Microsatellite data can help double impact of agricultural interventions

Study of smallholder wheat farmers in India shows data from small satellites can quantify and enhance yield gains

This story by Mandira Banerjee was originally posted in the University of Michigan Newsroom.

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 or 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 (220 pounds) 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 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.

Collecting the crop-cut measures of yield. Photo courtesy of: CIMMYT
Collecting the crop-cut measures of yield. Photo: CIMMYT

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.

Women applying fertilizer via traditional method. Photo courtesy of: CIMMYT
Women applying fertilizer via traditional method. Photo: CIMMYT

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. 

A fresh look at the genes behind grain weight in spring bread wheat

New study provides an extensive field-test validation of existing genetic markers for thousand grain weight; finds both surprises and promising results

To meet the demand for wheat from a rising and quickly urbanizing population, wheat yields in farmers’ fields must increase by an estimated 1.5% each year through 2030. 

Of all the factors that influence yield, grain weight is the trait that is most stable and heritable for use in breeding improved wheat varieties.  Breeders measure this by thousand grain weight (TGW).

Over the years, molecular scientists have made efforts to identify genes related to increased TGW, in order to speed up breeding through marker-assisted selection (MAS). Using MAS, breeders can select parents that contain genes related to the traits they are looking for, increasing the likelihood they will be passed on and incorporated in a new variety. 

Guillermo Garcia Barrios, a co-author of the study and student at Colegio de Postgraduados in Montecillo, Mexico with a PHERAstar machine used to validate genetic markers.
Photo: Marcia MacNeil/CIMMYT

There have been some limited successes in these efforts: in the past years, a few genes related to increased TGW have been cloned, and a set of genetic markers have been determined to be used for MAS. However, the effects of most of these candidate genes (CGs) have not yet been validated in diverse sets of wheat germplasm throughout the world that represent the full range of global wheat growing environments.

A group of wheat geneticists and molecular breeders from the International Maize and Wheat Improvement Center (CIMMYT) has recently conducted a thorough study to confirm the effects of the favorable alleles reported for these genes on TGW in CIMMYT wheat,   — and to identify new genetic determinants of this desired trait.

They found some good news and some bad.

First, the good news:  focusing on more than 4000 lines of CIMMYT wheat germplasm they found 15 haplotype blocks significantly associated with TGW.  Four haplotype blocks associated with TGW were also associated with grain yield – a grand prize for breeders, because in general the positive association of grain yield with TGW is less profound and sometimes even negative. However, of the 14 genes that had been previously reported to increase TGW, only one in CIMMYT’s 2015-2016 Elite Yield Trial and two in Wheat Associative Mapping Initiative panel were shown to have significant TGW associations.

The scientists also found that the alleles — pairs of genes on a chromosome that determine heredity – that were supposedly favorable to TGW actually decreased it.   These candidate genes also appear to vary in their TGW effects with genetic background and/or environment.

Thus, these findings also provide a foundation for more detailed investigations, opening the door for more studies on the genetic background dependence and environment sensitivity of the known candidate genes for TGW. 

Thousand Gain Weight is measured in this machine at CIMMYT’s administrative headquarters at El Batan, Mexico.
Photo: Marcia MacNeil/CIMMYT

 “Our findings indicate that it will be challenging to use MAS based on these existing markers across individual breeding programs,” said Deepmala Sehgal, CIMMYT wheat geneticist and the primary author of the study.

However, efforts to identify new genetic determinants of TGW were promising.  The authors’ study of CIMMYT germplasm found one locus on chromosome 6A that showed increases of up to 2.60 grams in TGW and up to 258 kilograms per hectare in grain yield.

This discovery expands opportunities for developing diagnostic markers to assist in multi-gene pyramiding – a process that can derive new and complementary allele combinations for enhanced wheat TGW and grain yield.

Most of all, the study highlights the strong need for better and more validation of the genes related to this and other traits, so that breeders can be sure they are using material that is confirmed to increase wheat grain weight and genetic yield.

“Our findings are very promising for future efforts to efficiently develop more productive wheat in both grain weight and grain yield,” said Sehgal. “This ultimately means more bread on household tables throughout the world.”

 “Validation of Candidate Gene-Based Markers and Identification of Novel Loci for Thousand-Grain Weight in Spring Bread Wheat” in Frontiers in Plant Science by Deepmala Sehgal, Suchismita Mondal, Carlos Guzman, Guillermo Garcia Barrios, Carolina Franco, Ravi Singh and Susanne Dreisigacker was supported by funding from the CGIAR Research Program on Wheat (WHEAT), the Delivering Genetic Gain in Wheat (DGGW) project funded by the Bill & Melinda Gates Foundation and the UK Department for International Development (DFID), and the US Agency for International Development (USAID) Feed the Future Innovation Lab for Applied Wheat Genomics.

Read the full article here: https://doi.org/10.3389/fpls.2019.01189


Wheat grains prepared for placement in TGW machine. Photo: Marcia MacNeil/CIMMYT

Borlaug Fellowship highlights longterm Washington State University-CIMMYT collaboration

The Norman Borlaug International Agricultural Science and Technology Fellowship Program at Washington State University, sponsored by the U.S. Department of Agriculture, facilitates international collaboration to fight soil borne pathogens

Cereal cyst nematodes

Soil borne pathogens (SBPs) are microorganisms that thrive in the soil and attack cereal crops, notably wheat. They cause high yield losses and reduce grain quality and quantity. SBPs include nematodes, a kind of round worm — including the Heterodera species of cereal cyst nematode and Pratylenchus species of root lesion nematodes — and crown rot caused by the Fusarium species, all of which attack roots of cereal crops.  Drought and monoculture farming exacerbate this damage.

Although chemical, biological and other options can be used to keep pathogen population levels low, the most environmentally friendly and biologically effective method of control is through a resistant crop variety.  However, up to now, only a few resistance genes have been identified against the cereal cyst nematode, Heterodera filipjevi, and this resistance is not yet present in high yielding cultivars.  

For nearly 20 years, research to fight these pathogens has benefited from a productive collaboration between the International Maize and Wheat Improvement Program (CIMMYT) in Turkey and Washington State University (WSU) and the U.S. Department of Agriculture’s Agricultural Research Service (USDA-ARS) in the United States through a fellowship program named after CIMMYT founder and Green Revolution pioneer Norman Borlaug. CIMMYT wheat breeders in Turkey have been working with breeders in Pullman, Washington to find stronger resistance genes to cereal cyst nematodes identify pathotypes, and other research areas that strengthen both CIMMYT and WSU wheat breeding programs.

CIMMYT pathologist and Turkey Country Representative Abdelfattah Dababat has been working with WSU and USDA-ARS since 2010. Dababat, who joined CIMMYT as a postdoctoral student studying soil borne pathogens (SBPs) in 2009, recently spent two months in Pullman as a Norman Borlaug International Agricultural Science and Technology Fellow, sponsored by the U.S. Department of Agriculture’s Agricultural Research Service (USDA-ARS). There he was able to share CIMMYT work with members of the WSU Department of Plant Pathology, USDA-ARS, exchange ideas with well-known pathologists, and even travel to Cleveland, Ohio to attend the meeting of the American Phytopathological Society.

“My experience at WSU has been productive and inspiring.” said Dababat. “I have learned from some of the best minds in plant pathology, and worked on SBP issues that plague farmers both in my region and theirs.

“I would like to thank CIMMYT, especially Dr. Hans Braun, for the opportunity to obtain this great fellowship visit to WSU.”

The CIMMYT-WSU relationship was strengthened when the two institutions collaborated on a proposal for an Ethiopian PhD student at the University of Ankara, Turkey to work on SBPs. Through the sponsorship of a Borlaug Leadership Enhancement in Agriculture Program (LEAP) scholarship, Elfinesh Shikur Gebremariam spent four months at WSU in 2013-14 to learn about molecular aspects related to crown rot diseases. She published three peer-reviewed papers in high impact factor journals.

From left to right: Abdelfattah Dababat, Timothy Paulitz and WSU wheat breeding postdoctoral student Nuan Wen during a survey for cereal cyst nematodes in Pullman, Washington

Timothy Paulitz, a research plant pathologist with USDA-ARS and an adjunct professor in WSU’s Department of Plant Pathology has also been an active member in this collaboration, contributing to two master classes on soil borne pathogens in cereals at CIMMYT’s Turkey research station.

“Dr. Paulitz has made tremendous impact in our region,” said Dababat. “He trained more than 50 young scientists who are now in a high scientific and or managerial positions and are contributing not only to their own food security but also to international food security.”

SBP resistance progress and challenges

CIMMYT screens hundreds of wheat germplasm lines each year against SBPs at its research station in Eskisehir, Turkey, in collaboration with the Grain Research Development Corporation of Australia. Using association mapping, CIMMYT researchers have been able to identify new sources of resistance to cereal cyst nematodes, and many new lines have been approved as moderately resistant to resistant compared known varieties.  As a result, hundreds of lines of winter and spring wheat germplasm moderately resistant to SBPs are available.

Cereal cyst nematodes (CCN) are a persistent problem, however. Among the most damaging nematode pests to small grain cereal production, CCN are common from the Middle East, North Africa and Central Asia to the Pacific Northwest of the U.S. These nematodes alone are estimated to reduce production of crops by 10% globally.  Breeding for resistance is difficult because breeders must use live nematodes to phenotype, or measure, the lines, and there are few molecular markers linked to the resistance genes against the major CCN species to help identify them.

However, CIMMYT research — involving targeted genetic exploitations, classical selection breeding of resistant genotypes discovery of quantitative trait loci (QTLs) associated with resistance genes, as well as recent genome-wide association studies (GWAS) to associate nematode resistance or susceptibility with particular regions of the genome — has seen some success. One important source for disease-resistance genes is found in wheat’s wild relatives.  So far, 11 resistance genes have been reported. Nine of these were transferred into common wheat from its wild relatives (like Aegilops or goat grass, and other Triticum species) to enhance resistance against the H. avenae species of nematode.

Dababat and Wen in the lab while extracting DNA from wheat lines at the WSU laboratories.

Recently, CIMMYT and the University of Bonn, Germany performed GWAS on 161 winter wheat accessions and identified 11 QTL associated with resistance against the H. filipjevi species of nematode. These QTLs were intercrossed into susceptible winter wheat germplasm and the first generation material (F1) along with the parents were sent to WSU as part of the Borlaug fellowship.  CIMMYT and WSU also conducted several surveys in countries including Azerbaijan and Kazakhstan to detect SBPs in cereals.

This joint research will help both institutes to find stronger resistance genes to the cereal cyst nematodes.

The Washington State-based part of Dababat’s Borlaug fellowship is drawing to a close, but the collaboration and relationship between the two institutions remains. In June of next year, Paulitz will visit him in Turkey to follow up on his research progress.

“The international collaboration between CIMMYT and WSU shows how much progress we can make when we work together,” said Dababat. “I look forwarding to continuing our partnership to help farmers around the world find resistance to SBPs.”

Large-scale genomics will improve the yield, climate-resilience, and quality of bread wheat, new study shows

Scientists identified significant new chromosomal regions for wheat yield and disease resistance, which will speed up global breeding efforts.

This story by Mike Listman was originally posted on CIMMYT.org

Bread wheat improvement using genomic tools will be critical to accelerate genetic gains in the crop's yield, disease resistance, and climate resilience. (Photo: Apollo Habtamu/CIMMYT)
Bread wheat improvement using genomic tools will be critical to accelerate genetic gains in the crop’s yield, disease resistance, and climate resilience. (Photo: Apollo Habtamu/CIMMYT)

Using the full wheat genome map published in 2018, combined with data from field testing of wheat breeding lines in multiple countries, an international team of scientists has identified significant new chromosomal regions for wheat yield and disease resistance and created a freely-available collection of genetic information and markers for more than 40,000 wheat lines.

Reported today in Nature Genetics, the results will speed up global efforts to breed more productive and climate-resilient varieties of bread wheat, a critical crop for world food security that is under threat from rising temperatures, rapidly-evolving fungal pathogens, and more frequent droughts, according to Philomin Juliana, wheat scientist at the International Maize and Wheat Improvement Center (CIMMYT) and first author of the new study.

“This work directly connects the wheat genome reference map with wheat lines and extensive field data from CIMMYT’s global wheat breeding network,” said Juliana. “That network in turn links to over 200 breeding programs and research centers worldwide and contributes to yield and other key traits in varieties sown on nearly half the world’s wheat lands.”

The staple food for more than 2.5 billion people, wheat provides 20% of human dietary calories and protein worldwide and is critical for the nutrition and food security of hundreds of millions of poor persons in regions such as North Africa and South Asia.

“Farmers and societies today face new challenges to feed rising and rapidly-urbanizing populations, and wheat epitomizes the issues,” said Ravi Singh, CIMMYT wheat breeder and corresponding author of the study. “Higher temperatures are holding back yields in major wheat-growing areas, extreme weather events are common, crop diseases are spreading and becoming more virulent, and soil and water are being depleted.”

Juliana said the study results help pave the way to apply genomic selection, an approach that has transformed dairy cow husbandry, for more efficient wheat breeding.

“Molecular markers are getting cheaper to use; meanwhile, it’s very costly to do field testing and selection involving many thousands of wheat plants over successive generations,” Juliana said. “Genome-wide marker-based selection can help breeders to precisely identify good lines in early breeding generations and to test plantlets in greenhouses, thereby complementing and streamlining field testing.”

The new study found that genomic selection could be particularly effective in breeding for wheat end-use quality and for resistance to stem rust disease, whose causal pathogen has been evolving and spreading in the form of highly-virulent new races.

The new study also documents the effectiveness of the global public breeding efforts by CIMMYT and partners, showing that improved wheat varieties from this work have accumulated multiple gene variants that favor higher yields, according to Hans-Joachim Braun, director of CIMMYT’s global wheat program.

“This international collaboration, which is the world’s largest publicly-funded wheat breeding program, benefits farmers worldwide and offers high-quality wheat lines that are released directly to farmers in countries, such as Afghanistan, that are unable to run a full-fledged wheat breeding program,” Braun explained.

The study results are expected to support future gene discovery, molecular breeding, and gene editing in wheat, Braun said.

Together with more resource-efficient cropping systems, high-yielding and climate-resilient wheat varieties will constitute a key component of the sustainable intensification of food production described in Strategy 3 of the recent EAT-Lancet Commission recommendations to transform the global food system. Large-scale genomics will play a key role in developing these varieties and staying ahead of climate- and disease-related threats to food security.

Funders of this work include USAID’s Feed the Future Innovation Lab for Applied Wheat Genomics. Contributing to the research described are research teams engaged in wheat improvement at CIMMYT, and the lab of Jesse Poland, Associate Professor at Kansas State University and Director of the USAID Applied Wheat Genomics Innovation Lab.

Smallholder farmers’ multi-front strategy combats rapidly evolving wheat rust in Ethiopia

Researchers found farmers who increased both the area growing resistant varieties and the number of wheat varieties grown per season saw the biggest yield increases.

This story by  Simret Yasabu was originally posted on CIMMYT.org.

New research shows that smallholder farmers in Ethiopia used various coping mechanisms apart from fungicides in response to the recent wheat rust epidemics in the country. Scientists from the International Maize and Wheat Improvement Center (CIMMYT) and the Ethiopian Institute of Agricultural Research (EIAR) call for continuous support to research and extension programs to develop and disseminate improved wheat varieties with resistant traits to old and newly emerging rust races.

Rising wheat yields cannot catch up rising demand

Wheat is the fourth largest food crop in Ethiopia cultivated by smallholders, after teff, maize and sorghum. Ethiopia is the largest wheat producer in sub-Saharan Africa and average farm yields have more than doubled in the past two decades, reaching 2.74 tons per hectare on average in 2017/18. Farmers who use improved wheat varieties together with recommended agronomic practices recorded 4 to 6 tons per hectare in high-potential wheat growing areas such as the Arsi and Bale zones. Yet the country remains a net importer because demand for wheat is rapidly rising.

The Ethiopian government has targeted wheat self-sufficiency by 2023 and the country has huge production potential due to its various favorable agroecologies for wheat production.

However, one major challenge to boosting wheat production and yields is farmers’ vulnerability to rapidly evolving wheat diseases like wheat rusts.

The Ethiopian highlands have long been known as hot spots for stem and yellow wheat rusts caused by the fungus Puccinia spp., which can spread easily under favorable climatic conditions. Such threats may grow with a changing climate.

Ethiopian wheat planting. (Photo: CIMMYT)

Recurrent outbreaks of the two rusts destroyed significant areas of popular wheat varieties. In 2010, a yellow rust epidemic severely affected the popular Kubsa variety. In 2013/14, farmers in the Arsi and Bale zones saw a new stem rust race destroy entire fields of the bread wheat Digalu variety.

In response to the 2010 yellow rust outbreak, the government and non-government organizations, seed enterprises and other development supporters increased the supply of yellow rust resistant varieties like Kakaba and Danda’a.

Fungicide is not the only solution for wheat smallholder farmers

Two household panel surveys during the 2009/10 main cropping season, before the yellow rust epidemic, and during the 2013/14 cropping season analyzed farmers’ exposure to wheat rusts and their coping mechanisms. From the survey, 44% of the wheat farming families reported yellow rust in their fields during the 2010/11 epidemic.

Household data analysis looked at the correlation between household characteristics, their coping strategies against wheat rust and farm yields. The study revealed there was a 29 to 41% yield advantage by increasing wheat area of the new, resistant varieties even under normal seasons with minimum rust occurrence in the field. Continuous varietal development in responding to emerging new rust races and supporting the deployment of newly released rust resistant varieties could help smallholders cope against the disease and maintain improved yields in the rust prone environments of Ethiopia.

The case study showed that apart from using fungicides, increasing wheat area under yellow rust resistant varieties, increasing diversity of wheat varieties grown, or a combination of these strategies were the main coping mechanisms farmers had taken to prevent new rust damages. Large-scale replacement of highly susceptible varieties by new rust resistant varieties was observed after the 2010/11 epidemic.

The most significant wheat grain yield increases were observed for farmers who increased both area under resistant varieties and number of wheat varieties grown per season.

The additional yield gain thanks to the large-scale adoption of yellow rust resistant varieties observed after the 2010/11 epidemic makes a very strong case to further strengthen wheat research and extension investments, so that more Ethiopian farmers have access to improved wheat varieties resistant to old and newly emerging rust races.

Read the full study on PLOS ONE:
https://doi.org/10.1371/journal.pone.0219327

Meet Lucia Nevescanin Moreno, first PhD recipient of the HeDWIC fellowship

The International Maize and Wheat Improvement Center (CIMMYT’s) own Lucia Nevescanin Moreno is the first recipient of a new scholarship sponsored by the Heat and Drought Wheat Improvement Consortium (HeDWIC) for its doctoral training program.

The HeDWIC Doctoral Training Program evolved out of the MasAgro-Trigo project, thanks to funding from the Mexican Secretariat of Agriculture and Rural Development (SADER) and National Council for Science and Technology (Consejo Nacional de Ciencia y Tecnología, CONACYT). The idea of the initiative is to provide young scientists from climate or food security vulnerable regions with opportunities to conduct research at advanced institutes internationally, to boost heat and drought tolerance of wheat in their home country. The program is expected to expand to other climate vulnerable regions through similar efforts to train talented young scientists who wish to be involved in improving the climate resilience of crops.

Lucia, who is currently working as an assistant research associate with CIMMYT, will be pursuing a PhD on wheat root function under abiotic stress under the supervision of University of Nottingham professor of Plant Sciences Malcom Bennett starting in October.

We asked Lucia a few questions about her research and the importance of heat and drought resilience.

How did you hear about CIMMYT?

A professor from my master’s program told me about it. I was doing a master’s in Natural Resources in the Instituto Tecnologico de Sonora, working specifically on tropical dry forest in Northwest Mexico but I always wanted to do science in a more applied way. I wanted to work on something that could help other people. Food security is something that people need to pay a lot of attention to. I started working for CIMMYT in February 2018 as an assistant research associate in the Global Wheat Program, conducting experiments in different conditions and I really learned a lot and am still learning a lot.

How did you hear about HeDWIC?

I was working with [CIMMYT Remote Sensing Specialist] Francisco Pinto on wheat root research here at CIMMYT and he asked me if I wanted to continue with my studies. I told him that I wanted to do a PhD and he showed me this opportunity with HeDWIC and the University of Nottingham. So I applied and I got it. Actually, I was very surprised to learn that I am the first PhD recipient of the HeDWIC scholarship. It’s a lot of pressure!

What will you be working on?

I will be studying wheat root function under abiotic stress under the supervision of Malcom Bennett at the University of Nottingham. I will be doing field-based phenotyping at Yaqui Valley in Mexico to determine what root characteristics are underlying plant performance under a range of environments including heat stress and water stress conditions. I will be using techniques like x-ray and laser ablation tomography in controlled conditions at the University of Nottingham to measure the physiology and anatomy of the wheat roots. I will also be working with Francisco Pinto and Matthew Reynolds from CIMMYT, Darren Wells and Craig Sturrock from the University of Nottingham and Jonathan Lynch from Penn State University.

Why do you think a consortium like HeDWIC is important for food security?

With climate change occurring at such a rapid pace, we really need to adapt to these new conditions. The population is also growing and so the demand for food needs serious attention. In HeDWIC they are working with external conditions like drought and heat and they are looking at how crops can adapt to these conditions. I think that just looking at how to increase yield is not enough, we need to look at how the crop will respond in the different environmental conditions we will go through.

What advice would you give to young women interested in a career in science?

I think it’s more difficult for women to adapt to this environment of work but we just need to be brave and show that we can do it! I was really interested in working in science because I wanted to know how things work and why. Maybe with my research and with research in general we can help people in power to make important decisions that can help other people. I think that should be the principle purpose of science.

Lucia’s PhD is supported by the CONACYT-Government of Mexico, SADER’s MasAgro Trigo and the University of Nottingham.

Bottlenecks between basic and applied plant science jeopardize life-saving crop improvements

International collaboration and a visionary approach by both researchers and funders are urgently needed to translate primary plant research results into real impact in the fields, argue crop improvement experts.

Visitors at the CIMMYT’s experimental station in Obregon, Mexico, where elite wheat lines are tested for new traits.

For a number of reasons – including limited interdisciplinary collaboration and a dearth of funding, revolutionary new plant research findings are not being used to improve crops.

 “Translational research” — efforts to convert basic research knowledge about plants into practical applications in crop improvement – represents a necessary link between the world of fundamental discovery and farmers’ fields.  This kind of research is often seen as more complicated and time consuming than basic research and less sexy than working at the “cutting edge” where research is typically divorced from agricultural realities in order to achieve faster and cleaner results; however, modern tools — such as genomics, marker-assisted breeding, high throughput phenotyping of crop traits using drones, and speed breeding techniques – are making it both faster and cost-effective.

In a new article in Crop Breeding, Genetics, and Genomics, wheat physiologist Matthew Reynolds of the International Maize and Wheat Improvement Center (CIMMYT) and co-authors make the case for increasing not only funding for translational research, but the underlying prerequisites: international and interdisciplinary collaboration towards focused objectives and a visionary approach by funding organizations. 

“It’s ironic,” said Reynolds. “Many breeding programs have invested in the exact technologies — such as phenomics, genomics and informatics — that can be powerful tools for translational research to make real improvements in yield and adaptation to climate, disease and pest stresses.  But funding to integrate these tools in front-line breeding is quite scarce, so they aren’t reaching their potential value for crop improvement.” 

Many research findings are tested for their implications for wheat improvement by the International Wheat Yield Partnership (IWYP) at the IWYP Hub — a centralized technical platform for evaluating innovations and building them into elite wheat varieties, co-managed by CIMMYT at its experimental station in Obregon, Mexico.

IWYP has its roots with the CGIAR Research Program on Wheat (WHEAT), which in 2010 formalized the need to boost both wheat yield potential as well as its adaptation to heat and drought stress. The network specializes in translational research, harnessing scientific findings from around the world to boost genetic gains in wheat, and capitalizing on the research and pre-breeding outputs of WHEAT and the testing networks of the International Wheat Improvement Network (IWIN). These efforts also led to the establishment of the Heat and Drought Wheat Improvement Consortium (HeDWIC).

Members of the International Wheat Yield Partnership which focuses on translational research to boost wheat yields.

“We’ve made extraordinary advances in understanding the genetic basis of important traits,“ said IWYP’s Richard Flavell, a co-author of the article.  “But if they aren’t translated into crop production, their societal value is lost.”

 The authors — all of whom have proven track records in both science and practical crop improvement — offer examples where exactly this combination of factors led to the impactful application of innovative research findings.

  • Improving the Vitamin A content of maize: A variety of maize with high Vitamin A content has the potential to reduce a deficiency that can cause blindness and a compromised immune system. This development happened as a result of many translational research efforts, including marker-assisted selection for a favorable allele, using DNA extracted from seed of numerous segregating breeding crosses prior to planting, and even findings from gerbil, piglet and chicken models  — as well as long-term, community-based, placebo-controlled trials with children — that helped establish that Vitamin A maize is bioavailable and bioefficacious.
  • Flood-tolerant rice: Weather variability due to climate change effects is predicted to include both droughts and floods. Developing rice varieties that can withstand submergence in water due to flooding is an important outcome of translational research which has resulted in important gains for rice agriculture.  In this case, the genetic trait for flood tolerance was recognized, but it took a long time to incorporate the trait into elite germplasm breeding programs. In fact, the development of flooding tolerant rice based on a specific SUB 1A allele took over 50 years at the International Rice Research Institute in the Philippines (1960–2010), together with expert molecular analyses by others. The translation program to achieve efficient incorporation into elite high yielding cultivars also required detailed research using molecular marker technologies that were not available at the time when trait introgression started.

Other successes include new approaches for improving the yield potential of spring wheat and the discovery of traits that increase the climate resilience of maize and sorghum. 

One way researchers apply academic research to field impact is through phenotyping. Involving the use of cutting edge technologies and tools to measure detailed and hard to recognize plant traits, this area of research has undergone a revolution in the past decade, thanks to more affordable digital measuring tools such as cameras and sensors and more powerful and accessible computing power and accessibility.

An Australian Pine on CIMMYT’s El Batan Experimental Station commemorates the 4th Symposium of the International Plant Phenotyping Network.

Scientists are now able to identify at a detailed scale plant traits that show how efficiently a plant is using the sun’s radiation for growth, how deep its roots are growing to collect water, and more — helping breeders select the best lines to cross and develop.

Phenotyping is key to understanding the physiological and genetic bases of plant growth and adaptation and has wide application in crop improvement programs.  Recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases allows scientists to collect information about traits such as plant development, architecture, plant photosynthesis, growth or biomass productivity from hundreds to thousands of plants in a single day. This revolution was the subject of discussion at a 2016 gathering of more than 200 participants at the International Plant Phenotyping Symposium hosted by CIMMYT in Mexico and documented in a special issue of Plant Science.

There is currently an explosion in plant science. Scientists have uncovered the genetic basis of many traits, identified genetic markers to track them and developed ways to measure them in breeding programs. But most of these new findings and ideas have yet to be tested and used in breeding programs – wasting their potentially enormous societal value.

Establishing systems for generating and testing new hypotheses in agriculturally relevant systems must become a priority, Reynolds states in the article. However, for success, this will require interdisciplinary, and often international, collaboration to enable established breeding programs to retool.  Most importantly, scientists and funding organizations alike must factor in the long-term benefits as well as the risks of not taking timely action. Translating a research finding into an improved crop that can save lives takes time and commitment. With these two prerequisites, basic plant research can and should positively impact food security.

Authors would like to acknowledge the following funding organizations for their commitment to translational research.

The International Wheat Yield Partnership (IWYP) is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) in the UK; the U. S. Agency for International Development (USAID) in the USA; and the Syngenta Foundation for Sustainable Agriculture (SFSA) in Switzerland.

The Heat and Drought Wheat Improvement Consortium (HeDWIC) is supported by the Sustainable Modernization of Traditional Agriculture (MasAgro) Project by the Ministry of Agriculture and Rural Development (SADER) of the Government of Mexico; previous projects that underpinned HeDWIC were supported by Australia’s Grains Research and Development Corporation (GRDC).

The Queensland Government’s Department of Agriculture and Fisheries in collaboration with The Grains Research and Development Corporation (GRDC) have provided long-term investment for the public sector sorghum pre-breeding program in Australia, including research on the stay-green trait. More recently, this translational research has been led by the Queensland Alliance for Agriculture and Food Innovation (QAAFI) within The University of Queensland.

ASI validation work and ASI translation and extension components with support from the United Nations Development Programme (UNDP) and the Bill and Melinda Gates Foundation, respectively.

Financial support for the maize proVA work was partially provided by HarvestPlus (www.HarvestPlus.org), a global alliance of agriculture and nutrition research institutions working to increase the micronutrient density of staple food crops through biofortification. The CGIAR Research Program MAIZE (CRP-MAIZE) also supported this research.

The CGIAR Research Program on Wheat (WHEAT) is led by the International Maize and Wheat Improvement Center (CIMMYT), with the International Center for Agricultural Research in the Dry Areas (ICARDA) as a primary research partner. Funding comes from CGIAR, national governments, foundations, development banks and other agencies, including the Australian Centre for International Agricultural Research (ACIAR),  the UK Department for International Development (DFID) and the United States Agency for International Development (USAID).

Scientists use DNA fingerprinting to gauge the spread of modern wheat in Afghanistan

New study finds that wheat farmers often do not accurately identify their varieties.

Wheat is Afghanistan’s number-one staple crop, but the country does not grow enough and must import millions of tons of grain each year to satisfy domestic demand.

Despite the severe social and political unrest that constrain agriculture in Afghanistan, many farmers are growing high-yielding, disease resistant varieties developed through international, science-based breeding and made available to farmers as part of partnerships with national wheat experts and seed producers.

These and other findings have emerged from the first-ever large-scale use of DNA fingerprinting to assess Afghanistan farmers’ adoption of improved wheat varieties, which are replacing less productive local varieties and landraces, according to a paper published yesterday in the science journal BMC Genomics.

The study is part of an activity supported between 2003 and 2018 by the Australian Department of Foreign Affairs and Trade, through which the Agricultural Research Institute of Afghanistan and the International Maize and Wheat Improvement Center (CIMMYT) introduced, tested, and released improved wheat varieties.

“As part of our study, we established a ‘reference library’ of released varieties, elite breeding lines, and Afghan wheat landraces, confirming the genetic diversity of the landraces and their value as a genetic resource,” said Susanne Dreisigacker, wheat molecular breeder at CIMMYT and lead author of the new paper.

“We then compared wheat collected on farmers’ fields with the reference library. Of the 560 wheat samples collected in 4 provinces during 2015-16, farmers misidentified more than 40%, saying they were of a different variety from that which our DNA analyses later identified.”

Wheat is the most important staple crop in Afghanistan — more than 20 million of the country’s rural inhabitants depend on it — but wheat production is unstable and Afghanistan has been importing between 2 and 3 million tons of grain each year to meet demand.

Over half of the population lives below the poverty line, with high rates of malnutrition. A key development aim in Afghanistan is to foster improved agronomic practices and the use of high quality seed of improved wheat varieties, which together can raise yields by over 50%.

“Fungal diseases, particularly yellow rust and stem rust, pose grave threats to wheat in the country,” said Eric Huttner, research program manager for crops at the Australian Centre for International Agricultural Research (ACIAR) and co-author of the present paper. “It’s crucial to know which wheat varieties are being grown where, in order to replace the susceptible ones with high-performing, disease resistant varieties.”

Varietal adoption studies typically rely on questionnaires completed by breeders, extension services, seed producers, seed suppliers, and farmers, but such surveys are complicated, expensive, and often inaccurate.

“DNA fingerprinting resolves uncertainties regarding adoption and improves related socioeconomic research and farm policies,” Huttner explained, adding that for plant breeding this technology has been used mostly to protect intellectual property, such as registered breeding lines and varieties in more developed economies.

This new study was commissioned by ACIAR as a response to a request from the Government of Afghanistan for assistance in characterizing the Afghan wheat gene bank, according to Huttner.

“This provided the reference library against which farmers’ samples could be compared,” he explained. “Accurately identifying the varieties that farmers grow is key evidence on the impact of introducing improved varieties and will shape our future research

Joint research and development efforts involving CIMMYT, ACIAR, the Food and Agriculture Organization (FAO) of the United Nations, the International Centre of Agricultural Research in Dry Areas (ICARDA), French Cooperation, and Afghanistan’s Ministry of Agriculture, Irrigation and Livestock (MAIL) and Agricultural Research Institute (ARIA) have introduced more than 400 modern, disease-resistant wheat varieties over the last two decades. Nearly 75% of the wheat grown in the areas surveyed for this study comes from these improved varieties.

“New gene sequencing technologies are increasingly affordable and their cost will continue to fall,” said Dreisigacker. “Expanded use of DNA fingerprinting can easily and accurately identify the wheat cultivars in farmers’ fields, thus helping to target breeding, agronomy, and development efforts for better food security and farmer livelihoods.”


For more information, or to arrange interviews with the researchers, please contact:

Marcia MacNeil, Wheat 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

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 CGIAR 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.

About ACIAR
As Australia’s specialist international agricultural research for development agency, the Australian Centre for International Agricultural Research (ACIAR) brokers and funds research partnerships between Australian scientists and their counterparts in developing countries. Since 1982, ACIAR has supported research projects in eastern and southern Africa, East Asia, South and West Asia and the Pacific, focusing on crops, agribusiness, horticulture, forestry, livestock, fisheries, water and climate, social sciences, and soil and land management. ACIAR has commissioned and managed more than 1,500 research projects in 36 countries, partnering with 150 institutions along with more than 50 Australian research organizations.

About Afghanistan’s Ministry of Agriculture, Irrigation and Livestock
The Ministry of Agriculture, Irrigation and Livestock (MAIL) of the Islamic Republic of Afghanistan works on the development and modernization of agriculture, livestock and horticulture. The ministry launches programs to support the farmers, manage natural resources, and strengthen agricultural economics. Its programs include the promotion and introduction of higher-value economic crops, strengthening traditional products, identifying and publishing farm-tailored land technologies, boosting cooperative programs, agricultural economics, and export with marketing.

Alternatives to burning can increase Indian farmers’ profits and cut pollution, new study shows

Published in Science, the article provides evidence for national policies that block stubble burning and promote no-till mechanization to manage crop residues.

This story by Mike Listman was originally posted on the website of the International Maize and Wheat Improvement Center (CIMMYT).

India’s farmers feed millions of people. (Photo: Dakshinamurthy Vedachalam)

The new study compares the costs and benefits of 10 distinct land preparation and sowing practices for northern India’s rice-wheat cropping rotations, which are spread across more than 4 million hectares. The direct seeding of wheat into unplowed soil and shredded rice residues was the best option — it raises farmers’ profits through higher yields and savings in labor, fuel, and machinery costs.

The study, conducted by a global team of eminent agriculture and environmental scientists, was led by researchers from The Nature Conservancy, the International Maize and Wheat Improvement Center (CIMMYT), the Indian Council of Agricultural Research (ICAR), the Borlaug Institute for South Asia (BISA) and the University of Minnesota.

A new economic study in the journal Science shows that thousands of farmers in northern India could increase their profits if they stop burning their rice straw and adopt no-till practices to grow wheat. Alternative farming practices could also cut farmers’ greenhouse gas emissions from on-farm activities by as much as 78% and help lower air pollution in cities like New Delhi.

A burning issue

To quickly and cheaply clear their fields to sow wheat each year, farmers in northern India burn an estimated 23 million tons of straw from their rice harvests. That enormous mass of straw, if packed into 20-kilogram 38-centimeter-high bales and piled on top of each other, would reach a height of over 430,000 kilometers — about 1.1 times the distance to the moon.

Regulations are in place in India to reduce agricultural fires but burning continues because of implementation challenges and lack of clarity about the profitability of alternate, no-burn farming.

Farmers have alternatives, the study shows. To sow wheat directly without plowing or burning rice straw, farmers need to purchase or rent a tractor-mounted implement known as the “Happy Seeder,” as well as attach straw shredders to their rice harvesters. Leaving straw on the soil as a mulch helps capture and retain moisture and also improves soil quality, according to M.L. Jat, CIMMYT Principal Scientist, cropping systems specialist and a co-author of the study.

A combine harvester (left) equipped with the Super Straw Management System, or Super SMS, works alongside a tractor fitted with a Happy Seeder. (Photo: Sonalika Tractors)

Win-win

The Science study demonstrates that it is possible to reduce air pollution and greenhouse gas emissions in a way that is profitable to farmers and scalable.

The paper shows that Happy Seeder-based systems are on average 10%–20% more profitable than straw burning options.

“Our study dovetails with 2018 policies put in place by the government of India to stop farmers from burning, which includes a US$166 million subsidy to promote mechanization to manage crop residues within fields,” said Priya Shyamsundar, Lead Economist, Global Science, of The Nature Conservancy and first author of the study.

Shyamsundar noted that relatively few Indian farmers currently sow their wheat using the Happy Seeder but manufacturing of the Seeder had increased in recent years. “Less than a quarter of the total subsidy would pay for widespread adoption of the Happy Seeder, if aided by government and NGO support to build farmer awareness and impede burning.”

“With a rising population of 1.6 billion people, South Asia hosts 40% of the world’s poor and malnourished on just 2.4% of its land,” said Jat, who recently received India’s prestigious Rafi Ahmed Kidwai Award for outstanding and impact-oriented research contributions in natural resource management and agricultural engineering. “Better practices can help farmers adapt to warmer winters and extreme, erratic weather events such as droughts and floods, which are having a terrible impact on agriculture and livelihoods. In addition, India’s efforts to transition to more sustainable, less polluting farming practices can provide lessons for other countries facing similar risks and challenges.”

In November 2017, more than 4,000 schools closed in Delhi due to seasonal smog. This smog increases during October and November when fields are burned. It causes major transportation disruptions and poses health risks across northern India, including Delhi, a city of more than 18 million people.

Some of these problems can be resolved by the use of direct sowing technologies in northwestern India.

“Within one year of our dedicated action using about US$75 million under the Central Sector Scheme on ‘Promotion of agriculture mechanization for in-situ management of crop residue in the states of Punjab, Haryana, Uttar Pradesh and NCT of Delhi,’ we could reach 0.8 million hectares of adoption of Happy Seeder/zero tillage technology in the northwestern states of India,” said Trilochan Mohapatra, director general of the Indian Council of Agricultural Research (ICAR). “Considering the findings of the Science article as well as reports from thousands of participatory validation trials, our efforts have resulted in an additional direct farmer benefit of US$131 million, compared to a burning option,” explained Mohapatra, who is also secretary of India’s Department of Agricultural Research and Education.

Read the full study in Science

This research was supported by the Susan and Craig McCaw Foundation, the Institute on the Environment at the University of Minnesota, the CGIAR Research Program on Wheat (WHEAT), and the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS). The Happy Seeder was originally developed through a project from the Australian Centre for International Agricultural Research (ACIAR).

For more information, or to arrange interviews with the researchers, please contact:

Rodrigo Ordóñez, Communications Manager, CIMMYT
r.ordonez@cgiar.org, +52 5558042004 ext. 1167


Cranking, a thing of the past

In Bangladesh, a newly available device takes the hassle out of starting the engine of two-wheel tractors, particularly for women entrepreneurs.

This post was originally published on cimmyt.org on July 10, 2019 by M. Shahidul Haque Khan and Sultana Jahan.

Halima Begum wanted to increase her income by providing mechanization services to other farmers in Bangladesh’s Chuadanga district, but she was limited by the level of physical effort required. Starting the engine of her tractor was difficult and embarrassing — cranking it required a lot of strength and she had to rely on others to do it for her. She was also afraid she would get injured, like other local service providers.

Women in rural areas of Bangladesh are often hesitant to work in the fields. Social norms, limited mobility, physical exertion, lack of time and other constraints can cause aspiring female entrepreneurs to step back, despite the prospect of higher income. The few women like Halima who do step out of their comfort zone and follow their dreams often have to overcome the physical effort required to operate these machines.

Starting the tractor is a daunting task on its own and the possibility of having to do it multiple times a day adds to the reluctance of ownership.

To make manual cranking a thing of the past for Bangladeshi women entrepreneurs, and to encourage others, the International Maize and Wheat Improvement Center (CIMMYT), through the Cereal Systems Initiative for South Asia-Mechanization and Irrigation (CSISA-MI), is supporting small businesses who manufacture and sell affordable mechanical self-starter attachments for two-wheel tractors.

The self-starter is a simple spring-loaded device mounted over the old crank handle socket, which allows users to start the engine with the flick of a lever.

Halima Begum operates her two-wheel tractor, equipped with a self-starter device. (Photo: Mostafa Kamrul Hasan/CIMMYT)

For women like Begum, manually starting a tractor was a difficult task that is now gone forever.

“I used to struggle quite a lot before, but now I can easily start the machine, thanks to this highly convenient self-starter,” Begum said.

The self-starter reduces the risk of accidents and coaxes hesitant youth and women to become entrepreneurs in the agricultural mechanization service industry.

CIMMYT is supporting businesses like Janata Engineering, which imports self-starter devices and markets them among local service providers in the district of Sorojgonj, Chuadanga district. The project team worked with the owner, Md. Ole Ullah, to organize field demonstrations for local service providers, showing how to use and maintain the self-starter device.

The Cereal Systems Initiative for South Asia-Mechanization and Irrigation (CSISA-MI) is led by the International Maize and Wheat Improvement Center (CIMMYT) and funded by the United States Agency for International Development (USAID). The project focuses on upstream market interventions in Bangladesh, ensuring technologies are reliably available in local markets and supported by an extensive value chain.