funder_partner: Diversity Arrays Technology (DArT)

A CIMMYT technician cuts a leaf sample for DNA extraction. (Photo: CIMMYT)

Breeders take quantum leap

Written by Rodrigo Ordóñez on February 19, 2021. Posted in News.

Wheat breeders from across the globe took a big step towards modernizing their molecular breeding skills at a recent workshop sponsored by the Wheat Initiative, with the CGIAR Excellence in Breeding Platform (EiB) and the International Maize and Wheat Improvement Center (CIMMYT).

The workshop focused on three open-source tools used in molecular breeding: GOBii-GDM for genomic data management, Flapjack for data visualization and breeding analysis, and Galaxy for Genomic Selection. These tools help breeders make selections more quickly and precisely, and ultimately lead to more cost effective and efficient improvement of varieties.

The Wheat Initiative — a global scientific collaboration whose goals are to create improved wheat varieties and disseminate better agronomic practices worldwide — and its Breeding Methods and Strategies expert working group had planned to host these trainings during the 2020 Borlaug Global Rust Initiative Technical Workshop in the United Kingdom. After it became obvious that in-person trainings were not possible, the course organizers — including CIMMYT molecular wheat breeder Susanne Dreisigacker and EiB Adoption Lead and former GOBii project director Elizabeth Jones — decided to come together to host online workshops.

Many of the tools will be incorporated into EiB’s Enterprise Breeding System (EBS), a new integrated data management system being developed for CGIAR breeders. Jones plans to also design training modules for these molecular breeding tools that will be accessible to anyone through the EiB Toolbox.

In the meantime, the tools used in the workshop are all freely available: DArTView, Flapjack (training videos), GOBii-GDM (request access through the web form or by email), and Galaxy Genomic Selection.

The first session of the workshop “Transforming Wheat Breeding Through Integrated Data Management with GOBii and Analysis in Flapjack” benefited breeders from Australia, Canada, Ethiopia, France, India, Ireland, Italy, Morocco, Pakistan, Switzerland, Tunisia, the United Kingdom and the United States.

Susanne Dreisigacker presents during one of the sessions of the workshop.

Powering data analysis around the world

The workshop series, “Transforming Wheat Breeding Through Integrated Data Management with GOBii and Analysis in Flapjack,” aimed to benefit breeders from wheat producing countries all over the world, with sessions over two different time zones spread out over three days to reduce “Zoom fatigue.” Participants joined the first session from Australia, Canada, Ethiopia, France, India, Ireland, Italy, Morocco, Pakistan, Switzerland, Tunisia, the United Kingdom and the United States.

“It was wonderful to see the diversity of participants that we were able to train through an online workshop, many of whom otherwise might not have been able to travel to the UK for the original meeting,” said Jones. “Participants were very engaged, making the workshop so rewarding.”

The workshop was guided by Teresa Saavedra, Wheat Initiative coordinator. Apart from Dreisigacker and Jones, other trainers explained specific tools and approaches. Iain Milne from the James Hutton Institute in Scotland gave more details about the Flapjack genotyping visualization tool, which includes analysis for pedigree verification, marker assisted backcrossing and forward breeding. Andrew Kowalczyk, developer at Diversity Arrays Technology, spoke about the genotyping data QC tool DArTView.

A CIMMYT technician performs one of the steps to extract DNA samples from plants. (Photo: CIMMYT)

Clay Sneller, wheat breeder at Ohio State University, contributed training materials for important molecular breeding tools. Carlos Ignacio, previously based at the International Rice Research Center (IRRI) and now working on a PhD in Genomic Selection at Ohio State University, contributed his experience as a GOBii team member and a major contributor towards the design of Flapjack tools. Star Gao, application specialist with GOBii and now a requirements analyst for the Enterprise Breeding System, also facilitated the sessions.

Gilles Charmet, research director at the France’s National Research Institute for Agriculture, Food and Environment (INRAE), introduced the sessions in the Americas/Europe time zone with welcome remarks and overview of the goals of the Wheat Initiative. Alison Bentley, director of the CIMMYT Global Wheat Program, briefed on the achievements and goals of the CIMMYT Wheat program and the Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project.

“This training will contribute towards us reaching our AGG goals of accelerating gains in wheat, by sharing technical knowledge, and allowing our beneficiary partners to have state-of-the-art know-how in the use of genetic and genomic data,” Bentley said.

Participant Stéphane Boury from Caussade Semences, France commented, “This was a very effective way to learn about new tools in wheat breeding.”

The sessions continue in Australasia next week, and will be introduced by Peter Langridge, chair of the Scientific Board for the Wheat Initiative, and EiB director Michael Quinn. Sanjay Kumar Singh, incoming chair of the Breeding expert working group for the Wheat Initiative, will close the event.

Wheat fields in the Arsi highlands, Ethiopia, 2015. (Photo: CIMMYT/ Peter Lowe)

Rust-resistant bread wheat varieties widely adopted in Ethiopia

Written by Emma Orchardson on November 11, 2020. Posted in Press releases.

A state-of-the-art study of plant DNA provides strong evidence that farmers in Ethiopia have widely adopted new, improved rust-resistant bread wheat varieties since 2014.

The results — published in Nature Scientific Reports — show that nearly half (47%) of the 4,000 plots sampled were growing varieties 10 years old or younger, and the majority (61%) of these were released after 2005.

Four of the top varieties sown were recently-released rust-resistant varieties developed through the breeding programs of the Ethiopian Institute for Agricultural Research (EIAR) and the International Maize and Wheat Improvement Center (CIMMYT).

Adoption studies provide a fundamental measure of the success and effectiveness of agricultural research and investment. However, obtaining accurate information on the diffusion of crop varieties remains a challenging endeavor.

DNA fingerprinting enables researchers to identify the variety present in samples or plots, based on a comprehensive reference library of the genotypes of known varieties. In Ethiopia, over 94% of plots could be matched with known varieties. This provides data that is vastly more accurate than traditional farmer-recall surveys.

This is the first nationally representative, large-scale wheat DNA fingerprinting study undertaken in Ethiopia. CIMMYT scientists led the study in partnership with EIAR, the Ethiopian Central Statistical Agency (CSA) and Diversity Array Technologies (DArT).

“When we compared DNA fingerprinting results with the results from a survey of farmers’ memory of the same plots, we saw that only 28% of farmers correctly named wheat varieties grown,” explained Dave Hodson, a principal scientist at CIMMYT and lead author of the study.

The resulting data helps national breeding programs adjust their seed production to meet demand, and national extension agents focus on areas that need better access to seed. It also helps scientists, policymakers, donors and organizations such as CIMMYT track their impact and prioritize funding, support, and the direction of future research.

“These results validate years of international investment and national policies that have worked to promote, distribute and fast-track the release of wheat varieties with the traits that farmers have asked for — particularly resistance to crop-destroying wheat rust disease,” said Hodson.

Ethiopia is the largest wheat producer in sub-Saharan Africa. The Ethiopian government recently announced its goal to become self-sufficient in wheat, and increasing domestic wheat production is a national priority.

Widespread adoption of these improved varieties, demonstrated by DNA fingerprinting, has clearly had a positive impact on both economic returns and national wheat production gains. Initial estimates show that farmers gained an additional 225,500 tons of production — valued at $50 million — by using varieties released after 2005.

The study results validate investments in wheat improvement made by international donor agencies, notably the Bill & Melinda Gates Foundation, the Ethiopian government, the UK Foreign, Commonwealth and Development Office (FCDO, formerly DFID), the US Agency for International Development (USAID) and the World Bank. Their success in speeding up variety release and seed multiplication in Ethiopia is considered a model for other countries.

“This is good news for Ethiopian farmers, who are seeing better incomes from higher yielding, disease-resistant wheat, and for the Ethiopian government, which has put a high national priority on increasing domestic wheat production and reducing dependence on imports,” said EIAR Deputy Director General Chilot Yirga.

The study also confirmed CGIAR’s substantial contribution to national breeding efforts, with 90% of the area sampled containing varieties released by Ethiopian wheat breeding programs and derived from CIMMYT and the International Center for Agricultural Research in the Dry Areas (ICARDA) germplasm. Varieties developed using germplasm received from CIMMYT covered 87% of the wheat area surveyed.

“This research demonstrates that DNA fingerprinting can be applied at scale and is likely to transform future crop varietal adoption studies,” said Kindie Tesfaye, a senior scientist at CIMMYT and co-author of the study. “Additional DNA fingerprinting studies are now also well advanced for maize in Ethiopia.”

This research is supported by the Bill and Melinda Gates Foundation and CGIAR Fund Donors. Financial support was provided through the “Mainstreaming the use and application of DNA Fingerprinting in Ethiopia for tracking crop varieties” project funded by the Bill & Melinda Gates Foundation (Grant number OPP1118996).

RELATED PUBLICATIONS:

Ethiopia’s Transforming Wheat Landscape: Tracking Variety Use through DNA Fingerprinting

FOR FURTHER INFORMATION OR INTERVIEW REQUESTS:

Dave Hodson, International Maize and Wheat Improvement Center (CIMMYT), d.hodson@cgiar.org

ABOUT CIMMYT:

The International Maize and What Improvement Center (CIMMYT) is the global leader in publicly-funded maize and wheat research and related farming systems. Headquartered near Mexico City, CIMMYT works with hundreds of partners throughout the developing world to sustainably increase the productivity of maize and wheat cropping systems, thus improving global food security and reducing poverty. CIMMYT is a member of the CGIAR System and leads the CGIAR programs on Maize and Wheat and the Excellence in Breeding Platform. The Center receives support from national governments, foundations, development banks and other public and private agencies. For more information visit staging.cimmyt.org

Ethiopian policymakers consider wider use of DNA fingerprinting

Written by Rodrigo Ordóñez on September 12, 2019. Posted in Features. 1 Comment on Ethiopian policymakers consider wider use of DNA fingerprinting

How to track adoption and assess the impact of maize and wheat varieties? Some of the methods used until now, like farmers’ recall surveys, have various limitations. In addition to relying exclusively on people’s memory and subjectivity, they are difficult to replicate and prone to errors.

DNA fingerprinting, on the other hand, allows objective evaluation and is considered the “gold standard” method for adoption and impact assessments.

It consists of a chemical test that shows the genetic makeup of living things, by separating strands of DNA and revealing the unique parts of their genome. The results show up as a pattern of stripes that can be matched against other samples.

This technique is extremely helpful in tracking crop varieties and monitoring their adoption. It can be used to assess the impact of research-for-development investments, guide breeding and seed system strategies, implement the intellectual property rights of breeders, assess the use of crop genetic resources, and informing policy.

On June 25, 2019, the International Maize and Wheat Improvement Center (CIMMYT) held a half-day workshop in Addis Ababa to discuss the use and application of DNA fingerprinting in Ethiopia for the tracking of crop varieties.

High-level government officials and major players in the agricultural sector were interested in learning more about the policy implications of this tool and how to mainstream its use.

CIMMYT’s Socioeconomics Program Director, Olaf Erenstein (left), talks to Eyasu Abraha, Minister of Agriculture and Natural Resources (center), and Mandefro Nigussie, Director General of the Ethiopian Institute of Agricultural Research.

Introducing DNA fingerprinting in Ethiopia

The main DNA fingerprinting project in Ethiopia has been in operation since January 2016, focusing on the country’s two major staple crops: wheat and maize. The project covers the Amhara, Oromia, SNNPR, and Tigray regions, which together account for 92% and 79% of the national wheat and maize production.

The Bill & Melinda Gates Foundation has funded the project, which was jointly implemented by CIMMYT, the Ethiopian Institute of Agricultural Research (EIAR), Ethiopia’s Central Statistical Agency (CSA) and Diversity Arrays Technology (DArT).

The main objective of the project was to generate a knowledge base for the practical use of DNA fingerprinting, to mainstream the use of this technology, and to offer policy options and recommendations.

CIMMYT scientists Dave Hodson (left), Bekele Abeyo (center) and Sarah Hearne participated in the workshop.

Better monitoring for wheat self-sufficiency

At the workshop, researchers presented two policy briefs specific to Ethiopia: one focusing on policy implications of DNA fingerprinting for tracking bread wheat varieties and another one on how to revitalize the durum wheat sub-sector.

Speaking at the workshop, Eyasu Abraha, Minister of Agriculture and Natural Resources, noted that the government planned to achieve wheat grain self-sufficiency in the next few years by increasing wheat productivity in the highlands and expanding wheat production to the lowlands through irrigation. In this regard, improved crop variety development and dissemination is one of the key elements to increase agricultural productivity and improve the livelihood of millions of smallholder farmers.

According to Abraha, more than 130 wheat varieties have been released or registered in Ethiopia since the late 1960s, in collaboration with international research organizations. Public and private seed enterprises have multiplied and distributed these varieties to reach smallholder farmers.

Even though adoption studies have been conducted, there is still a strong need for more accurate and wider studies. In addition to tracking adoption and demand, using DNA fingerprinting could help understand the distribution of varieties across space and time.