Tag: genetic gains

Network develops optimized breeding pipelines for accelerated genetic gains in dryland crops

Written by Julian Bañuelos-Uribe on March 13, 2024. Posted in Blogs.

Participants from the breeding pipelines optimization meeting at the Safari Park Hotel, Nairobi, Kenya. (Photo: CIMMYT)

Partners from the Africa Dryland Crop Improvement Network (ADCIN) from 16 institutes in Africa came together for a four-day workshop in Nairobi, Kenya, during 19-22 September 2023, to critically review and optimize breeding pipelines for newly formed breeding programs. The meeting provided an opportunity for multidisciplinary scientists to better understand each other’s significant roles and contributions in achieving optimized breeding pipelines.

Nine female and 28 male scientists working across 14 countries made up the group of experts at the workshop, which included crop breeders, quantitative geneticists, crop protection scientists, genomics experts, and data analysts. Together, they collaboratively developed, assessed, and refined the various stages and processes of breeding pipelines. Most participants were crop breeding leads from the national agricultural research and extension systems (NARES) and CGIAR Research Centers, as well as members of the Breeding Informatics Working Group A, the first of its kind as a strategic leadership group of crop breeding experts.

The workshop sponsored by CIMMYT focused on improving genetic gains across six crops: chickpea, pigeon pea, finger millet, pearl millet, groundnut, and sorghum. The workshop was organized by CIMMYT experts, Abhishek Rathore, breeding data and informatics expert, Keith Gardner, quantitative geneticist, and Roma Rani Das, biometrician, and quantitative geneticist experts from the CGIAR Accelerated Breeding Initiative, Dorcus Gemenet and Christian Werner.

Multidisciplinary expertise in action

Under the guidance of the Associate Program Director and the Breeding Lead for Dryland Crops, Harish Gandhi, participants engaged in an array of advanced genetic approaches, statistical techniques, and quantitative concepts presented by the participating experts from CIMMYT and CGIAR Accelerated Breeding.

Each breeding program schema was reviewed from detailed quantitative genetic aspects and agreed project criteria, including choosing parents, the optimum number of parents, crossing designs, the number of generations, methodologies, testing strategies, and analytical frameworks. The group deliberated on the breeding strategies tailored for respective market segments and target product profiles to further improvise and optimize breeding pipelines to enhance the programs’ efficiency.

Agreements were reached on the number of founder parents, the number of crosses and progenies in various generations, line development method, evaluation and testing strategy, time until parental selection (cycle time), marker assisted selection (MAS), genomic selection (GS) strategy, making routine use of molecular markers for QA/QC. The team also finalized the breeding strategies tailored for respective market segments and target product profiles to further improvise and optimize breeding pipelines aimed at higher genetic gains.

In coordination with crop breeders from CIMMYT, the NARES dryland crop breeding leads presented the current schematics of breeding pipelines for both line and hybrid breeding, highlighting the market segment, Target Product Profile (TPP) and Target Product Environment (TPE).

The breeding informatics team also showcased the upcoming Dryland Crops Trial Information System dashboard, a one stop shops to capture, host, and provide information on the trials organized by the network’s NARES breeders across Africa.

Collaboration for genetic gains

Crop breeding experts discuss strategies for breeding pipeline optimization. (Photo: CIMMYT)

The value of partnership working was frequently highlighted by the speakers. Michael Quinn, lead of the CGIAR Accelerated Breeding Initiative, gave an overview of the initiative’s objectives and high-level goals in 2023, emphasizing the need to foster dialogue and alignment across breeding teams. He also underlined the importance of such hand-in-hand meetings for fostering cross-regional and cross-institute learning.

“Plant breeding has always been at the center stage of crop improvement, but it has become more and more important lately, and there is a need to bring more collaborative efforts across disciplines to realize higher genetic gains in our breeding programs,” said Kevin Pixley, Dryland Crops program director and Wheat program director during his virtual presentation.

“Interaction with the breeding leads from CIMMYT and the NARES in East and Southern Africa (ESA) and West and Central Africa (WCA) and other experts helped in cross learning from the advanced breeding programs,” said Maryam Dawud, plant breeder at the Lake Chad Research Institute in Nigeria. Such workshops are needed for developing optimized breeding pipelines, and we will need more such in-person workshops on advanced data analysis.”

Next steps for dryland crops

During the workshop, network partners came up with an optimized breeding pipeline incorporating advanced quantitative genetic and statistical principles aligned with the latest scientific advancements and market demands. The group further developed a six-month actionable plan split by region to address common bottlenecks across the crops, such as capacity building in data analysis, modernizing digital infrastructure, training and enhancing human capacity in the use of equipment, and managing staff turnover.

All these deliberations provided the network partners with better insights and hands-on-experience to design their breeding pipeline, outlining specific steps, responsibilities, and timelines for implementing the identified optimizations. This preparatory work will ensure there is a targeted and coordinated effort toward pipeline enhancement and accelerated genetic gain for dryland crops in the region.

Happy Daudi, head, Groundnut Research Program at Tanzania Agricultural Research Institute (TARI), who participated in the workshop, stated, “Bringing in multidisciplinary experts provided a great opportunity to integrate various concepts of population improvement, product development, and deploying advanced statistical approaches for optimizing our breeding pipeline for achieving higher genetic gains, and accelerated variety turn over.”

Thank you to the Bill and Melinda Gates Foundation, the United States Agency for International Development (USAID), and CGIAR, for their generous funding which made this workshop possible.

Advancing wheat breeding through rapid marker-selectable trait introgression

Written by Julian Bañuelos-Uribe on February 22, 2024. Posted in Blogs.

The experimental research station in Toluca, Mexico. (Photo: S. Herrera/CIMMYT)

In the ever-evolving field of agriculture, AGG-WHEAT is leading a transformative approach through rapid marker-selectable trait introgression in wheat breeding programs. This method aims to streamline the process of integrating desirable traits into various genetic backgrounds.

At the core of AGG-WHEAT’s strategy is the establishment of a centralized marker-selectable trait introgression pipeline. This initiative seeks to facilitate the transfer of specific genes from a centralized source into various genetic backgrounds within plant breeding programs. Molecular markers play a crucial role in efficiently identifying and selecting target traits.

The merits of a centralized trait introgression pipeline extend beyond convenience. This approach ensures a more uniform and controlled transfer of genetic material, enhancing the precision of trait introgressions across diverse breeding lines. Molecular markers streamline the selection process, improving the accuracy of desired trait incorporation into wheat varieties.

Speed breeding facilities in Toluca, Mexico

AGG-WHEAT’s marker-selectable trait introgression pipelines are implemented at the speed breeding facilities located at the CIMMYT research station in Toluca, Mexico. These facilities serve as the incubators for innovation, where new selection candidates are evaluated based on various criteria. The decision-making process involves an expert panel comprising geneticists, trait specialists, and breeders. This panel annually determines the selection candidates, considering factors such as trait demand, genetic diversity, evidence of Quantitative Trait Loci (QTL) effects, selection efficiency, and available funding.

The decision-making process involves a multifaceted evaluation of potential selection candidates. Documented trait pipelines and product profiles guide decision-making to ensure alignment with the overarching goals of wheat breeding programs. Considerations include the need for phenotypic variation and the existence of limited genetic diversity for the trait under consideration.

The decision-making process also explores existing in-house or external evidence of QTL effects and the underlying gene mechanisms. Selection efficiency, contingent on the availability of accurate molecular markers and a known purified donor parent, further refines the pool of potential candidates. Established phenotypic protocols for product testing and the crucial element of available funding complete the decision-making criteria.

Achievements

In a significant step towards innovation, the products of the first marker-selectable trait introgression pipelines entered yield trials in 2023. This marks a transition from conceptualization to tangible impact, reflecting the efficacy of AGG-WHEAT’s approach. A total of 97 F5-lines, cultivated through the marker-assisted backcross (MABC) scheme, now grace the fields.

These lines carry novel genes associated with fusarium head blight and rust resistance, derived from wheat genetic resources and wild relatives. The choice of these traits underscores AGG-WHEAT’s commitment to addressing challenges faced by wheat crops, ensuring improved resilience and sustainability in the face of evolving environmental conditions.

The success of these initial trait introgression pipelines represents more than a scientific achievement; it marks a pivotal moment in the trajectory of wheat breeding. The 97 F5-lines, standing as testaments to enhanced resistance traits, are poised to make a transition into mainstream breeding pipelines. This marks the commencement of a broader dissemination strategy, where these lines will be distributed for testing at National Agricultural Research and Extension Services (NARES).

The journey from the experimental fields to mainstream adoption involves a meticulous process. These lines, having undergone rigorous evaluation and selection, now hold the potential to catalyze changes in commercial wheat varieties. The lessons learned from their cultivation will shape future breeding strategies and contribute to the resilience of wheat crops in diverse agricultural landscapes.

AGG-WHEAT’s lasting impact

AGG-WHEAT’s marker-selectable trait introgression stands as an innovative approach in wheat breeding. The centralized approach, the strategic use of molecular markers, and the meticulous decision-making process exemplify the commitment to excellence and precision. The journey from concept to reality—marked by the entry of 97 F5-lines into yield trials—signals a new era in wheat breeding.

As these lines traverse from experimental fields to mainstream adoption, they carry the promise of transforming the landscape of commercial wheat varieties. AGG-WHEAT’s lasting impact goes beyond the scientific realm; it extends to the fields where farmers strive for sustainable and resilient wheat crops. In the tapestry of agricultural progress, AGG-WHEAT has woven a thread of innovation that holds the potential to redefine the future of wheat cultivation.

Enhancing wheat breeding efficiency in South Asia through early germplasm access

Written by Julian Bañuelos-Uribe on February 19, 2024. Posted in Blogs.

In the dynamic landscape of wheat breeding, early access to germplasm emerges as a strategic catalyst for accelerating variety turnover and meeting the evolving challenges faced by farmers in South Asia. Since its inception, the Accelerating Genetic Gains in Maize and Wheat (AGG) project has pioneered new tools to optimize the wheat breeding process. One such tool, the efficient and low-cost 3-year breeding cycle, has been fine-tuned in Mexico, using the Toluca screenhouse and field advancement in Obregón, laying the groundwork for faster variety turnover.

The inaugural set of lines generated through this enhanced breeding cycle is already undergoing Stage 1 trials in the Obregón 2023-24 season. However, the innovation doesn’t stop there; to expedite the variety release process and garner robust data from the Target Population of Environments (TPE), Stage 2 lines are being rigorously tested at over 20 sites in South Asia through collaboration with National Agricultural Research and Extension Services (NARES) partners. In the seasons spanning 2021-2024, a total of 918 Stage 2 lines underwent rigorous trials, aiming to provide early access to improved wheat lines for testing and release by NARES and establish a genetic correlation matrix between Obregón selection environments and diverse sites across South Asia.

These extensive trials serve a dual purpose. Firstly, they facilitate early access to improved wheat lines for testing and release by NARES, bolstering the agricultural landscape with resilient and high-yielding varieties. Secondly, they contribute to the establishment of a genetic correlation matrix between the selection environments in Obregón and the diverse sites across South Asia. This matrix becomes a guiding compass, aiding in selecting the most promising lines for broader TPEs in South Asia and beyond.

Transformative impact on wheat varieties in South Asia

Through the support of our partners and funders from the Bill & Melinda Gates Foundation, the Foundation for Food and Agriculture Research (FFAR), the UK Foreign, Commonwealth & Development Office (FCDO), and the US Agency for International Development (USAID), great achievements have been recorded throughout the region. India, a prominent player in wheat cultivation, stands as a testament to the transformative impact of early access to advanced lines. The top three varieties, namely DBW187, DBW303, and DBW 222, covering over 6 million hectares, trace their roots to CIMMYT varieties. Adopting a fast-track approach through early-stage testing of these advanced lines at BISA sites in India, supported by the Delivering Genetic Gain in Wheat (DGGW) project, facilitated the release of these varieties two years ahead of the regular testing process. This expedited varietal release was complemented by the innovative early seed multiplication and dissemination approach introduced by the Indian Council of Agricultural Research (ICAR). Recent additions to this accelerated channel include varieties such as DBW 327, DBW 332, DBW 370, and 371, promising further advancements in wheat cultivation.

Pakistan

In Pakistan, the early access to advanced lines has been a catalyst for releasing high-yielding, climate-resilient, and nutritious wheat varieties. In 2023 alone, 12 new varieties were released, with the renowned ‘Akbar-19,’ introduced in 2019, covering a substantial 42% of cultivated land in Punjab. Data released by the Ayub Agricultural Research Institute (AARI), shows that this variety, known for its high yield potential, disease resistance, and enriched zinc content, has significantly contributed to increased wheat production in the region.

Nepal

Guided by policy interventions in the national varietal testing process, Nepal has experienced the fast-track commercialization of high-yielding and climate-resilient wheat varieties. Allowing multilocation testing of CIMMYT nurseries and advanced elite lines, Nepal released six biofortified zinc wheat varieties in 2020. The expeditious seed multiplication of these released and pre-release varieties has facilitated the rapid spread of new and improved wheat varieties.

The strategic utilization of early access to wheat germplasm in South Asia holds promise in accelerating variety turnover, offering farmers resilient and high-performing wheat varieties. Collaborative efforts between research institutions, government bodies, and international organizations exemplify the power of innovation in transforming agriculture. With an ongoing dedication to refining breeding cycles, expanding testing initiatives, and fostering collaboration, the AGG project contributes to building a sustainable and resilient agricultural future in South Asia. Early access to wheat germplasm emerges as a practical approach in this scientific endeavor, laying the foundation for a climate-resilient and food-secure region. The successes witnessed in India, Pakistan, and Nepal underscore the transformative potential of this approach, offering tangible benefits for agricultural communities in South Asia and beyond. In navigating the complexities of a changing climate and growing food demand, early access to wheat germplasm remains a pragmatic ally, propelling agricultural innovation and resilience to new heights.

Building capacities for advanced modern breeding programs in Africa

Written by Susan Otieno on June 14, 2023. Posted in News.

In December 2022, more than 40 scientists from African National Agricultural Research Institutes (NARI) and Small and Medium Enterprise (SME) seed companies received training on the design and implementation of modern maize breeding programs.

The training, explains Yoseph Beyene, project leader in the Accelerating Genetic Gains (AGG) – Maize project, was designed to improve maize breeders’ knowledge of the most advanced technologies and methodologies in order to increase genetic gains in their respective breeding programs. It was supported by AGG-Maize and the CGIAR Accelerated Breeding Initiative (ABI) and formed part of ongoing efforts to modernize NARI breeding programs under AGG-Maize.

Yoseph Beyene, Accelerating Genetic Gains-Maize Project leader, makes introductory remarks at the start of the Senior Breeders Training in Nairobi, Kenya. (Photo: Susan Otieno/CIMMYT)

Over the course of five days in Nairobi, Kenya, participants from 13 countries where AGG-Maize is implemented worked to develop their skills in the use of new technologies and approaches to improving genetic gains and breeding efficiencies. Topics covered included the prioritization of market segmentation and product profile development, application of quantitative genetics principles in maize breeding, seed production research, improved designs for regional on-farm trials, and much more.

“The training was an eye opener supported by detailed explanations on applications of diverse research methodologies in maize breeding,” said Isiah Aleri, a research assistant for the International Maize and Wheat Improvement Center’s (CIMMYT) Maize Program in Kenya. “I met teams who had different views on some breeding techniques, but later received guided explanations from trainers on why certain standards and requirements are set for effective decision making.”

Veronica Ogugo, a research associate in the same CIMMYT program, agreed saying: “It was very educative and in-depth in all the areas that were covered by the different specialists. The best part was that each of the components complimented one another.” She added that the training also offered a good opportunity for interaction with other experts.

B.M. Prasanna, CIMMYT Global Maize Program director, speaks at the Senior Breeders Training in Nairobi, Kenya. (Photo: Susan Otieno/CIMMYT)

What and whom to breed for

In his opening remarks at the training, B.M. Prasanna, Global Maize Program director at CIMMYT, noted the need for efficient use of limited resources, and encouraged scientists to work smartly, for instance, by leveraging available germplasm across phenotyping networks from other regions to diversify germplasm base for increased genetic gains. He emphasized the importance of clearly determining market segments and developing product profiles that have clear objectives, as well as the key traits to be considered, such as tolerance to drought, heat, and pests and diseases like fall armyworm.

Prasanna highlighted zinc as an example of an important feature to focus on, pointing out the micronutrient’s vital role in mental well-being and its immune boosting properties, especially in children. “Different geographies have different ways of using maize,” he explained. “In general, maize provides 15-56% of total calorie intake in the rain-fed tropics, hence its importance for improving not only smallholder farmer incomes but also food and nutrition security.”

He also outlined how important partnerships with national programs and seed companies are for achieving the fullest impact of CIMMYT’s work. “The strong regional collaborative maize breeding and seed systems is fundamental for impact,” he said. “It is also the reason for arguably the largest public sector maize germplasm testing network in the Global South, in rain-fed stress-prone tropical environments.”

AGG-Maize project registers impressive progress

Written by Susan Otieno on October 4, 2022. Posted in News.

Participants of the AGG Maize Mid-Term Review and Planning Meeting at CIMMYT’s Maize Lethal Necrosis Screening Facility in Naivasha, Kenya. (Photo: Dokta Jonte Photography)

The Accelerating Genetic Gains in Maize and Wheat (AGG) Project, which is halfway through its implementation, continues to register impressive achievements. At a meeting focusing on the project’s Maize component, held in Nairobi during July 25-28, B.M. Prasanna, Director of the Global Maize Program at the International Maize and Wheat Improvement Center (CIMMYT), highlighted the project’s major achievements in the opening session.

“One of the most important achievements of this project is increasing use of powerful tools and technologies to increase genetic gains in maize breeding pipelines in Africa,” said Prasanna. He noted that the AGG partners are showing keen interest in doubled haploid-based maize breeding. Prasanna pointed out that currently work is ongoing to produce third-generation tropicalized haploid inducers which, in combination with molecular markers, will support accelerated development of improved maize germplasm, a key objective of the AGG Project.

Prasanna also pointed out a significant increase in adoption of stress-tolerant maize in Africa – from less than half a million hectares cultivated under stress tolerant maize varieties in 2010, to 7.2 million hectares currently in 13 African countries, benefitting 44.5 million people. He explained that drought-tolerant maize is not only a productivity enhancing tool but also an innovation for improving the welfare of farmers. “It reduces the probability of crop failure by 30 percent and provides an extra income to farmers at a rate of approximately $240 USD per hectare, equivalent to about nine months of food for a family at no additional cost,” he said, adding that the essence of research is taking improved genetics to farmers and impacting their lives.

He noted there is remarkable progress in maize varietal turnover in sub-Saharan Africa, pointing out particularly efforts in Ethiopia, Uganda, Zambia and Zimbabwe, where old maize varieties, some dating as far back as 1988, have been replaced with newer climate-resilient varieties. Prasanna highlighted the need to engage with policy makers to put in place appropriate legislation that can accelerate replacement of old or obsolete varieties with improved genetics.

Prasanna stressed on the importance of rapid response to transboundary diseases and insect-pests. CIMMYT has established fall armyworm (FAW) screening facility at Kiboko, Kenya, and that more than 10,000 maize germplasm entries have been screened over the last three years. He applauded South Sudan for being the first country in sub-Saharan Africa to recently release three CIMMYT-developed FAW-tolerant hybrids. He said CIMMYT’s FAW-tolerant inbred lines have been shared with 92 institutions, both public and private, in 34 countries globally since 2018.

Kevin Pixley, CIMMYT Global Genetic Resources Director and Deputy Director General, Breeding and Genetics, encouraged the participants to continuously reflect on making innovative contributions through the AGG project, to serve smallholder farmers and other stakeholders, and to offer sustainable solutions to the food crisis that plagues the world.

B.M. Prasanna addresses partners at the KALRO Kiboko Research station in Kenya during an AGG field visit. (Photo: Dokta Jonte Photography)

Synergies across crops and teams

Pixley pointed out that though the meeting’s focus was on maize, the AGG Project has both maize and wheat components, and the potential for learning between the maize and wheat teams would benefit many, especially with the innovative strides in research from both teams.

Pixley referenced a recent meeting in Ethiopia with colleagues from the International Institute of Tropical Agriculture (IITA), the International Center for Tropical Agriculture (CIAT) and CIMMYT, where discussions explored collaboration among CGIAR centers and other stakeholders in strengthening work on cowpea, chickpea, beans, sorghum, millet and groundnut crops. He noted that maize, wheat and the aforementioned crops are all critical in achieving the mission of CGIAR.

“CIMMYT has been requested, since August of last year, by CGIAR to initiate research projects on sorghum, millet and groundnut because these crops are critical to the success of achieving the mission of CGIAR,” said Pixley. “So, we have recently initiated work on the Accelerated Varietal Improvement and Seed Systems in Africa (AVISA) project together with partners. This is the first step towards OneCGIAR. It’s about synergies across crops and teams.”

Collaborative research commended

The meeting’s Chief Guest, Felister Makini, Deputy Director General – Crops of the Kenya Agricultural and Livestock Research Organisation (KALRO), commended the collaborative research undertaken by CIMMYT and other CGIAR partners. She noted that the partnerships continue to build on synergies that strengthen institutional financial, physical and human resources. She attested that collaboration between KALRO and CGIAR dates back to the 1980s, beginning with training in maize breeding, and then subsequent collaboration on developing climate-adaptive improved maize varieties and training of KALRO technicians in maize lethal necrosis (MLN) screening and management among other areas.

Maize and wheat are staple food sources in Kenya and sub-Saharan Africa and as the population increases, new methods and approaches must be found to accelerate development and deployment of improved maize and wheat varieties. She challenged the partners to intensify research and come out with high-yielding varieties that are resistant or tolerant to a wide range of biotic and abiotic stresses.

The Inaugural Session also featured remarks from the representatives of the AGG funders – Gary Atlin from the Bill & Melinda Gates Foundation, Jonna Davis from the Foundation for Food and Agriculture Research (FFAR), and John Derera from IITA, an AGG project partner.

A total of 116 participants, including representatives from National Agricultural Research Systems (NARS) in 13 AGG-Maize partner countries in Africa and seed companies, participated in the meeting. Participants also visited the KALRO-CIMMYT MLN Screening Facility at Naivasha, and KALRO-CIMMYT maize experiments at Kiboko, Kenya, including the work being done at the maize doubled haploid and FAW facilities.