In crop research fields, drones and other high-tech sensing tools are now a common sight. They collect high-resolution data on a wide range of traits — from simple measurement of canopy temperature to complex 3D reconstruction of photosynthetic canopies.
This technological approach to collecting precise plant trait information, known as phenotyping, is becoming ubiquitous. According to experts at the International Maize and Wheat Improvement Center (CIMMYT) and other research institutions, breeders can profit much more from these tools, when used judiciously.
Examples of different classes and applications of breeder friendly phenotyping. (Image: M. Reynolds et al.)
In a new article in the journal Plant Science, CIMMYT Wheat Physiologist Matthew Reynolds and colleagues explain the different ways that phenotyping can assist breeding — from simple to use, “handy” approaches for large scale screening, to detailed physiological characterization of key traits to identify new parental sources — and why this methodology is crucial for crop improvement. The authors make the case for breeders to invest in phenotyping, particularly in light of the imperative to breed crops for warmer and harsher climates.
Members of the Enterprise Breeding System advisory committee listen to a presentation from Tom Hagen. (Photo: Alfonso Cortés/CIMMYT)
Members of the Enterprise Breeding System (EBS) advisory committee met on January 17-18, 2019, to review progress on the development of a full-spectrum breeding data management software.
CGIAR plant breeders currently rely on a suite of different software projects to make use of the data that is crucial to developing better varieties. Developed under the CGIAR Excellence in Breeding Platform (EiB), the EBS aims to provide a single solution that links data across new and existing applications so that the entire breeding data workflow — from experiment creation to analytics — can be accessed from a single user-friendly dashboard.
Development of the system is well underway, with the goal of providing a “minimum viable implementation” to pilot users at the International Maize and Wheat Improvement Center (CIMMYT) and the International Rice Research Institute (IRRI) in 2020. More advanced functions, institutions and crops will be added to the EBS over the next three years.
Working between breeders and developers to ensure needs are translated into software functions, the EBS team has trained CIMMYT staff and consultants as requirements analysts, five of whom presented to members of the EBS advisory committee the meeting on progress in the five “domains” of breeding software functions.
Sharing bits and bytes
Rosemary Shresthra introduced experiment creation, where users can quickly select the type of experiment they wish to run and automatically set up all the steps needed to complete it in the EBS.
Kate Dreher took the attendees through field implementation, where it is possible to map fields in the system and connect them to a range of plot data collection tools developed by external projects.
Ricardo León outlined the germplasm management component of the system, where the seed inventory is kept, and new entries made after trials are harvested to go on to the next stage.
Pedro Medeiros explained how an analytics request manager will allow EBS users to push their data to different analytics tools that support decision-making and, ultimately, their ability to deliver better varieties that meet farmers’ needs.
Finally, Star Gao, a breeding informatics specialist for the Genomic and Open-Source Breeding Informatics Initiative (GOBii), showed how users will be able to request phytosanitary, genotypic and quality analysis of samples from their trials through the EBS system. The system will provide an overview of the status of all samples submitted for analysis with different service providers, in addition to the ability to connect with various databases.
“We can do all this because all information in the EBS is treated the same way, from experiment creation through implementation,” said EBS coordinator Tom Hagen in summary.
The EBS advisory group, which includes user representatives from CIMMYT and IRRI breeding teams alongside EiB staff, ended the day by discussing and prioritizing new functions that could be added to the EBS over the next three years.
An international team of scientists is working with farmers in the Yaqui Valley, in Mexico’s Sonora state, to develop and test a new mobile technology that aims to improve wheat and sugarcane productivity by helping farmers manage factors that cause the yield gap between crop potential and actual field performance.
Scientists have been developing and testing a smartphone app where farmers can record their farming activities — including sowing date, crop type and irrigation — and receive local, precise crop management advice in return.
This project is a private-public partnership known as Mexican COMPASS, or Mexican Crop Observation, Management & Production Analysis Services System.
Research has shown that proper timing of irrigation is more important to yields than total water amounts. Earlier planting times have also been shown to improve wheat yields. Having optimum dates for both activities could help farmers improve yields and stabilize their incomes.
The COMPASS smartphone app uses earth observation satellite data and in-situ field data captured by farmers to provide information such as optimum sowing date and irrigation scheduling.
“Sowing and irrigation timing are well known drivers of yield potential in that region — these are two features of the app we’re about to validate during this next season,” explained Francelino Rodrigues, Precision Agriculture Scientist at the International Maize and Wheat Improvement Center (CIMMYT).
Sound data
Technological innovation for crop productivity is needed now more than ever with threats to food security increasing and natural resources becoming scarcer. Farmers are under increasing pressure to produce more with less, which means greater precision is needed in their agricultural practices.
The Yaqui Valley, Mexico’s biggest wheat producing area, is located in the semi-arid Sonoran Desert in the northern part of Mexico. Water security is a serious challenge and farmers must be very precise in their irrigation management.
The Mexican COMPASS consortium, which is made up of the geospatial data analytics company Rezatec, the University of Nottingham, Booker Tate, CIMMYT and the Colegio de Postgraduados (COLPOS) in Mexico, evolved as a way to help Mexican farmers improve their water use efficiency.
“Yaqui Valley farmers are very experienced farmers, however they can also benefit by using an app that is designed locally to inform and record their decisions,” Rodrigues explained.
The smartphone app will also allow farmers to record and schedule their crop management practices and will give them access to weekly time-series Normalized Difference Vegetation Index (NDVI) maps, that will allow farmers to view their fields at any time from any location.
“All of this information is provided for free! That’s the exciting part of the project. The business model was designed so that farmers will not need to pay for access to the app and its features, in exchange for providing their crop field data. It’s a win-win situation,” said Rodrigues.
CIMMYT research assistant Lorena Gonzalez (center) helps local farmers try out the new COMPASS app during the workshop in Ciudad Obregon, Sonora state, Mexico. (Photo: Alison Doody/CIMMYT)
Farmer-centered design
The app is now in the validation stage and COMPASS partners are inviting farmers to test the technology on their own farms. A workshop on October 21 in Ciudad Obregon provided farmers with hands-on training for the app and allowed them to give their feedback.
Over 100 farmers attended the workshop, which featured presentations from Saravana Gurusamy, project manager at Rezatec, Iván Ortíz-Monasterio, principal scientist at CIMMYT, and representatives from local farmer groups Asociación de Organismos de Agricultores del Sur de Sonora (AOASS) and Distrito de Riego del Río Yaqui (DRRYAQUI). The workshop featured a step-by-step demonstration of the app and practical exercises for farmers to test it out for themselves.
“We need technology nowadays because we have to deal with many factors. The profit we get for wheat is getting smaller and smaller each year, so we have to be very productive. I hope that this app can help me to produce a better crop,” said one local wheat farmer who attended the workshop.
User feedback has played a key role in the development of the app. COMPASS interviewed dozens of farmers to see what design worked for them.
“Initially we came up with a really complicated design. However, when we gave it to farmers, they didn’t know how to use it,” explained Rezatec project manager, Saravana Gurusamy. The team went back to the drawing board and with the feedback they received from farmers, came up with a simple design that any farmer, regardless of their experience with technology or digital literacy, could use.
A farmer who attended the workshop talks about his experience and the potential benefits of the app. See full video on YouTube.
Sitting down with Gurusamy after the workshop, he outlined his vision for the future of the app.
“My vision is to see all the farmers in Sonora, working in wheat using the app. The first step is to prove the technology here, then roll it out to all of Mexico and eventually internationally.”
Mexican COMPASS is a four year project funded by the UK Space Agency’s International Partnership Programme (IPP-UKSA) and the CGIAR Research Program on Wheat (WHEAT). It is a collaboration between Rezatec, the University of Nottingham and Booker Tatein the UK,and the International Maize and Wheat Improvement Center (CIMMYT) and the Colegio de Postgraduados (COLPOS) in Mexico.
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)
“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.
Researchers visit maize fields in Ethiopia’s Wondo Genet Agricultural Research Center. (Photo: Peter Lowe/CIMMYT)
One major reason why maize productivity in sub-Saharan Africa is very low is poor soil health. Soil acidity is often mentioned because of its impact on crop yields and the extent of acid soils in the region. A recent soil mapping exercise, conducted by the Ethiopian Soil Information System (EthioSIS) under the administration of the Ethiopian Agricultural Transformation Agency (ATA), estimated that 43% of arable lands were affected by acid soils and that 3.6 million people, about 10% of the total rural population, live in areas with acidic soils.
Very acid soils — those with a pH below 5.5, roughly one hundred times more acidic than neutral soils — are associated with certain toxicities, like aluminum and iron excess, and some nutrient deficiencies. Soil acidity pushes soil nutrients out of reach of the plant, leading to stunting of root system and plant. As a result, the plant becomes also less tolerant to drought.
Soil acidification depends on soil nature, agroecology and farming systems. It happens through natural leaching of CO2 after rainfall and excess application of nitrogenous fertilizer or organic matter, for instance.
As a result, soil acidity significantly affects maize yields. In Ethiopia, studies have revealed substantial impacts on crop productivity related to acid soils and the importance of acid soil management for Ethiopia’s food security. The Ethiopian Institute of Agricultural Research (EIAR) estimated that soil acidity on wheat production alone costed the country over 9 billion Ethiopian Birr, about $300 million per year.
Acidic soils in the limelight
Preliminary analysis led by the International Food Policy Research Institute (IFPRI) suggests that yields of major cereal crops, such as wheat and barley, could increase by 20 to 40% with the application of lime in acidic areas of the country.
While these preliminary results are significant, we need to know more about local farmers’ experience with acidic soil and their mitigation strategies. Such impact assessments are however typically determined at either the national or experimental plot level and do not map where mitigating against acid soils would be the most profitable.
To improve acid soils, farmers may apply lime on their fields to raise the pH, a practice known as liming. How much lime to apply will depend on the crop, soil type but also on the quality of lime available. Liming has multiple beneficial effects like improving nitrogen fixation of legume nodules, boosting yields of legume crops.
But liming has a cost. It can quickly become a very bulky affair as we need to apply 3 to 4 tons per hectare for sandy soils and up to 8 tons per hectare for clay and humifere soils.
Furthermore, existing lime markets are quite limited or even non-existent in many areas, even those where acidic soils are prevalent. Developing supply chains from scratch is difficult and costly. Understanding the costs and potential returns to such investments is important. There are many questions to ask at different levels, from the farm and farming system to the lime supply chain. What are the available lime sources — calcitic, dolomite or blend — and lime quality? Where are the lime processing units and how could you assess the transport cost to the farms? What could be the crop yield response depending on the lime application?
User-friendly and scalable dashboard
IFPRI, in collaboration with EIAR, the International Maize and Wheat Improvement Center (CIMMYT) and the German aid agency GIZ, developed a pilot in Ethiopia’s Amhara region to help better target lime interventions for a greater impact. Amhara region was chosen because of the importance of acid soils, and access to extensive soil data.
Combination of several spatial datasets on soil quality, agroecological, weather, long-term agronomic trials and crop modelling tools enabled to generate at scale, georeferenced estimates of crop yield responses for different lime applications. Calibration of this spatial model for wheat estimated a yield increase of approximately 30% increasing the pH from 5.5 to 6.5, which is relatively consistent with general research data and expert opinion.
Mapped estimates of the grain prices and the delivered costs of lime, based on the location of the lime crushers in the region and transport costs, enables then to map out the spatial profitability of lime operations.
Initial calculations revealed a great variability of lime costs at the farmgate, with transportation representing at least half of total lime costs. It showed also that farmers often do not use the most cost-effective combination of inputs to tackle soil acidity.
Another possible application is to determine maize growing areas where lime benefits outweigh the costs, which would be ideal sites for demonstrating to farmers the positive impact lime applications could have to their livelihoods.
This Amhara lime dashboard prototype demonstrated its scalability. A national dashboard is currently being developed, which includes lime sources GPS location, grain prices and district-level soil quality mapping. This approach is tested also in Tanzania.
CIMMYT and its partners plan to package such tool in a user-friendly open-access web version that can be rapidly updated and customized depending on the area of intervention, for instance integrating a new lime source, and applied for different crops, and across the Eastern African region. Such dashboards will help development organizations and government make better informed decisions regarding lime investments.
Surveyors in Mexico collect data from farmers. (Photo: CIMMYT)
CIMMYT’s projects in Latin America feature in a new report that aims to help countries use data to design public policies and projects that help achieve the Sustainable Development Goals (SDGs) by 2030.
The Counting on The World to Act report was released on September 23, 2019, by the Sustainable Development Solutions Network (SDSN) and the Thematic Research Network on Data and Statistics (TReNDS) during the 74th session of the United Nations General Assembly (UNGA 74) in New York City.
The report describes CIMMYT’s data management systems and tools as examples of “frontier technologies” for data gathering, management and analysis that effectively contribute to sustainable farming in Colombia, Guatemala and Mexico.
“As part of the data revolution, efficiencies are being derived from lower-tech approaches such as using citizen-generated data and smartphones to speed up existing survey-based approaches,” reads the introduction to CIMMYT’s sidebar story in Chapter 4, Incentives for Innovation.
The MasAgro Electronic Log that field technicians use to monitor crop cycles and management practices, and the AgroTutor application that offers farmers more specific and timely recommendations are some of the new affordable tools for data management that CIMMYT is successfully implementing in Latin America.
At the African Green Revolution Forum 2019, global and African leaders come together to develop actionable plans that will move African agriculture forward. This year, the forum is taking place in Ghana on the week of September 3, 2019, under the theme “Grow digital: Leveraging digital transformation to drive sustainable food systems in Africa.” Participants will explore the practical application of the emerging elements of the digital era such as big data, blockchain, digital IDs, drones, machine learning, robotics, and sensors.
CIMMYT’s work in this area is showcased in a new leaflet entitled “Data-driven solutions for Africa: Using smart tools to combat climate change.” The leaflet highlights innovations such as crowdsourced crop disease tracking and response systems in Ethiopia, low-cost imaging tools to speed up the development of hardier varieties, and combining geospatial data with crop models to predict climate change and deliver personalized recommendations to farmers.
A new publication highlights the diverse ways in which CIMMYT’s research is propelling the digital transformation of agriculture in Africa.
Speaking at the conference attended by 2,000 delegates and high-level dignitaries, CIMMYT Director General Martin Kropff will give the keynote remarks during the session “Digital innovations to strengthen resilience for smallholders in African food systems” on September 3. This panel discussion will focus on how the data revolution can support African smallholder farmers to adapt quickly challenges like recurrent droughts or emerging pests, including the invasive fall armyworm. The Global Resilience Partnership (GRP), the Food and Agriculture Organization of the United Nations (FAO), CABI, and the Minister of Agriculture of Burkina Faso will be among the other panelists in the session.
The same day, CIMMYT will also participate to an important “Agronomy at scale through data for good” panel discussion with speakers from the Bill & Melinda Gates Foundation, research organizations and private companies. The session will highlight how digital agriculture could help deliver better targeted, site-specific agronomic advice to small farmers.
During the forum, the CIMMYT delegation will seek collaborations in other important drivers of change like gender transformation of food systems and smallholder mechanization.
They will join public sector leaders, researchers, agri-preneurs, business leaders and farmers in outlining how to leverage the growth in digital technologies to transform food systems and agricultural livelihoods in Africa.
“Knowing which strain you have is critical information that can be incorporated into early warning systems and results in more effective control of disease outbreaks in farmer’s fields” said Dr. Dave Hodson, a rust pathologist at CIMMYT in Ethiopia and co-author of the paper “MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens.” Read more here.
MARPLE (Mobile and Real-time PLant disEase) Diagnostics is a revolutionary mobile lab developed by a team from the John Innes Centre (JIC), the International Maize and Wheat Improvement Center (CIMMYT) and the Ethiopian Institute of Agricultural Research (EIAR). It uses nanopore sequence technology to rapidly diagnose and monitor wheat rust in farmers’ fields.
Designed to be used without constant electricity and in varying temperatures, the suitcase-sized lab allows researchers to identify wheat rust to strain level in just 48 hours — something that used to take months using other tools.
The MARPLE team was recognized as Innovator of the Year for international impact in 2019 by the UK Biotechnology and Biological Sciences Research Council (BBSRC).
A new video from the John Innes Centre shows how the MARPLE Diagnostics kit will allow Ethiopia to quickly identify wheat rust strains, instead of sending samples to labs abroad.
Profitability under different fertilization recommendation scenarios in Ethiopia and Tanzania, measured in U.S. dollars per hectare.
What fertilizer application will give me the best returns? What maize crop variety should I use?
Each farmer faces constraints related to weather uncertainty, soil fertility management challenges, or access to finance and markets. To improve their yields and incomes, African smallholder farmers need agronomic advice adapted to their specific circumstances. The challenge is even greater in sub-Saharan Africa, where agricultural production landscapes are highly diverse. Yet traditional agronomic research was not designed to fit with complex agroecological regions and farming systems. Compounding the problem, research organizations often have limited resources to develop the necessary experiments to generate farm- and site-specific agronomic advice at scale.
“Agronomic research is traditionally not equipped to consider spatial or socio-economic diversity among the millions of farmers it targets,” said Sebastian Palmas, data scientist at the International Maize and Wheat Improvement Center (CIMMYT) in Nairobi, Kenya.
Palmas presented some of the learnings of the Taking Maize Agronomy to Scale in Africa (TAMASA) project during a science seminar called “A spatial ex ante framework for guiding agronomic investments in sub-Saharan Africa” on March, 4, 2019.
The project, funded by the Bill & Melinda Gates Foundation, has used data to improve the way agronomic research for development is done. Researchers working on the TAMASA project addressed this challenge by using available geospatial information and other big data resources, along with new data science tools such as machine learning and Microsoft’s AI for Earth. They were able to produce and package information that can help farmers, research institutions and governments take better decisions on what agronomic practices and investments will give them the best returns.
By adapting the Quantitative Evaluation of the Fertility of Tropical Soils (QUEFTS) model to the conditions of small farmers in TAMASA target countries (Ethiopia, Nigeria and Tanzania), using different layers of information, CIMMYT and its partners have developed a versatile geospatial tool for evaluating crop yield responses to fertilizer applications in different areas of a given country. Because calculations integrate spatial variation of fertilizer and grain prices, the tool evaluates the profitability — a key factor influencing farmers’ fertilizer usage — for each location. The project team can generate maps that show, for instance, the estimated agronomic and economic returns to different fertilizer application scenarios.
The TAMASA team plans to publish the code and user-friendly interface of this new geospatial assessment tool later this year. (Photo: CIMMYT)
Making profits grow
These tools could potentially help national fertilizer subsidy programs be more targeted and impactful, like the ambitious Ethiopia’s Fertilizer Blending initiative which distributes up to 250,000 tons of fertilizer annually. Initial calculations showed that, by optimizing diammonium phosphate (DAP) and urea application, the profitability per hectare could improve by 14 percent on average, compared to the current fertilizer recommendations.
Such an approach could generate farm-specific advice at scale and boost farmers’ incomes. It could also provide insights on many different issues, like estimating market demand for a new fertilizer blend, or the estimated quantity of additional fertilizer required to bring about a targeted maize yield increase.
Future extensions of the framework may incorporate varietal differences in nutrient management responses, and thus enable seed companies to use the framework to predict where a new maize hybrid would perform best. Similarly, crop breeders could adapt this ex ante assessment tool to weigh the pros and cons of a specific trait and the potential impact for farmers.
The TAMASA team plans to publish the code and user-friendly interface of this new geospatial assessment tool later this year.
Maize ears from CIMMYT’s collection, showing a wide variety of colors and shapes. CIMMYT’s germplasm bank contains about 28,000 unique samples of cultivated maize and its wild relatives, teosinte and Tripsacum. These include about 26,000 samples of farmer landraces — traditional, locally-adapted varieties that are rich in diversity. The bank both conserves this diversity and makes it available as a resource for breeding. (Photo: Xochiquetzal Fonseca/CIMMYT)
Imagine walking through a grocery store, doing your weekly shopping. Everything seems normal, but as you pick up a can, there’s no label. There’s nothing to tell you what the product is, and now you can’t reliably choose anything to eat this week.
Now switch gears and imagine a germplasm bank. Without the right labeling on these different varieties, it’s difficult to tell what’s new and what’s already been discovered when working on new research projects.
About nine years ago, the International Maize and Wheat Improvement Center (CIMMYT) started an initiative called the Seeds of Discovery (SeeD). This initiative facilitates easier access to and use of maize and wheat genetic resources.
SeeD achieves impact through five main components: genotyping, phenotyping, software tools, pre-breeding and capacity building.
“One of the aims of Seeds of Discovery was to best characterize germplasm,” says Sarah Hearne, a molecular geneticist and maize lead of SeeD. “At CIMMYT, our international germplasm bank holds in trust one of the largest and most diverse publicly available maize collections in the world.”
However, Hearne says this germplasm bank used to look like a grocery store without any labels or without labels that would allow someone to select a can of value. To combat this, SeeD decided to work on a labeling process for the germplasm bank: the Molecular Maize Atlas.
The Molecular Maize Atlas is an information platform that brings genotypic data resources and associated tools together. This genotypic data provides unifying information across landraces and acts as a common backbone, which other valuable information, like phenotypic data, can be added to.
Mainassara Zaman-Allah conducts a demonstration of the use of unmanned aerial vehicles (UAV) at the Chiredzi research station in Zimbabwe.
To keep up with growing maize demand, breeders aim at optimizing annual yield gain under various stress conditions, like drought or low fertility soils. To that end, they identify the genetic merit of each individual plant, so they can select the best ones for breeding.
To improve that process, researchers at the International Maize and Wheat Improvement Center (CIMMYT) are looking at cost-effective ways to assess a larger number of maize plants and to collect more accurate data related to key plant characteristics. Plant phenotyping looks at the interaction between the genetic make-up of a plant with the environment, which produces certain characteristics or traits. In maize, for example, this may manifest in different leaf angles or ear heights.
Recent innovations in digital imagery and sensors save money and time in the collection of data related to phenotyping. These technologies, known as high-throughput phenotyping platforms, replace lengthy paper-based visual observations of crop trials.
Authors of a recent review study on high-throughput phenotyping tools observe that obtaining accurate and inexpensive estimates of genetic value of individuals is central to breeding. Mainassara Zaman-Allah, an abiotic stress phenotyping specialist at CIMMYT in Zimbabwe and one of the co-authors, emphasizes the importance of improving existing tools and developing new ones. “Plant breeding is a continuously evolving field where new tools and methods are used to develop new varieties more precisely and rapidly, sometimes at reduced financial resources than before,” he said. “All this happens to improve efficiency in breeding, in order to address the need for faster genetic gain and reduction of the cost of breeding.”
“Under the Stress Tolerant Maize for Africa (STMA) project, we are working on implementing the use of drone-based sensing, among other breeding innovations, to reduce time and cost of phenotyping, so that the development of new varieties costs less,’’ said Zaman-Allah. “The use of drones cuts time and cost of data collection by 25 to 75 percent compared to conventional methods, because it enables to collect data on several traits simultaneously — for example canopy senescence and plant count,” he explained.
Another great innovation developed under this CIMMYT project is what Zaman-Allah calls the ear analyzer. This low-cost digital imaging app allows to collect maize ear and kernel trait data 90 percent faster. This implies higher productivity and rigor, as more time is dedicated to data analysis rather than time spent on data collection. Using digital image processing, the ear analyzer gives simultaneous data of more than eight traits, including ear size and number, kernel number, size and weight.
Measuring maize attributes such as ear size, kernel number and kernel weight is becoming faster and simpler through digital imaging technologies.
Scientists are exploring the use of different sensors for phenotyping, such as Red, Green and Blue (RGB) digital imaging or Light Detection and Ranging (LIDAR) devices. Infrared thermal and spectral cameras could lead to further progress towards faster maize breeding.
Such sensors can help collect numerous proxy data relating to important plant physiological traits or the plant environment, like plant height and architecture, soil moisture and root characteristics. This data can be used to assess the maize crop yield potential and stress tolerance.
Such breeding innovations are also making maize research more responsive to climate change and emerging pests and diseases.
Seed Assure app testing in the field in Kiboko, Kenya. (Photo: CIMMYT)
Many Kenyan maize farmers are busy preparing their seed stock for the next planting season. Sowing high quality seeds of stress-tolerant varieties is a cost-effective way for African smallholder farmers to boost their harvests while being resilient to evolving crop pests and diseases as well as an erratic climate. However, even if a majority of farmers buy their seeds, they are often of dubious quality or of old, outdated varieties, which do not cope well against increasing drought and heat shocks or emerging diseases.
Insufficient seed quality control
The African seed sector has long been plagued by counterfeit seeds and a complex and costly certification process, which hampers access to better, higher-yielding, wide-ranging varieties for farmers.
Since the 1990s, national agencies could not keep up with the seed trade growth to handle the certification processes. Backlogs of certification requests and erroneous seed checks make it costly for private seed companies to produce and commercialize new varieties. As a result, maize varieties grown by farmers in sub-Saharan Africa are old: 28 years old on average for hybrids and up to 40 years old for open-pollinated varieties.
“A lot of the national certification systems in the region are overwhelmed. They do not have enough seed inspectors with proper training and tools to carry out compliance checks effectively and in a timely manner. The licensing, labeling and branding protocols and regulations are equally not in full force, and much of the work still needs to be digitized. This slows the entire process,” said Kate Fehlenberg, Drought Tolerant Maize for Africa Seed Scaling (DTMASS) Project Manager at the International Maize and Wheat Improvement Center (CIMMYT), at a recent Common Market for Eastern and Southern Africa (COMESA) seed policies’ harmonization event in Nairobi.
Go digital
To solve this certification bottleneck, seed actors are looking at digital solutions for faster, more accurate seed quality checks for both seed producers and regulators. One Kenyan company, Cellsoft Ltd., has developed SeedAssure, a cloud-based platform that enables digital seed inspections. Data necessary for quality seed production, pest and disease surveillance, and the required checks to apply for a commercial license can be shared in real-time on a common platform that links seed companies, inspectors and local authorities. Such a tool not only enables optimal quality in seed production, but expedites the licensing, certification and trade processes with traceable data records.
SeedAssure is rapidly being rolled out across eastern and southern Africa with support across the seed value chain. This includes regional trade bodies like COMESA and the Southern African Development Community (SADC), national regulators such as the Seed Control and Certification Institute (SCCI), to research and development organizations like CIMMYT and the Alliance for a Green Revolution in Africa (AGRA). So far, 15 seed companies in seven countries in the region have been testing SeedAssure.
Transboundary data-sharing to boost regional seed trade
Visitors test SeedAssure on a smartphone during a field visit in Kiboko, Kenya. (Photo: CIMMYT)
To boost regional seed trade, all actors along the seed value chain and across the region must embrace this digital revolution and “speak the same language”. This means adopting the same rules to identify and register a new variety, and using a common platform to easily share data between countries.
Currently, despite efforts to harmonize seed trade policies across the region, such as the COMESA Seed Harmonization Implementation Program (COMSHIP), passed in 2014, most countries still use different protocols to name and register seed varieties. One variety could have a different name in each country it is sold in. Data used for quality control are still often on paper rather than online, with each country performing its own tests. Seed companies must apply for new variety registration, with new data for each country they operate in. This all costs them time and money.
Adopting a unique identifier for seed products and digitalization can help alleviate this harmonization issue, easing comparable data sharing across border. Since November 2017, CIMMYT has adopted a Variety Identification Number (VIN) system. It is like a unique barcode for each variety which contains information about the organization that produced the variety, the year of release, the crop and specific traits such as drought-tolerance, the country where it is produced, etc. SADC and COMESA have just adopted this VIN system. COMSHIP is setting digital seed variety catalogues using the VIN, and soon regional seed labels. It will facilitate cross-border seed trade and help track seed fraud.
The 2019 Global Forum for Food and Agriculture (GFFA) held this week in Berlin is debating how digitalization is transforming the farming sector. This is particularly relevant for the African seed sector as digital innovations could make seed certification and quality control cheaper, faster and more transparent, while narrowing the space for fake seed. Seed companies would then be encouraged to release more new improved varieties, and ultimately accelerate our research impact for African farmers.
Farmer Gudeye Leta harvests his local variety maize in Dalecho village, Gudeya Bila district, Ethiopia. (Photo: Peter Lowe/CIMMYT)
Ethiopia is Africa’s third largest producer of maize, after Nigeria and South Africa. Although the country produces around 6.5 million tons annually, the national average maize yield is relatively low at 3.5 tons compared to the attainable yield of 8.5 tons. This high yield gap — the difference between attainable and actual yields — can be attributed to a number of factors, including crop varieties used, farm management practices, and plant density.
The Taking Maize Agronomy to Scale (TAMASA) project aims to narrow maize yield gaps in Ethiopia, Nigeria and Tanzania through the development and scaling out of decision-support tools, which provide site-specific recommendations based on information held in crop and soil databases collected from each country. These help farmers to make decisions based on more accurate variety and fertilizer recommendations, and can contribute to improving maize production and productivity.
One such tool is Nutrient Expert, a free, interactive computer-based application. It can rapidly provide nutrient recommendations for individual farmers’ fields in the absence of soil-testing data. The tool was developed by the International Plant Nutrition Institute in collaboration with the International Maize and Wheat Improvement Center (CIMMYT), the International Institute of Tropical Agriculture (IITA), and research and extension service providers.
Nutrient Expert user interface.
In Ethiopia, regional fertilizer recommendations are widely used, but soil fertility management practices can vary greatly from village to village and even between individual farmers. This can make it difficult for farmers or extension agents to receive accurate information tailored specifically to their needs. Nutrient Expert fills this gap by incorporating information on available fertilizer blends and giving customized recommendations for individual fields or larger areas, using information on current farmer practices, field history and local conditions. It can also provide advice on improved crop management practices such as planting density and weeding, thereby helping farmers to maximize net returns on their investment in fertilizer.
Data calibration was based on the results of 700 multi-location nutrient omission trials conducted in major maize production areas in Ethiopia, Nigeria and Tanzania. These trials were designed as a diagnostic tool to establish which macro-nutrients are limiting maize growth and yield, and determine other possible constraints.
In Ethiopia, CIMMYT scientists working for the TAMASA project conducted nutrient omission trials on 88 farmer fields in Jimma, Bako and the Central Rift Valley in 2015 to produce a version of Nutrient Expert suitable for the country. Researchers trialed the app on six maize-belt districts in Oromia the following year, in which Nutrient Expert recommendations were compared with soil-test based and regional ones.
Researchers found that though the app recommended lower amounts of phosphorus and potassium fertilizer, overall maize yields were comparable to those in other test sites. In Ethiopia, this reduction in the use of NPK fertilizer resulted in an investment saving of roughly 80 dollars per hectare.
Results from Nutrient Expert trials in Ethiopia, Nigeria and Tanzania showed improved yields, fertilizer-use efficiency and increased profits, and the app has since been successfully adapted for use in developing fertilizer recommendations that address a wide variety of soil and climatic conditions in each of the target countries.
The World Bank’s 2016 Digital Dividends report states that we are currently “in the midst of the greatest information and communications revolution in human history.” This shifting digital landscape has significant implications for the ways in which stakeholders in the agricultural sector generate, access and use data. Amidst Africa’s burgeoning technology scene, CIMMYT’s TAMASA project demonstrates the transformative power of harnessing ICTs for agricultural development.
Learn more about different versions of Nutrient Expert and download the free software here.
TAMASA is a five-year project (2014-2019) funded by the Bill & Melinda Gates Foundation, seeking to improve productivity and profitability for small-scale maize farmers in Ethiopia, Nigeria and Tanzania. Read more about the project here.
KATHMANDU, Nepal (CIMMYT) — The International Maize and Wheat Improvement Center (CIMMYT) is working with Nepal’s Soil Management Directorate and the Nepal Agricultural Research Council (NARC) to aggregate historic soil data and, for the first time in the country, produce digital soil maps. The maps include information on soil PH, organic matter, total nitrogen, clay content and boron content. Digital soil mapping gives farmers and natural resource managers easy access to location-specific information on soil properties and nutrients, so they can make efficient and localized management decisions.
As part of CIMMYT’s Nepal Seed and Fertilizer (NSAF) project, researchers used new satellite imagery that enabled the resolution of the maps to be increased from 1×1 km to 250×250 m. They have updated the web portal to make it more user friendly and interactive. When loaded onto a smartphone, the map can retrieve the soil properties information from the user’s exact location if the user is within areas with data coverage. The project team is planning to produce maps for the whole country by the end of 2019.
CIMMYT scientist David Guerena talks about the role of the new digital maps to combat soil fertility problems in Nepal.
At a World Soil Day event in Nepal, CIMMYT soil scientist David Guerena presented the new digital soil maps to scientists, academics, policymakers and other attendees. Guerena explained the role this tool can play in combatting soil fertility problems in Nepal.
These interactive digital maps are not simply visualizations. They house the data and analytics which can be used to inform site-specific integrated soil fertility management recommendations.
The first high-resolution digital soil maps for the Terai region have been produced with support from the data assets from the National Land Use Project, developed by Nepal’s Ministry of Agriculture and Livestock Development. These maps will be used to guide field programming of the NSAF project, drive the development of market-led fertilizer products, and inform and update soil management recommendations. The government of Nepal can use the same information to align policy with the needs of farmers and the capacity of local private seed and fertilizer companies.
In 2017, 16 scientists from Nepal’s Soil Management Directorate, NARC and other institutions attended an advanced digital soil mapping workshop where they learned how to use different geostatistical methods for creating soil maps. This year, as part of the NSAF project, four NARC scientists attended a soil spectroscopy training workshop and learned about digitizing soil data management and using advanced spectral methods to convert soil information into fertilizer recommendations.
Soil data matters
Soil properties have a significant influence on crop growth and the yield response to management inputs. For farmers, having access to soil information can make a big difference in the adoption of integrated soil fertility management.
Farmer motivation and decision-making relies heavily on the perceived likeliness of obtaining a profitable return at minimized risk. This largely depends on the yield response to management inputs, such as improved seeds and fertilizers, which depends to a large extent on site-specific soil properties and variation in agro-ecological conditions. Therefore, quantitative estimates of the yield response to inputs at a given location are essential for estimating the risks associated with these investments.
The Nepal Seed and Fertilizer project is funded by the United States Agency for International Development (USAID) and is a flagship project in Nepal. The objective of the NSAF is to build competitive and synergistic seed and fertilizer systems for inclusive and sustainable growth in agricultural productivity, business development and income generation in Nepal.
KATHMANDU, Nepal (CIMMYT) — The International Maize and Wheat Improvement Center (CIMMYT) is working with Nepal’s Soil Management Directorate and the Nepal Agricultural Research Council (NARC) to aggregate historic soil data and, for the first time in the country, produce 