A number of scientists from the International Maize and Wheat Improvement Center (CIMMYT) presented this week at the International Plant and Animal Genome Conference (PAG) in San Diego, USA.

PAG is the largest agricultural genomics meeting in the world, bringing together over 3,000 leading genetic scientists and researchers from around the world to present their research and share the latest developments in plant and animal genome projects. It provides an important opportunity for CIMMYT scientists to highlight their work translating the latest molecular research developments into wheat and maize breeding solutions for better varieties. 

To meet global food demand by 2050, agricultural production must increase by 60% – while at the same time minimizing harm to the environment. This is the process of sustainable intensification, recommended by world organizations like the United Nations and the EAT Lancet Commission as a key strategy for transforming our struggling global food system.

Genomics is crucial to sustainable intensification. By studying a plant or animal’s genetic architecture, researchers can better understand what drives crop or livestock productivity, quality, climate-resilience and resistance to pests and diseases. With this information scientists can speed up efforts to develop better varieties and stay ahead of climate- and disease- related threats.

• Wheat Scientist Philomin Juliana shared her findings on successfully identifying significant new chromosomal regions for wheat yield and disease resistance using the full wheat genome map. Juliana and her colleagues have created a freely-available collection of genetic information and markers for more than 40,000 wheat lines which will accelerate efforts to breed superior wheat varieties. She also discussed the value of genomic and high-throughput phenotyping tools for current breeding strategies adopted by CIMMYT to develop climate resilient wheat.  

• Principal Scientist Sarah Hearne discussed the smarter exploration of germplasm banks for breeding. Genebanks are reserves of native plant variation representing the evolutionary history of the crops we eat. They are a vital source of genetic information, which can accelerate the development of better, more resilient crops. However, it is not easy for breeders and scientists to identify or access the genetic information they need. Using the whole genebank genotypic data, long-term climate data from the origins of the genebank seeds and novel analysis methods, Hearne and her colleagues were able to identify elite genetic breeding material for improved, climate resilient maize varieties. They are now extending this approach to test the value of these data to improve breeding programs and accelerate the development of improved crops.

• Distinguished Scientist Jose Crossa discussed the latest models and methods for combining phenomic and genomic information to accelerate the development of climate-resilient crop varieties. He highlighted the use of the Artificial Neural Network — a model inspired by the human brain — to model the relationship between input signals and output signals in crops. He also discussed a phenotypic and genomic selection index which can improve response to selection and expected genetic gains for all of an individual plant’s genetic traits simultaneously.

• Genomic Breeder Umesh Rosyara demonstrated the Genomic selection pipeline and other tools at a workshop on the genomic data management and marker application tool Galaxy. The software, developed by the Excellence in Breeding (EiB) platform, integrates a suite of bioinformatics analysis tools, R-packages – a free software environment for statistical computing and graphics –  and visualization tools to manage routine genomic selection (GS) and genome wide association studies (GWAS) analysis. This allows crop breeders and genomic scientists without a programming background to conduct these analyses and create crop-specific workflows.

“PAG is currently the main international meeting touching both crop and livestock genomics, so it’s an invaluable chance to connect and share insights with research and breeding colleagues around the world,” said Hearne. 

“It’s also an important forum to highlight how we are linking upstream and field, and help others do the same.”

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

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.

In a letter to the editors* of Nature, John R. Porter, Chair of the Independent Steering Committee for the CGIAR Research Program on Wheat, and Tony Fischer, Honorary Research Fellow, CSIRO Plant Industry, Australia, and former Director of the CIMMYT Wheat Program, along with other leading crop scientists, question where functional plant genomics research is headed. Their letter stems from a recent Editorial about reported progress in the 11th Plant Genomes Meeting. Porter et al. ask “what has been gained from decoding the alphabet of gene sequences,” and “when will the promise of genetics be translated into higher yields in farmers’ fields?”

“The best and most relevant research for crop science begins and ends in the field,” say Porter et al.

They call for an interdisciplinary approach aligning functional genomics with crop agronomy, while keeping food security in clear sight and contributing to the yield growth in crop production required to feed billions more consumers in coming decades.

* Full access requires a subscription to Nature or purchase of the letter.