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

Written by Mike Listman on . Posted in Press releases.

Wheat is Afghanistan’s number-one staple crop, but the country doesn’t grow enough and must import millions of tons of grain each year to satisfy domestic demand.
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 an extensive ‘reference library’ of released varieties, elite breeding lines, and Afghan wheat landraces,” 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 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.

L.M. Suresh

Written by Emma Orchardson on . Posted in Uncategorized.

L.M. Suresh leads CIMMYT’s maize pathology efforts in sub-Saharan Africa. He regularly contributes to Global Maize Program projects that have strategic significance in maize pathology, disease diagnosis, epidemiology and disease resistance.

Suresh also works on maize lethal necrosis (MLN) phenotyping with public and private partnership at CIMMYT and the Kenya Agricultural and Livestock Research Organization’s (KALRO) joint research station in Naivasha, Kenya. His team has phenotyped around 200,000 maize germplasm from various partners and 19 MLN resistant/tolerant hybrids have been released in east Africa so far. He has supported the training of more than 5000 researchers, students, extension workers, private seed company executives and farmers in rapid disease diagnosis and his contributions have helped to prevent further MLN spread throughout eastern and southern Africa.

Manje Gowda

Written by Emma Orchardson on . Posted in Uncategorized.

Manje Gowda is a maize molecular breeder based in Kenya with CIMMYT’s Global Maize Program. His current research focuses on the identification, validation and deployment of novel genetic variation into elite germplasm, integrating knowledge on plant breeding, quantitative genetics, and molecular breeding to improve maize breeding efficiency.

In close collaboration with CIMMYT maize breeders, he implements forward breeding and genomic selection in CIMMYT’s Eastern and Southern Africa maize breeding programs. He gives maize breeders access to the newest genotyping technologies and is involved in the development of high quality seeds through rigorous application of marker based QA&QC.

Xinyao He

Written by Mary Donovan on . Posted in Uncategorized.

Xinyao He joined CIMMYT in 2011 and since then his main research area has been Fusarium head blight (FHB) and its associated mycotoxins, including phenotypic screening for FHB resistance, breeding for FHB resistance, genetic dissection of resistance mechanisms, and integrated FHB management.

He has also been heavily involved in wheat blast research since 2016, including field disease screening, genetic studies and marker validation, as well as participating in research and breeding activities for other wheat diseases such as Septoria tritici blotch, Septoria nodorum blotch, spot blotch, tan spot and Karnal bunt.

Velu Govindan

Written by Emma Orchardson on . Posted in Uncategorized.

Velu Govindan is a senior wheat breeder at the CIMMYT’s Global Wheat Program in Mexico. He has been engaged in wheat improvement research for the past 15 years. During this period, he made significant contributions towards the development and release of more than 20 biofortified wheat varieties in South Asia with enhanced zinc and iron concentration, with tolerance to rusts & other foliar diseases and climate change-induced heat and drought stress.

Govindan is leading the two of the spring wheat breeding pipelines targeted to early maturing wheat environments with wheat yield potential, climate resilience and yield stability across diverse environments by combining traditional breeding and cutting-edge genomic tools. He is leading the CIMMYT breeding efforts towards mainstreaming grain Zn across elite wheat lines through accelerated breeding strategies. He has published more than 80 peer-reviewed journal articles and 15 book chapters. He received young scientist award from India.

Sridhar Bhavani

Written by Emma Orchardson on . Posted in Uncategorized.

Sridhar Bhavani is a Senior Scientist, Head of Rust Pathology and Molecular Genetics working at CIMMYT HQ.

He is a passionate researcher leader with over 15 years of experience working on wheat traits especially rust diseases. He has demonstrated leadership in executing multiple international projects and established strong networks and linkages in East Africa, Asia and various global wheat partners.

As the Head of Rust Pathology, he oversees pathology, molecular genetics, and breeding strategy components in major projects such as: Accelerating Genetic Gains in Maize and Wheat (AGGMW) funded by BMGF; DFID, FCDO, BMGF & DFID funded Zn mainstreaming project; GRDC and ACRCP funded projects on delivering genetic tools and knowledge required to breed wheat and barley with resistance to leaf rust, stripe rust and stem rust; USAID funded project on wheat rust breeding; NMBU-Norway funded project on sustainable management of rust diseases in wheat; and a project led by Kansas State on New Sources of Genetic Disease Resistance.

Xuecai Zhang

Written by Emma Orchardson on . Posted in Uncategorized.

Xuecai Zhang is a Senior Scientist and Maize Molecular Breeder with CIMMYT’s Global Maize Program. In 2011, he joined CIMMYT as an assistant breeder at the lowland tropical maize breeding program in Mexico. In 2015, he started to lead the maize molecular breeding lab in Mexico to implement modern molecular breeding tools and technologies for accelerating the genetic gain of the Latin American maize breeding pipelines. From 2024, he coordinates the maize collaborations between CIMMYT and China.

Aparna Das

Written by Emma Orchardson on . Posted in Uncategorized.

Aparna Das is a Technical Program Manager for the Global Maize Program, working with breeding teams to implement new strategies to improve the product delivery pipeline.

Claudio César Ayala Hernández

Written by Emma Orchardson on . Posted in Uncategorized.

Claudio Ayala is an experienced Data Management Coordinator with a demonstrated history of working in the research industry. He has a Master’s degree focused on Information Systems and Applied Computing and is skilled in analytics, database management, and the development of tools for effectively capturing, curating, storing and integrating different datasets.

Arun Kumar Joshi

Written by Rodrigo Ordóñez on . Posted in Uncategorized.

Arun Kumar Joshi is engaged in developing climate-resilient, high-yielding, nutritive wheat varieties for South Asia. In addition, he is engaged in various collaborations on climate-resilient agriculture and seed system. He has facilitated the development and release of more than five dozen wheat varieties in South Asia through a significant contribution to climate resilience, disease resistance, conservation agriculture, and Zinc rich biofortification. His research findings are published in 188 refereed journal articles, 212 extension articles and manuals, 10 books or book chapters, and 136 symposia proceedings, and has a patent.

Joshi, a former Professor of Banaras Hindu University, is a fellow of the three most prestigious science academies in India – the Indian National Science Academy (INSA), the National Academy of Science in India (NASI), and the National Academy of Agriculture Sciences (NAAS). In 2014, he was awarded the Jeanie Borlaug Laube WIT Mentor Award from the Borlaug Global Rust Initiative at Cornell University.

Breaking Ground: Susan Dreisigacker

Breaking Ground: Susanne Dreisigacker knows wheat inside out

Written by Courtney Brantley on . Posted in Features.

Breaking Ground: Susan DreisigackerEL BATAN, Mexico (CIMMYT) — Through pure coincidence, Susanne Dreisigacker fell into the world of agricultural science and landed in Mexico. Her interest in genetics and biology solidified when she arrived at the International Maize and Wheat Improvement Center (CIMMYT) through the University of Hohenheim in Germany to pursue her PhD work. Impressed by CIMMYT’s scientific endeavors and its mission, she found herself permanently back at the institution in 2005 as a resident scientist. Now, as the head of CIMMYT’s Wheat Molecular Breeding Lab, Dreisigacker ensures that wheat breeders use the appropriate wheat material to conduct gene profiling and genome sequencing.

Dreisigacker works to discover and validate molecular markers, or DNA segments, for traits of interest. This information helps breeders to develop improved crop varieties that feature those traits.

At its core, her position centers on defining best practices for genomic tool application in the wheat breeding program. These genomic tools serve as “…indirect selection criteria to ultimately assist breeders select improved outputs at the molecular level, such as disease resistance and enhanced nutritional quality in wheat,” explains Dreisigacker. Furthermore, her research amasses data on grain yield and its corresponding components — such as grain weight and other difficult traits to tackle in the wheat breeding world — to help breeders stabilize high yield rates.

On average, over 40,000 wheat lines a year are analyzed on behalf of breeders under Dreisigacker’s direction. The ultimate challenge is organizing this massive data outcome to effectively support the breeders.

Zooming out from the molecular level

Dreisigacker works to discover and validate molecular markers, or DNA segments, for traits of interest. (Photo: Darell Sison)
Dreisigacker works to discover and validate molecular markers, or DNA segments, for traits of interest. (Photo: Darell Sison)

Working in an environment with interdisciplinary characteristics such as a breeding program, it can be difficult to prioritize which traits merit the bulk of her time. Dreisigacker stresses that teamwork is paramount, from breeders to pathologists to quality specialists, as they all share mutual goals, so their efforts “need to intersect in order to be beneficial.” Dreisigacker enjoys interacting among the disciplines and sharing her work with the international wheat community.

Progress in the application of genomic tools and the push for their usefulness inspires Dreisigacker to continue her work with wheat at CIMMYT. Her work in the laboratory is the backbone of the transmission of better quality germplasm from breeders to farmers. “There is a need to more efficiently integrate gene profiling and genome sequencing into breeding. The transition from upstream genomic research to the processes of application and adaptability are overlooked,” says Dreisigacker.

When she is not looking at wheat at the molecular level, you can find her spending time with her husband and young daughter or teaching exercise classes in CIMMYT’s gymnasium.

Over 100,000 genes

Written by Mike Listman on . Posted in News.

After 13 years of research, an international team of more than 200 scientists recently cracked the full genome of bread wheat. Considering that wheat has five times more DNA than humans, this is a significant scientific breakthrough. The complete sequencing provides researchers with a map for the location of more than 100,000 genes which, experts say, will help accelerate the development of new wheat varieties.

Philomin Juliana, a Post-Doctoral Fellow in wheat breeding at the International Maize and Wheat Improvement Center (CIMMYT) talks about the relevance of the new map for the center, whose genetics figures in the pedigrees of wheat varieties grown on more than 100 million hectares worldwide.

Are you already using this resource, and how?

We have anchored the genotyping-by-sequencing marker data for about 46,000 lines from CIMMYT’s first-year wheat yield trials (2013-2018) to the new, International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (RefSeq v1.0) assembly of the bread wheat genome, with an overall alignment rate of 64%. This has provided valuable information on the location of key genome regions associated with grain yield, disease resistance, agronomic traits and quality in CIMMYT’s wheat germplasm, identified from genome-wide association mapping studies.

We have also used the new reference sequence to understand the impact of marker densities and genomic coverage on the genomic predictability of traits and have gained a better understanding of the contributions of diverse chromosome regions (distal, proximal, and interstitial) towards different phenotypes.

How will use of the new wheat reference sequence help CIMMYT and partners to develop improved wheat for traits of interest?

There are so many ways we can use this new tool! It provides valuable insights into trait genetics and genomics in bread wheat and will help us to more quickly identify candidate genes associated with traits of interest and to clone those genes. We will also be able to design molecular breeding strategies and precisely select and introgress target regions of the genome.

More generally, the reference sequence already has a range of markers — among them, simple sequence repeats (SSR), diversity array technologies (DArT) markers, and single nucleotide polymorphisms (SNPs) — anchored to it, which will facilitate comparisons between mapping studies and the quick development and validation of useful new markers.

It will also help to apply tools like gene-editing to obtain desired phenotypes and will allow us to better characterize the genetic diversity in CIMMYT’s wheat, to identify useful genes in key CIMMYT parent lines and rapidly introgress them into breeding lines.

With the annotated whole genome information, breeders can design crosses focused directly on desired combinations of genomic regions or predict the outcome of crosses involving gene combinations.

It will definitely speed varietal testing in partner countries through quick and accurate molecular screens for the presence of desired genes, instead of having to perform multiple generations of field testing.

Finally, it will help us to detect molecular-level differences between CIMMYT varieties released in different countries.

Which traits are being targeted by CIMMYT and partners?

We are using the new reference sequence to understand better the molecular bases of grain yield, heat and drought tolerance, rust resistance, flowering time, maturity, plant height, grain and flour protein, and various other quality traits.

Philomin Juliana

A recipient of Monsanto’s Beachell-Borlaug International Scholars Program Award, Juliana completed a Ph.D. in Plant Breeding and Genetics at Cornell University in 2016. Her work at CIMMYT seeks to identify the genetic bases of key traits in CIMMYT wheat germplasm and to assess high-throughput genotyping and phenotyping to increase the rate of genetic gain for yield in the center’s bread wheat breeding. In this work, she partners with the Cornell-led Delivering Genetic Gain in Wheat (DGGW) project and Jesse Poland of the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) and Kansas State University. Her research also forms part of USAID’s Feed the Future projects.

How to get your high-impact research published in leading journals: top tips from the Senior Editor of Nature Genetics

Written by on . Posted in Features.

At CIMMYT’s Science Week 2018, Nature Genetics Senior Editor Catherine Potenski spoke on how to publish plant genomics research that has broad, novel impact.

Catherine Potenski, Senior Editor of Nature Genetics, talks to participants of CIMMYT's Science Week on June 26, 2018. (Photo: Alfonso Cortés/CIMMYT)
Catherine Potenski, Senior Editor of Nature Genetics, talks to participants of CIMMYT’s Science Week on June 26, 2018. (Photo: Alfonso Cortés/CIMMYT)

Having research that is high-impact is not only critical to doing excellent science that has meaning, but also a premier way to let the research community know what you are doing and reach a broader audience, according to Catherine Potenski, Senior Editor at Nature Genetics, one of the more than 70 high-quality academic journals of publishing company Springer Nature.

“Plant genomics is an exciting field that is a priority for Nature Genetics given climate change and other challenges,” said Potenski. “We look for studies with novelty, a genetics scope and resource value.”

Nature Genetics is highly selective and publishes approximately 200 papers per year. Potenski wants to make the editorial review process more productive and simple for researchers so they can share their best work.

“You should organize your paper to highlight the impact of the findings and write a cover letter that places your work in context, highlighting what gap of knowledge it fills and how others will use this research,” explained Potenski. In addition, scientists should target the right journal for their research. In case of doubt, they can send a pre-submission inquiry and work with editors.

Impact is not always immediate, and the impact factor is not necessarily a good or proven metric. “The first CRISPR articles published in the early 2000s are now very impactful, but nobody knew the impact they would have then. Just because it is not in a high-impact journal, it does not mean it is not high-impact,” she said.

Potenski shared the six questions plant researchers should ask themselves when submitting research to Nature Genetics.

  1. Is my main approach genetic?

Your main analyses should be based on genetic screens, Quantitative Trait Locus (QTL) mapping, genome re-sequencing or other genetic approaches. If the main analysis of a paper is in transcriptomics, imaging or biochemistry, this could be considered off scope (but fine if they are secondary analyses).

  1. Are the findings highly novel?

Your research should reflect a new method or finding that is really groundbreaking. Findings that just provide insight into a known process, are confirmatory or incremental do not meet Nature’s standards. If the finding is only new for a specific crop, that might also not be sufficiently novel.

  1. Is there a large user group for the data?

Bigger is usually always better; you want your research to apply to or benefit as many people as possible. If the crop you are studying is widely consumed like wheat, or you have a large study scope such as large-scale GWAS (Genome-Wide Association Study) analysis, that will impact many more people than if you are studying watermelons using single QTL mapping.

  1. Is this a very large or unique dataset?

You want large, high-quality datasets and analyses that are unique and other groups cannot easily repeat. Ideally this leads to a new approach in your field. Data that are open and easily available, and studies using the latest technologies also get priority.

  1. Do the findings provide biological insights?

You want people reading your study to learn something new about plant biology. Instead of merely reporting domestication patterns, you want something new about the mechanisms of evolution or adaptation. Editors look for comprehensive, molecular mechanistic insight into the processes studied.

  1. Is there evidence for crop improvement?

Editors prioritize studies with potential for crop improvement, especially in the context of climate change and food security. You want your research to be demonstrated in a crop plant, ideally in the physical plant and not in a model simulation.