of wheat stem rust emerged in eastern Africa in the late 1990s and spawned 13 new strains that eventually appeared in 13 countries of Africa and beyond. Adding to wheat’s adversity, a devastating malady from the Americas known as “wheat blast” suddenly appeared in Bangladesh in 2016, causing wheat crop losses as high as 30% on a large area and threatening to move quickly throughout South Asia’s vast wheat lands.

In both cases, quick international responses such as the Borlaug Global Rust Initiative, have been able to monitor and characterize the diseases and, especially, to develop and deploy resistant wheat varieties.

A community volunteer of an agricultural cooperative (left) uses the Plantix smartphone app to help a farmer diagnose pests in his maize field in Bardiya district, Nepal. (Photo: Bandana Pradhan/CIMMYT)
A community volunteer of an agricultural cooperative (left) uses the Plantix smartphone app to help a farmer diagnose pests in his maize field in Bardiya district, Nepal. (Photo: Bandana Pradhan/CIMMYT)

Partners and funders of CIMMYT’s climate research

A global leader in publicly-funded maize and wheat research and related farming systems, CIMMYT is a member of CGIAR and leads the South Asia Regional Program of the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS).

CIMMYT receives support for research relating to climate change from national governments, foundations, development banks and other public and private agencies. Top funders include CGIAR Research Programs and Platforms, the Bill & Melinda Gates Foundation, Mexico’s Secretary of Agriculture and Rural Development (SADER), the United States Agency for International Development (USAID), the UK Department for International Development (DFID), the Australian Centre for International Agricultural Research (ACIAR), Cornell University, the German aid agency GIZ, the UK Biotechnology and Biological Sciences Research Council (BBSRC), and CGIAR Trust Fund Contributors to Window 1 &2.

First steps taken to unify breeding software

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

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

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

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

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

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

Stacked software

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

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

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

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

A cross-institution DevOps culture

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

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

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

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

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

Scientists develop an early warning system that delivers wheat rust predictions directly to farmers’ phones

One of the researchers behind the study, Yoseph Alemayehu, carries out a field survey in Ethiopia by mobile phone. (Photo Dave Hodson/CIMMYT)
One of the researchers behind the study, Yoseph Alemayehu, carries out a field survey in Ethiopia by mobile phone. (Photo Dave Hodson/CIMMYT)

TEXCOCO, Mexico — Using field and mobile phone surveillance data together with forecasts for spore dispersal and environmental suitability for disease, an international team of scientists has developed an early warning system which can predict wheat rust diseases in Ethiopia. The cross-disciplinary project draws on expertise from biology, meteorology, agronomy, computer science and telecommunications.

Reported this week in Environmental Research Letters, the new early warning system, the first of its kind to be implemented in a developing country, will allow policy makers and farmers all over Ethiopia to gauge the current situation and forecast wheat rust up to a week in advance.

The system was developed by the University of Cambridge, the UK Met Office, the Ethiopian Institute of Agricultural Research (EIAR), the Ethiopian Agricultural Transformation Agency (ATA) and the International Maize and Wheat Improvement Center (CIMMYT). It works by taking near real-time information from wheat rust surveys carried out by EIAR, regional research centers and CIMMYT using a smartphone app called Open Data Kit (ODK).

This is complemented by crowd-sourced information from the ATA-managed Farmers’ Hotline. The University of Cambridge and the UK Met Office then provide automated 7-day advance forecast models for wheat rust spore dispersal and environmental suitability based on disease presence.

All of this information is fed into an early warning unit that receives updates automatically on a daily basis. An advisory report is sent out every week to development agents and national authorities. The information also gets passed on to researchers and farmers.

Example of weekly stripe rust spore deposition based on dispersal forecasts. Darker colors represent higher predicted number of spores deposited. (Graphic: University of Cambridge/UK Met Office)
Example of weekly stripe rust spore deposition based on dispersal forecasts. Darker colors represent higher predicted number of spores deposited. (Graphic: University of Cambridge/UK Met Office)

Timely alerts

“If there’s a high risk of wheat rust developing, farmers will get a targeted SMS text alert from the Farmers’ Hotline. This gives the farmer about three weeks to take action,” explained Dave Hodson, principal scientist with CIMMYT and co-author of the research study. The Farmers’ Hotline now has over four million registered farmers and extension agents, enabling rapid information dissemination throughout Ethiopia.

Ethiopia is the largest wheat producer in sub-Saharan Africa but the country still spends in excess of $600 million annually on wheat imports. More can be grown at home and the Ethiopian government has targeted to achieve wheat self-sufficiency by 2023.

“Rust diseases are a grave threat to wheat production in Ethiopia. The timely information from this new system will help us protect farmers’ yields, and reach our goal of wheat self-sufficiency,” said EIAR Director Mandefro Nigussie.

Wheat rusts are fungal diseases that can be dispersed by wind over long distances, quickly causing devastating epidemics which can dramatically reduce wheat yields. Just one outbreak in 2010 affected 30% of Ethiopia’s wheat growing area and reduced production by 15-20%.

The pathogens that cause rust diseases are continually evolving and changing over time, making them difficult to control. “New strains of wheat rust are appearing all the time — a bit like the flu virus,” explained Hodson.

In the absence of resistant varieties, one solution to wheat rust is to apply fungicide, but the Ethiopian government has limited supplies. The early warning system will help to prioritize areas at highest risk of the disease, so that the allocation of fungicides can be optimized.

Example of weekly stripe rust environmental suitability forecast. Yellow to Brown show the areas predicted to be most suitable for stripe rust infection. (Graphic: University of Cambridge/UK Met Office)
Example of weekly stripe rust environmental suitability forecast. Yellow to Brown show the areas predicted to be most suitable for stripe rust infection. (Graphic: University of Cambridge/UK Met Office)

The cream of the crop

The early warning system puts Ethiopia at the forefront of early warning systems for wheat rust. “Nowhere else in the world really has this type of system. It’s fantastic that Ethiopia is leading the way on this,” said Hodson. “It’s world-class science from the UK being applied to real-world problems.”

“This is an ideal example of how it is possible to integrate fundamental research in modelling from epidemiology and meteorology with field-based observation of disease to produce an early warning system for a major crop,” said Christopher Gilligan, head of the Epidemiology and Modelling Group at the University of Cambridge and a co-author of the paper, adding that the approach could be adopted in other countries and for other crops.

“The development of the early warning system was successful because of the great collaborative spirit between all the project partners,” said article co-author Clare Sader-Allen, currently a regional climate modeller at the British Antarctic Survey.

“Clear communication was vital for bringing together the expertise from a diversity of subjects to deliver a common goal: to produce a wheat rust forecast relevant for both policy makers and farmers alike.”


RELATED PUBLICATIONS:

An early warning system to predict and mitigate wheat rust diseases in Ethiopia
https://doi.org/10.1088/1748-9326/ab4034

INTERVIEW OPPORTUNITIES:

Dave Hodson, Senior Scientist, International Maize and Wheat Improvement Center (CIMMYT)

FOR MORE INFORMATION, OR TO ARRANGE INTERVIEWS, CONTACT:

Marcia MacNeil, Communications Officer, CIMMYT. m.macneil@cgiar.org, +52 (55) 5804 2004 ext. 2070.

Rodrigo Ordóñez, Communications Manager, CIMMYT. r.ordonez@cgiar.org, +52 (55) 5804 2004 ext. 1167.

ACKNOWLEDGEMENTS:

This study was made possible through the support provided by the BBSRC GCRF Foundation Awards for Global Agriculture and Food Systems Research, which brings top class UK science to developing countries, the Delivering Genetic Gains in Wheat (DGGW) Project managed by Cornell University and funded by the Bill & Melinda Gates Foundation and the UK Department for International Development (DFID). The Government of Ethiopia also provided direct support into the early warning system. This research is supported by CGIAR Fund Donors.

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.

ABOUT THE ETHIOPIAN INSTITUTE OF AGRICULTURAL RESEARCH (EIAR):

The Ethiopian Institute of Agricultural Research (EIAR) is one of the oldest and largest agricultural research institutes in Africa, with roots in the Ethiopian Agricultural Research System (EARS), founded in the late 1940s. EIAR’s objectives are: (1) to generate, develop and adapt agricultural technologies that focus on the needs of the overall agricultural development and its beneficiaries; (2) to coordinate technically the research activities of Ethiopian Agricultural Research System; (3) build up a research capacity and establish a system that will make agricultural research efficient, effective and based on development needs; and (4) popularize agricultural research results. EIAR’s vision is to see improved livelihood of all Ethiopians engaged in agriculture, agro-pastoralism and pastoralism through market competitive agricultural technologies.

The man who fed the world

Norman Borlaug was awarded the Nobel Peace Prize in 1970 in recognition of his contributions to world peace through increasing food production. In the latest episode of the BBC radio show Witness History, Rebecca Kesby interviews Ronnie Coffman, student and friend of Norman Borlaug.

Among other stories, Coffman recalls the moment when Borlaug was notified about the Nobel Prize — while working in the wheat fields in Mexico — and explores what motivated Borlaug to bring the Green Revolution to India.

Spurt in stubble burning in Pakistan raises heat in Punjab

The Punjab government is working on war footing to curb farm fires ahead of the celebrations of 550 birth anniversary of Guru Nanak, but rising incidents of stubble burning in Pakistan, particularly near border areas of Punjab, have raised concern among scientists at Punjab remote sensing center (PRSC) and Punjab agricultural university (PAU).

Experts from Cornell and International Maize and Wheat Improvement Center (CIMMYT) in a recent study ‘Tradeoffs Between Groundwater Conservation and Air Pollution From Agricultural Fires in Northwest India’ stated that pollution, particularly caused by stubble burning, leads to an estimated 16,000 premature deaths caused every year in New Delhi capital region, with an aggregate reduction in life expectancy of 6 years.

Read more here.

Microsatellite data can help double impact of agricultural interventions

A young man uses a precision spreader to distribute fertilizer in a field. (Photo: Mahesh Maske/CIMMYT)
A young man uses a precision spreader to distribute fertilizer in a field. (Photo: Mahesh Maske/CIMMYT)

Data from microsatellites can be used to detect and double the impact of sustainable interventions in agriculture at large scales, according to a new study led by the University of Michigan (U-M).

By being able to detect the impact and target interventions to locations where they will lead to the greatest increase of yield gains, satellite data can help increase food production in a low-cost and sustainable way.

According to the team of researchers from U-M, the International Maize and Wheat Improvement Center (CIMMYT), and Stanford and Cornell universities, finding low-cost ways to increase food production is critical, given that feeding a growing population and increasing the yields of crops in a changing climate are some of the greatest challenges of the coming decades.

“Being able to use microsatellite data, to precisely target an intervention to the fields that would benefit the most at large scales will help us increase the efficacy of agricultural interventions,” said lead author Meha Jain, assistant professor at the U-M School for Environment and Sustainability.

Microsatellites are small, inexpensive, low-orbiting satellites that typically weigh 100 kilograms or less.

“About 60-70% of total world food production comes from smallholders, and they have the largest field-level yield gaps,” said Balwinder Singh, senior researcher at the International Maize and Wheat Improvement Center (CIMMYT).

To show that the low-cost microsatellite imagery can quantify and enhance yield gains, the researchers conducted their study in smallholder wheat fields in the Eastern Indo-Gangetic Plains in India.

They ran an experiment on 127 farms using a split-plot design over multiple years. In one half of the field, the farmers applied nitrogen fertilizer using hand broadcasting, the typical fertilizer spreading method in this region. In the other half of the field, the farmers applied fertilizer using a new and low-cost fertilizer spreader.

To measure the impact of the intervention, the researchers then collected the crop-cut measures of yield, where the crop is harvested and weighed in field, often considered the gold standard for measuring crop yields. They also mapped field and regional yields using microsatellite and Landsat satellite data.

They found that without any increase in input, the spreader resulted in 4.5% yield gain across all fields, sites and years, closing about one-third of the existing yield gap. They also found that if they used microsatellite data to target the lowest yielding fields, they were able to double yield gains for the same intervention cost and effort.

“Being able to bring solutions to the farmers that will benefit most from them can greatly increase uptake and impact,” said David Lobell, professor of earth system science at Stanford University. “Too often, we’ve relied on blanket recommendations that only make sense for a small fraction of farmers. Hopefully, this study will generate more interest and investment in matching farmers to technologies that best suit their needs.”

The study also shows that the average profit from the gains was more than the amount of the spreader and 100% of the farmers were willing to pay for the technology again.

Jain said that many researchers are working on finding ways to close yield gaps and increase the production of low-yielding regions.

“A tool like satellite data that is scalable and low-cost and can be applied across regions to map and increase yields of crops at large scale,” she said.

Read the full study:
The impact of agricultural interventions can be doubled by using satellite data

The study is published in the October issue of Nature Sustainability. Other researchers include Amit Srivastava and Shishpal Poonia of the International Maize and Wheat Improvement Center in New Delhi; Preeti Rao and Jennifer Blesh of the U-M School of Environment and Sustainability; Andrew McDonald of Cornell; and George Azzari and David Lobell of Stanford. 


For more information, or to arrange interviews, please contact CIMMYT’s media team.

Scientist Bekele Abeyo details research in Africa with BBC

CIMMYT’s representative in Ethiopia, Bekele Abeyo, gives an interview for Ethiopian media. (Photo: Jérôme Bossuet/CIMMYT)
CIMMYT’s representative in Ethiopia, Bekele Abeyo, gives an interview for Ethiopian media. (Photo: Jérôme Bossuet/CIMMYT)

Most African countries have good potential for boosting wheat production if they are supported with technology, innovation and research, said Bekele Abeyo, a senior scientist with the International Maize and Wheat Improvement Center (CIMMYT).

Abeyo, who is based in Ethiopia, which is one of the top wheat-producing countries in Africa, was speaking to BBC Newsday from the International Wheat Congress in the city of Saskatoon in Canada’s western wheat growing province of Saskatchewan.

Interview starts at 31:00:
https://www.bbc.co.uk/sounds/play/w172wpkb45wc459

In Ethiopia, a third of local demand is satisfied by imports, Abeyo said, adding that to reduce import bills, the government is trying to expand wheat production and irrigation in the lowlands where there is high potential for wheat production.

Climate change in Ethiopia and across sub-Saharan Africa is affecting yields, so scientists are working on producing drought-tolerant varieties of wheat. They are also producing biofortified varieties of wheat to help meet nutritional demand for zinc and iron.

More than 800 delegates, including researchers from the CGIAR Research Program on Wheat, CIMMYT, the International Center for Agricultural Research in the Dry Areas (ICARDA), the International Wheat Yield Partnership (IWYP), Cornell University’s Delivering Genetic Gain in Wheat project (DGGW), the University of Saskatchewan and many other organizations are discussing the latest research on wheat germplasm.

The CGIAR Research Program on Wheat (WHEAT), led by the International Maize and Wheat Improvement Center (CIMMYT), is a founding member of the G20 Wheat Initiative, a co-host of the conference.

Wheat provides 20% of all human calories consumed worldwide. In the Global South, it is the main source of protein and a critical source of life for 2.5 billion people who live on less than $2 a day. Wheat is central to conversations about the rural environment, agricultural biodiversity and global food security.