Tag: molecular markers

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.

CGIAR research highlighted among climate innovations to meet net zero emissions

Written by Sam Storr on April 18, 2022. Posted in News.

Agriculture is one of the five main greenhouse gas-emitting sectors where innovations can be found to reach net zero emissions, according to the new documentary and ten-part miniseries “Solving for Zero: The Search for Climate Innovation.” The documentary tells the stories of scientists and innovators racing to develop solutions such as low-carbon cement, wind-powered global transportation, fusion electricity generation and sand that dissolves carbon in the oceans.

Three CGIAR scientists are featured in the documentary, speaking about the contributions being made by agricultural research.

Whereas all sectors of the global economy must contribute to achieve net zero emissions by 2050 to prevent the worse effects of climate change, agricultural innovations are needed by farmers at the front line of climate change today.

CIMMYT breeder Yoseph Beyene spoke to filmmakers about the use of molecular breeding to predict yield potential. (Image: Wondrium.com)

Breeding climate-smart crops

“Climate change has been a great disaster to us. Day by day it’s getting worse,” said Veronica Dungey, a maize farmer in Kenya interviewed for the documentary.

Around the world, 200 million people depend on maize for their livelihood, while 90% of farmers in Africa are smallholder farmers dependent on rainfall, and facing drought, heatwaves, floods, pests and disease related to climate change. According to CGIAR, agriculture must deliver 60% more food by 2050, but without new technologies, each 1°C of warming will reduce production by 5%.

“Seed is basic to everything. The whole family is dependent on the produce from the farm,” explained Yoseph Beyene, Regional Maize Breeding Coordinator for Africa and Maize Breeder for Eastern Africa at the International Maize and Wheat Improvement Center (CIMMYT). As a child in a smallholder farming family with no access to improved seeds, Beyene learned the importance of selecting the right seed from year to year. It was at high school that Beyene was shown the difference between improved varieties and the locally-grown seed, and decided to pursue a career as a crop breeder.

Yoseph Beyene examines breeding lines. (Image: Wondrium.com)

Today, the CIMMYT maize program has released 200 hybrid maize varieties adapted for drought conditions in sub-Saharan Africa, called hybrids because they combine maize lines selected to express important traits over several generations. Alongside other CGIAR Research Centers, CIMMYT continues to innovate with accelerated breeding approaches to benefit smallholder farmers.

“Currently we use two kinds of breeding. One is conventional breeding, and another one is molecular breeding to accelerate variety development. In conventional breeding you have to evaluate the hybrid in the field,” Beyene said. “Using molecular markers, instead of phenotypic evaluation in the field, we are evaluating the genetic material of a particular line. We can predict based on marker data which new material is potentially good for yield.”

Such innovations are necessary considering the speed and the complexity of challenges faced by smallholder farmers due climate change, which now includes fall armyworm. “Fall armyworm is a recent pest in the tropics and has affected a lot of countries,” said Moses Siambi, CIMMYT Regional Representative for Africa. “Increased temperatures have a direct impact on maize production because of the combination of temperature of humidity, and then you have these high insect populations that lead to low yield.”

Resistance to fall armyworm is now included in new CIMMYT maize hybrids alongside many other traits such as yield, nutrition, and multiple environmental and disease resistances.

Ana María Loboguerrero, Research Director for Climate Action at the Alliance of Bioversity and CIAT, spoke about CGIAR’s community-focused climate work. (Image: Wondrium.com)

Building on CGIAR’s climate legacy

Ana María Loboguerrero, Research Director for Climate Action at the Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), told the filmmakers about CGIAR’s community-focused climate work, which includes Climate-Smart Villages and Valleys. Launched in 2009, these ongoing projects span the global South and effectively bridge the gap between innovation, research and farmers living with the climate crisis at their doorsteps.

“Technological innovations are critical to food system transformation,” said Loboguerrero, who was a principal researcher for the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS). “But if local contexts are not considered, even the best innovations may fail because they do not respond to beneficiaries needs.”

CCAFS’s impressive legacy — in research, influencing policy and informing $3.5 billion of climate-smart investments, among many achievements — is now being built upon by a new CGIAR portfolio of initiatives. Several initiatives focus on building systemic resilience against climate and scaling up climate action started by CCAFS that will contribute to a net-zero carbon future.

Loboguerrero pointed to other innovations that were adopted because they addressed local needs and were culturally appropriate. These include the uptake of new varieties of wheat, maize, rice and beans developed by CGIAR Research Centers. Taste, color, texture, cooking time and market demand are critical to the success of new varieties. Being drought-resistant or flood-tolerant is not enough.

Local Technical Agroclimatic Committees, another CCAFS innovation that is currently implemented in 11 countries across Latin America, effectively delivers weather information in agrarian communities across the tropics. Local farmers lead these committees to receive and disseminate weather information to better plan when they sow their seeds. “This success would not have been possible if scientists hadn’t gotten out of their labs to collaborate with producers in the field,” Loboguerrero said.

Climate adaptation solutions

Across CGIAR, which represents 13 Research Centers and Alliances, and a network of national and private sector partners, the goal is to provide climate adaptation solutions to 500 million small-scale farmers around the world by 2030. This work also covers reducing agricultural emissions, environmental impacts and even the possibility of capturing carbon while improving soil health.

Interested in learning more? The documentary “Solving for Zero: The Search for Climate Innovation” is available at Wondrium.com alongside a 10-part miniseries exploring the ongoing effort to address climate change.

A farmer in Tanzania holds a handful of drought-tolerant maize seed. (Photo: Anne Wangalachi/CIMMYT)

Molecular breeding speeds development of better seeds

Written by Emma Orchardson on November 27, 2020. Posted in Features.

To adequately confront rapidly changing plant pests and diseases and safeguard food security for a growing population, breeders — in collaboration with their partners — have to keep testing and applying new breeding methods to deliver resilient seed varieties at a much faster rate using minimal resources. Molecular markers are essential in this regard and are helping to accelerate genetic gains and deliver better seed to smallholders across sub-Saharan Africa in a much shorter timeframe.

Progress made so far in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a deeper understanding on the role of molecular markers and greatly complemented breeding strategies. However, phenotyping remains the single most costly process in plant breeding, thus limiting options to increase the size of breeding programs.

Application of molecular markers increases the ability to predict and select the best performing lines and hybrids, prior to selection in the field. “This enables breeders to expand the size of a breeding program or the populations they work on using the same amount of resources,” says Manje Gowda, a maize molecular breeder at the International Maize and Wheat Improvement Center (CIMMYT).

“There are three stages in the use of molecular markers: discovery, validation and deployment,” he explains. “At the discovery phase, the objective is to find molecular markers associated or tightly linked with the trait of interest, while also assessing whether the trait is more complex or easier to handle with few markers for selection.”

The molecular markers identified at the discovery stage are validated in independent bi-parental or backcross populations, and the marker trait associations — which are consistent across different genetic backgrounds and diverse environments — are then moved to the deployment stage. Here, they are considered for use in breeding either as part of marker assisted selection or forward breeding, marker assisted back crossing and marker assisted recurrent selection.

Screening for resistance markers

CIMMYT scientists have discovered several marker trait associations for crop diseases including maize lethal necrosis (MLN), maize streak virus (MSV), corn rust and turcicum leaf blight. All these trait-associated markers have been validated in biparental populations.

For MLN, after screening several thousands of lines, researchers identified a few with resistance against the viral disease, namely KS23-5 and KS23-6. These lines were obtained from synthetic populations developed by Kasetsart University in Thailand and serve as trait donors. Researchers were able to use these as part of forward breeding, producing doubled haploid (DH) lines by using KS23-6 as one parent and screening for the presence of MLN resistance genes.

“This screening helps eliminate the lines that may carry susceptible genes, without having to phenotype them under artificial inoculation,” says Gowda. “These markers are also available to all partners to screen for MLN resistance, thereby saving on costs related to phenotyping.”

Scientists also used these MLN resistance markers to introgress the MLN resistance into several elite lines that are highly susceptible to the disease but have other desirable traits such as high grain yield and drought tolerance. The marker-assisted backcrossing technique was used to obtain MLN resistance from the KS23-5 and KS23-6 donor lines. This process involves crossing an elite, commercial line — as a recurrent parent in the case of CIMMYT elite lines — with a donor parent line (KS23) with MLN resistance. These were then backcrossed over two to three cycles to improve the elite line carrying MLN resistance genes. In the past three years, more than 50 lines have been introgressed with the MLN resistance gene from KS23-6 donor line.

Aida Zewdu Kebede, a PhD student at the University of Hohenheim, sits next to an experimental plot for doubled haploid maize in Agua Fría, Mexico. (Photo: Thomas Lumpkin/CIMMYT)

An impetus to breeding programs

“The work Manje Gowda has been carrying out is particularly important in that it has successfully moved from discovery of valuable markers and proof-of-concept experiments to scalable breeding methods which are being used effectively,” says CIMMYT Trait Pipeline and Upstream Research Coordinator Mike Olsen. “Enabling routine implementation of molecular markers to increase selection efficiency of breeding programs in the context of African maize improvement is quite impactful.”

At CIMMYT, Gowda’s team applied genomic selection at the early stage of testing the breeding pipeline for different product profiles. “The objective was to testcross and phenotype 50% of the Stage One hybrids and predict the performance of remaining 50% of the hybrids using molecular markers,” Gowda explains.

The team have applied this strategy successfully each year since 2017, and the results of this experiment show that selection efficiency is the same as when using phenotypic selection, but using only 32% of the resources. From 2021 onwards, the aim is to use the previous year’s Stage One phenotypic and genotypic data to predict 100% of the lines. This will not only save the time but improve efficiency and resource use. The previous three-year Stage One historical data is helping to reduce the phenotyping of lines from 50% to 15%, with an increase in saving resources of up to 50%.

For the commercial seed sector, integrating molecular marker-based quality control measures can help deploy high-quality seeds, an important factor for increasing crop yields. In sub-Saharan Africa, awareness on marker-based quality has improved due to increased scientist and breeder trainings at national agricultural research systems (NARS), seed companies and national plant protection organizations, as well as regulators and policymakers.

Currently, many NARS and private sector partners are making it mandatory to apply marker-based quality control to maintain high-quality seeds. Since NARS and small- and medium-sized seed companies’ breeding programs are smaller, CIMMYT is coordinating the collection of samples from different partners for submission to service providers for quality control purposes. CIMMYT staff are also helping to analyze quality control data and interpret results to sharing with partners for decision-making. For the sustainability of this process, CIMMYT is training NARS partners on quality control, from sample collection to data analyses and interpretation, and this will support them to work independently and produce high-quality seed.

Such breeding improvements have become indispensable in supporting maize breeding programs in the public and private sectors to develop and deliver improved maize varieties to smallholder farmers across sub-Saharan Africa.

A farmer in Tanzania stands in front of her maize plot where she grows improved, drought tolerant maize variety TAN 250. (Photo: Anne Wangalachi/CIMMYT)

Wheat grains prepared for placement in a Thousand Grain Weight machine. (Photo: Marcia MacNeil/CIMMYT)

A fresh look at the genes behind grain weight in spring bread wheat

Written by Marcia MacNeil on October 9, 2019. Posted in News.

Guillermo Garcia Barrios, a co-author of the study and student at Colegio de Postgraduados in Montecillo, Mexico, with a PHERAstar machine used to validate genetic markers. (Photo: Marcia MacNeil/CIMMYT)

To meet the demand for wheat from a rising and quickly urbanizing population, wheat yields in farmers’ fields must increase by an estimated 1.5% each year through 2030.

Of all the factors that influence yield, grain weight is the trait that is most stable and heritable for use in breeding improved wheat varieties. Breeders measure this by thousand grain weight (TGW).

Over the years, molecular scientists have made efforts to identify genes related to increased TGW, in order to speed up breeding through marker-assisted selection (MAS). Using MAS, breeders can select parents that contain genes related to the traits they are looking for, increasing the likelihood they will be passed on and incorporated in a new variety.

There have been some limited successes in these efforts: in the past years, a few genes related to increased TGW have been cloned, and a set of genetic markers have been determined to be used for MAS. However, the effects of most of these candidate genes have not yet been validated in diverse sets of wheat germplasm throughout the world that represent the full range of global wheat growing environments.

A group of wheat geneticists and molecular breeders from the International Maize and Wheat Improvement Center (CIMMYT) has recently conducted a thorough study to confirm the effects of the favorable alleles reported for these genes on TGW in CIMMYT wheat, and to identify new genetic determinants of this desired trait.

They found some good news and some bad news.

First, the good news: focusing on more than 4,000 lines of CIMMYT wheat germplasm they found 15 haplotype blocks significantly associated with TGW. Four haplotype blocks associated with TGW were also associated with grain yield — a grand prize for breeders, because in general the positive association of grain yield with TGW is less profound and sometimes even negative. However, of the 14 genes that had been previously reported to increase TGW, only one in CIMMYT’s 2015-2016 Elite Yield Trial and two in Wheat Associative Mapping Initiative panel were shown to have significant TGW associations.

The scientists also found that the alleles — pairs of genes on a chromosome that determine heredity — that were supposedly favorable to TGW actually decreased it. These candidate genes also appear to vary in their TGW effects with genetic background and/or environment.

Thus, these findings also provide a foundation for more detailed investigations, opening the door for more studies on the genetic background dependence and environment sensitivity of the known candidate genes for TGW.

“Our findings indicate that it will be challenging to use MAS based on these existing markers across individual breeding programs,” said Deepmala Sehgal, CIMMYT wheat geneticist and the primary author of the study.

However, efforts to identify new genetic determinants of TGW were promising. The authors’ study of CIMMYT germplasm found one locus on chromosome 6A that showed increases of up to 2.60 grams in TGW and up to 258 kilograms per hectare in grain yield.

Thousand Grain Weight is measured in this machine at CIMMYT’s global headquarters in Texcoco, Mexico. (Photo: Marcia MacNeil/CIMMYT)

This discovery expands opportunities for developing diagnostic markers to assist in multi-gene pyramiding — a process that can derive new and complementary allele combinations for enhanced wheat TGW and grain yield.

Most of all, the study highlights the strong need for better and more validation of the genes related to this and other traits, so that breeders can be sure they are using material that is confirmed to increase wheat grain weight and genetic yield.

“Our findings are very promising for future efforts to efficiently develop more productive wheat in both grain weight and grain yield,” said Sehgal. “This ultimately means more bread on household tables throughout the world.”

“Validation of Candidate Gene-Based Markers and Identification of Novel Loci for Thousand-Grain Weight in Spring Bread Wheat” in Frontiers in Plant Science by Deepmala Sehgal, Suchismita Mondal, Carlos Guzman, Guillermo Garcia Barrios, Carolina Franco, Ravi Singh and Susanne Dreisigacker was supported by funding from the CGIAR Research Program on Wheat (WHEAT), the Delivering Genetic Gain in Wheat (DGGW) project funded by the Bill & Melinda Gates Foundation and the UK Department for International Development (DFID), and the US Agency for International Development (USAID) Feed the Future Innovation Lab for Applied Wheat Genomics.

Read the full article here: https://doi.org/10.3389/fpls.2019.01189

Breaking Ground: Susanne Dreisigacker knows wheat inside out

Written by Courtney Brantley on November 14, 2018. Posted in Features.

EL 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)*

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.