Posts Tagged ‘DGGW project’

Harnessing the potential of state-of-the-art genomic technologies for accelerating the rate of genetic gain in wheat

This blog by Philomin Juliana was originally published on the Borlaug Global Rust Initiative website.

Genomic breeding technologies offer exciting opportunities for wheat improvement amidst escalating challenges like changing climates, unpredictable temperatures, reduced precipitation and biotic stresses. Recognizing the need for accelerating the rate of genetic gain in wheat, the Delivering Genetic Gain in Wheat and the USAID Feed the Future projects have contributed extensively to the phenotyping and genotyping of an impressive number of 74,403 CIMMYT wheat breeding lines, generating more than a million phenotyping datapoints and 3 billion marker datapoints. These big datasets have been leveraged for evaluating state-of-the-art genomic technologies like genomic selection, genome-wide association mapping, and genomic fingerprinting that have empowered the CIMMYT wheat breeding program to efficiently deliver high-yielding, climate resilient and disease resistant varieties.

Genomic selection, a genomics-based selection strategy where genomic-estimated breeding values obtained from genome-wide molecular markers are used for the selection of individuals has gained burgeoning interest in recent years and is advocated as an approach that can dramatically accelerate genetic gains and change the role of phenotyping in breeding. Since it can be beneficial for CIMMYT and other wheat breeding programs, particularly in developing countries that are constrained in their ability to evaluate a large number of breeding lines due to limited resources, we have done a comprehensive evaluation of genomic selection for 35 key traits in wheat evaluated by CIMMYT and national partners.

Our results have provided strong evidence that genomic selection will be a very powerful tool for end-use quality related traits like alveograph, mixing time, grain protein, flour yield, flour sedimentation, loaf volume etc. and some diseases, that were well predicted using historic training populations. Hence, genomic estimated breeding values for these traits have been routinely integrated into selection decisions and selections have been scaled up to un-phenotyped early-generations using predicted values. This has led to a paradigm shift in integrating genomic breeding tools into CIMMYT’s wheat breeding pipeline and has resulted in better selection efficiency and high phenotyping cost-savings to the program.

We have also explored several genomic selection implementation scenarios for grain yield and determined the prospects of using genomic selection for minimizing the number of lines, years and sites tested by borrowing information from relatives, correlated years and sites. For this, we leveraged a large dataset of 61,064 grain yield observations from 1,974 yield trials evaluated by CIMMYT and national partners at 100 locations in 34 countries including Afghanistan, Algeria, Angola, Argentina, Bangladesh, Canada, Chile, China, Egypt, Ethiopia, Greece, India, Iran, Iraq, Libya, Mexico, Morocco, Myanmar, Nepal, Nigeria, Pakistan, Paraguay, Portugal, South Africa, Spain, Sudan, Taiwan, Tanzania, Tunisia, Turkey, Ukraine, Venezuela, Zambia and Zimbabwe. We also applied a quantitative genetics framework to explore the relationships between grain yield predictabilities and estimated heritabilities, variance components, phenotypic and genetic correlations for grain yield evaluated in different environments, all of which provided substantial insights into the challenges of predicting grain yield and the prospects for designing future genomic selection schemes.

We also performed a large genome-wide association study that led to a significant breakthrough in understanding the genetic-architecture of key traits like phenology, plant height, lodging, resistance to rusts and other foliar diseases, grain color, kernel weight, dough strength, bread-making quality, protein content and grain yield in wheat. We have identified hundreds of significant marker-trait associations and delineated 142 unique linkage-based QTLs, among which 55.6% were novel. One of the extremely intriguing and novel co-locations identified in our study was the association of the 2NS translocation from Aegilops ventricosa with grain yield in 10 different environments, stem rust seedling resistance to many races, stripe rust in Mexico, wheat blast, and lodging, demonstrating its remarkable value for wheat breeding. We also anchored about 542 significant trait-associated markers and 118 previously reported genes in proximity to the significant markers onto a powerful reference phenotype-genotype map aligned to the refence genome of bread wheat, which is a valuable resource providing new opportunities for accelerating genomics-assisted wheat breeding through a targeted selection of desired regions.

We have fingerprinted 44,624 wheat lines for 195 traits-associated markers, generating over 7.6 million data-points, which is a phenomenal resource to the global wheat community for enhancing productivity and stress-resilience in wheat. The fingerprinted panel comprises several key varieties cultivated worldwide, parents from CIMMYT’s crossing blocks 2009-2018 and is a quantum leap in understanding the genetic basis of traits in superior varieties. For example, a benchmark high-yielding CIMMYT-derived Mexican variety, BORLAUG100 F2014 was found to be rich in grain yield favorable alleles and a key stem rust QTL against the Ug99 lineage was traced back to old Kenyan (Kenya Fahari, Kenya Swara) and Ethiopian (FH6-1-7) varieties.

Furthermore, we also examined the marker allele frequency dynamics for key traits over 15 years to characterize the role of selection at CIMMYT in shaping patterns of allelic variation over time. While there was a spectacular increase in favorable allele frequencies for many traits over years due to selection, the results also emphasized the need for a continued effort to introduce novel sources of favorable alleles and the importance of integrating genomic tools in achieving accelerated enrichment of favorable alleles. Overall, our research has facilitated extending the frontiers of genomics-assisted breeding in wheat and will be very beneficial for future diagnostic marker development, gene discovery, marker-assisted selection and genomic selection in wheat.

Philomin Juliana’s 5 May 2020 seminar is here.

Borlaug Global Rust Initiative announces 2020 Women in Triticum prize winners

2020 Women in Triticum Award winners. Graphic: BGRI

The Borlaug Global Rust Initiative (BGRI) announced its 2020 cohort of Jeanie Borlaug Laube Women in Triticum (WIT) awardees honoring next-generation women scientists and mentors who have worked to increase gender parity in agriculture.

Five women wheat scientists from China, Ethiopia, Germany, India and Uruguay were named WIT Early Career Award winners, and a scientist in Australia was recognized with the 2020 WIT Mentor Award. The winners will be celebrated May 21 from 10-11 a.m. at the virtual event “The Changing Face of Leadership and Research in Wheat.” The event includes a keynote from World Food Prize president Barbara Stinson and a panel discussion with former WIT award winners.

“The future of wheat science depends on innovative, enthusiastic researchers,” said Maricelis Acevedo, associate director for science of the Delivering Genetic Gain in Wheat (DGGW) project and faculty member in Cornell University’s Department of Global Development.

“We are thrilled to honor these incredible scientists with a WIT award and continue the tradition of recognizing the next generation of top-notch scientists and the people who mentor them,” she said.

The BGRI is an international consortium based at Cornell with the goal to protect the world’s wheat supplies. The global network of scientists and farmers work to reduce the world’s vulnerability to fungal rust diseases in wheat and enhance global productivity to withstand future threats to the crop.

With this cohort, the BGRI has recognized 55 early career award winners since 2010.

“Building capacity within the scientific community by encouraging and supporting the training of young women scientists has always been one of the BGRI’s key goals,” Acevedo said. “Over the last decade, these scientists have emerged as leaders across the wheat community. We sincerely thank all the mentors who have supported these women’s efforts.”

The WIT Early Career Award provides early career women working in wheat with the opportunity for additional training, mentorship, and leadership opportunities. The WIT Mentor Award, first awarded in 2011, recognizes the efforts of men and women who have played a significant role in shaping the careers of women working in wheat and demonstrated a commitment to increasing gender parity in agriculture.

Five 2020 WIT Early Career Winners

Anna Elizabeth Backhaus, from Germany, has been interested in wheat genetics since she was 12 years old. A second-year PhD student at the John Innes Centre, where she is supervised by Cristobal Uauy and Richard Morris, Backhaus focuses on the genetic network in control of early spike development and trying to understand how developmental decisions are encoded in the wheat genome. As part of her project, she is performing RNA-sequencing on sections of the young wheat spike using single cell technologies, and using this approach to identify genetic networks in control of spikelet number and grain number, two interlinked traits that control final plant yield. She is phenotyping these yield traits in the Watkins collection of about 800 wheat landraces to identify novel genes for spike traits. Backhaus studied plant sciences at the University of East Anglia (Bsc) and University Bonn (Msc). She has also worked at the Max Planck Institute in Cologne and ICARDA.

Bharati Pandey, from India, is working as a scientific officer in the Bioscience Group, Bhabha Atomic Research Centre (BARC), Mumbai, Maharashtra, India. In 2015 she completed her doctoral degree from Birla Institute of Technology. In her doctoral thesis “Structural and functional analysis of wheat genome based on expressed sequence tags in relation to abiotic stress,” she worked on identifying and validating single nucleotide polymorphism (SNP) markers in abiotic stress-responsive genes, and identifying stress-induced microRNAs in wheat. As a Research Fellow at the ICAR-Indian Institute of Wheat and Barley Research Institute (IIWBR), she contributed to wheat genomics research by identifying and analyzing simple sequence repeat dynamics in three different rust fungi: stem, leaf and stripe rust. Pandey was also associated with the development and validation of microsatellite markers for wheat fungal pathogens including Karnal bunt and loose smut. Bharati and her team have designed and developed an Indian wheat database which allow users to retrieve information about molecular markers linked to rust resistance genes.

Yewubdar Ishetu Shewaye, from Ethiopia, works as a wheat breeder for the Ethiopian Institute of Agricultural Research (EIAR), at the Debre Zeit Agricultural Research Center. Her main objectives are to empower the farming community in Ethiopia and other developing nations in the fight against wheat rust diseases, to reduce production costs for resource-poor farmers, and to increase yield. She completed her BS in plant science in 2010 at Madawalabu University, Ethiopia, and her MS at Hawassa University, where she focused on the identification and characterization of stripe rust resistance genes in wheat using conventional and molecular marker approaches. This work involved associating phenotypic data with genotypic data to identify rust resistance genes in wheat genotypes, and identifying diagnostic molecular markers. Shewaye is deeply interested in research areas such as screening and characterizing wheat genotypes for rusts, association mapping for rust resistance, identifying diagnostic markers, understanding the mechanisms of host-pathogen interactions, selecting the best parent combinations for crosses to pyramid resistance genes, and mining wheat germplasm to discover more durable rust resistance genes that will be beneficial to the whole wheat breeding community.

Paula Silva, from Uruguay, received her BS at the School of Science of Universidad de la Républica, and her MS from the School of Agronomy, in Uruguay. Her master’s thesis focused on breeding wheat for adult plant resistance against leaf rust. Her MS advisor, Dr. Silvia Germán, instilled in her a true passion for wheat breeding for disease resistance. She was further mentored at CIMMYT by Dr. Sybil Herrera-Foessel. In 2015, while studying molecular tools for characterizing wheat rust resistance genes at the Plant Breeding Institute of the University of Sydney, Dr. Urmil Bansal encouraged Silva to pursue a PhD, a journey that has led Silva to study genetics at Kansas State University with Jesse Poland. There, she works on breeding for barley yellow dwarf and blast resistance by characterizing wild relatives of wheat to search for novel sources of resistance. In 2019, she was appointed at INIA to lead part of the disease resistance breeding program as well as coordinate the Precision Wheat Phenotypic Platform for Wheat Diseases in collaboration with CIMMYT.

Peipei Zhang, from China, completed her PhD degree in Plant Pathology in 2019 at Hebei Agricultural University, where she acquired her BS and MS degrees, and now works as a researcher. During her PhD from 2018-19, she studied under Dr. Sridhar Bhavani and Professor Caixia Lan in Ravi Singh’s research group in CIMMYT, participating in systematic breeding and research methods. For the last decade, Zhang’s research has focused on wheat rust genetics, specifically on gene discovery and QTL mapping resistance to both leaf rust and stripe rust using bi-parental mapping populations, identification of leaf rust resistance genes in wheat cultivars using genome-wide association mapping, and map-based gene cloning for leaf rust resistance gene. She has identified potentially new genes and the closely linked markers of these genes which can be used in marker assisted selection and wheat breeding. Zhang hopes that she will be able to transform her research outcomes to benefit millions of smallholder farmers in China and other countries to reduce wheat loss due to rust diseases.

The WIT Mentor Award

The 2020 WIT Mentor awardee is Evans Lagudah, a Chief Research Scientist at CSIRO, Australia, a Fellow of the Australian Academy of Science and an adjunct professor at the University of Sydney. Lagudah’s research interests cover basic studies on the molecular basis of multi-pathogen resistance genes, cloning of cereal immune receptors and genomic analyses/manipulation of targeted disease resistance traits. Among his research highlights are defining the molecular basis of adult plant rust resistance genes which represent novel classes of plant defense genes that function broadly in cereal crops against multiple pathogens. Lagudah operates at the interface between agriculture and fundamental molecular research, and his research ensures the rapid translation of new molecular discoveries into practical agriculture in the global grains industry. Lagudah continues to train and mentor PhD students, postdoctoral researchers and early- and mid-career scientists. He is a regular contributor to the West African Centre for Crop Improvement which trains the next generation of plant breeders in sub-Saharan Africa. He is among the world’s top 1% of most influential scientists as ranked by “Clarivate Analytics Highly Cited Researchers List” which identifies scientists who have demonstrated significant influence during the last decade.

More information about the winners can be found at the BGRI website.

Smarter deployment of disease-resistance genes critical for safeguarding world’s food supplies

This story by Matt Hayes was originally posted on the Borlaug Global Rust Initiative website.

Maricelis Acevedo inspects wheat samples with Murugasamy Sivasamy at the Indian Agricultural Research Institute, Regional station, Wellington. Photo: Matt Hayes / Cornell

In the worst years of the rust disease epidemic that decimated North American wheat fields in the 1950s, fungal spores riding wind currents across the continent reached into the sextillions — that’s a number with 21 zeros.

Severe wheat disease epidemics produce staggering numbers of spores containing incredible genetic diversity — and incalculable risks to global food supplies. If fungal spores encounter even a single susceptible wheat variety, natural selection positions the pathogen to take hold and proliferate, releasing more rounds of spores and spreading its own virulence genes across entire populations.  

Wheat breeders face a daunting task trying to defend against such a relentless barrage of evolving pathogens. In the battle, scientific ingenuity confronts biological innovation: wheat varieties that contain single disease-resistant genes can be easily overrun by rapidly evolving spores.

To safeguard food supplies and ensure durable disease resistance in wheat, scientists must embrace a globally integrated strategy that deploys resistant genes in a coordinated way, according to Maricelis Acevedo, associate director of science for the Delivering Genetic Gain in Wheat (DGGW) project.

“We need to be smart about gene deployment,” Acevedo said at the All India Wheat and Barley meeting Aug. 25 in Indore, Madhya Pradesh.

“If we don’t change our mentality, we risk reliving the worst horrors of the past and the widespread hunger that results when rust diseases wipe out the wheat supply,” she said.

Acevedo cautioned that the release of susceptible or vulnerable varieties at a national level weakens wheat resistance on a global scale. Varieties with only one major effective resistance gene, which may appear adequate to withstand disease pressure in a field trial, are at increased risk to disease pressure when released into circulation. Varieties with only a single resistance gene risk tainting an otherwise effective gene for everybody and imperiling the wheat crop around the world.

Varieties with five to six disease-resistance genes make it mathematically unlikely that spores will have the genetic ability to defeat the resistance. Minnesota scientists in 1985 calculated that the probability a pathogen contains virulence to all six major genes is more than four times greater than the number of spores released in a single year in the US under stem rust epidemic levels. 

To reduce the chances of selection in pathogen populations, often caused by major genes, breeders exploit combinations of genes that may provide partial resistance to a broader number of races.

Ravi Singh gives his presentation at the All India Wheat and Barley meeting in Indore. Photo: Matt Hayes / Cornell

While only releasing varieties with stacked genes is the most prudent breeding strategy, there are factors that incentivize shortcuts, according to Acevedo. Plant breeders in some countries are often promoted based on the numbers of varieties released — not for their long-term usefulness. And, in some countries, there are political incentives to provide farmers with new varieties year after year rather than release fewer, but more durable varieties.

Teams of plant breeders employed by National Agricultural Research Systems in countries around the world develop improved crop varieties. Many wheat breeders receive lines from CIMMYT, the International Maize and Wheat Improvement Center, which national scientists then cross with local varieties to adapt to local conditions. National scientists also breed their own from existing local varieties. The process to develop and release any new variety can take up to ten years and up to 15 years to make it to farmers fields.

 “A way to make varieties more durable for resistance to rusts is to use marker-assisted introgression of multiple resistance genes using speed breeding in recent varieties or promising varietal candidates, which also possess some of the known durable adult-plant resistance genes,” said Ravi Singh, distinguished scientist and head of Global Wheat Improvement at CIMMYT. The All India Wheat and Barley meeting was co-sponsored by CIMMYT and the International Center for Agricultural Research in the Dry Areas (ICARDA).

The Borlaug Global Rust Initiative (BGRI) was established at Cornell to reduce the world’s vulnerability to stem, yellow and leaf rusts of wheat. Acevedo said the BGRI’s main impacts have resulted from scientific collaboration, commitment to pathogen monitoring, and development and deployment of rust resistant varieties. The BGRI established a Gene Stewardship Award in 2012 to encourage the release of varieties with complex and diverse disease resistance.

In 2018, the Indian Council of Agricultural Research (ICAR), in New Delhi, India, and associated institutions, received the BGRI Gene Stewardship Award in part for replacing susceptible wheat varieties with resistant varieties.

Those efforts have proven successful: on Aug. 24, in a reported delivered at the All India Wheat and Barley meeting, ICAR announced that India for the first time produced more than 100 million tons of wheat in a year.

DGGW is funded by the Bill & Melinda Gates Foundation and UK Aid by the British people.