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Tag: genetic analysis

Afghan wheat landrace shows promise for rust resistance

Rust pathogens are the most ubiquitous fungal pathogens that continue to pose a serious threat to wheat production. The preferred strategy to combat these diseases is through breeding wheat varieties with genetic resistance.

Landraces are a treasure trove of trait diversity, offer an excellent choice for the incorporation of new traits into breeding germplasm, and serve as a reservoir of genetic variations that can be used to mitigate current and future food challenges. Improving selection efficiency can be achieved through broadening the genetic base through using germplasm pool with trait diversity derived from landraces.

In a recent study, researchers from the International Maize and Wheat Improvement Center (CIMMYT) used Afghan landrace KU3067 to unravel the genetic basis of resistance against Mexican races of leaf rust and stripe rust. The findings of this study not only showcase new genomic regions for rust resistance, but also are the first report of Lr67/Yr46 in landraces. This adult plant resistance (APR) gene confirms multi-pathogenic resistance to three rust diseases and to powdery mildew.

Using genotype sequencing and phenotyping, the authors also report an all-stage resistance gene for stripe rust on chromosome 7BL, temporarily designated as YrKU. The genetic dissection identified a total of six quantitative trait locus (QTL) conferring APR to leaf rust, and a further four QTL for stripe rust resistance.

Although use of landraces in wheat breeding has been practiced for a long time, it has been on a limited scale. This study represents a significant impact in breeding for biotic stresses, particularly in pest and disease resistance.

Read the full study here: Identification and Characterization of Resistance Loci to Wheat Leaf Rust and Stripe Rust in Afghan Landrace “KU3067”

Cover photo: Yellow rust screening takes place at a CIMMYT experimental station in Mexico. (Credit: Sridhar Bhavani/CIMMYT)

Fighting back against Ug99 wheat stem rust

Sridhar Bhavani, head of rust pathology and molecular genetics and the International Maize and Wheat Improvement Center (CIMMYT), shared potential solutions for fighting back against wheat stem rusts like Ug99.

More than 200 new wheat varieties released by CIMMYT over the last ten years have contributed to reducing the spread of wheat stem rust in East Africa, where the disease originated. Scientists identify genes resistant to Ug99 and breed new varieties that are not susceptible to stem rust pathogens.

For long-term success, combining multiple resistant genes within a single variety is the way to go.

Read more: Fighting back against Ug99 wheat stem rust

Understanding the role of organic material application in soil microbial community structures

While previous studies have demonstrated the importance of organic material in soil for sustainable agricultural practices, there has been limited research into how organic material application affects the soil microbial community structures.

Researchers from El Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) studied soil from the International Maize and Wheat Improvement Center’s (CIMMYT) long-term experiment in northwestern Mexico to determine the effect on the soil metagenome after adding easily decomposable organic residues. The soil was collected from plots where maize and wheat were cultivated without tillage on permanent beds with crop residue left on the soil surface since 1992.

Dried young maize plants were added to the soil in the laboratory. After three days of incubation, soil samples were analyzed using shotgun metagenomic sequencing to discover how the application of young maize plants affects the structure of microbial communities in arable soil, how the potential functioning of microbial communities is altered, and how the application affects the soil taxonomic and functional diversity.

Bacterial and viral groups were strongly affected by organic material application, whereas archaeal, protist and fungal groups were less affected. Soil viral structure and richness were impacted, as well as metabolic functionality. Further differences were recorded in cellulose degraders with copiotrophic lifestyle, which were enriched by the application of young maize plants, while groups with slow growing oligotrophic and chemolithoautotrophic metabolism performed better in unamended soil.

Given the importance of embedding and adopting sustainable agricultural practices as part of climate change adaptation and mitigation, the study improves our insight in a key aspect of sustainable agriculture, the management of crop residues.

Read the full study: Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study

Cover photo: Wheat crops growing at CIMMYT’s long-term experiment site in Ciudad Obregon, Mexico. (Credit: Nele Verhulst/CIMMYT)

Retrospective quantitative genetic analysis and genomic prediction of global wheat yields

The process for breeding for grain yield in bread wheat at the International Maize and Wheat Improvement Center (CIMMYT) involves three-stage testing at an experimental station in the desert environment of Ciudad Obregón, in Mexico’s Yaqui Valley. Because the conditions in Obregón are extremely favorable, CIMMYT wheat breeders are able to replicate growing environments all over the world and test the yield potential and climate-resilience of wheat varieties for every major global wheat growing area. These replicated test areas in Obregón are known as selection environments (SEs).

This process has its roots in the innovative work of wheat breeder and Nobel Prize winner Norman Borlaug, more than 50 years ago. Wheat scientists at CIMMYT, led by wheat breeder Philomin Juliana, wanted to see if it remained effective.

The scientists conducted a large quantitative genetics study comparing the grain yield performance of lines in the Obregón SEs with that of lines in target growing sites throughout the world. They based their comparison on data from two major wheat trials: the South Asia Bread Wheat Genomic Prediction Yield Trials in India, Pakistan and Bangladesh initiated by the U.S. Agency for International Development Feed the Future initiative and the global testing environments of the Elite Spring Wheat Yield Trials.

The findings, published in Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields, in Frontiers in Plant Science, found that the Obregón yield testing process in different SEs is very efficient in developing high-yielding and resilient wheat lines for target sites.

The authors found higher average heritabilities, or trait variations due to genetic differences, for grain yield in the Obregón SEs than in the target sites (44.2 and 92.3% higher for the South Asia and global trials, respectively), indicating greater precision in the SE trials than those in the target sites. They also observed significant genetic correlations between one or more SEs in Obregón and all five South Asian sites, as well as with the majority (65.1%) of the Elite Spring Wheat Yield Trial sites. Lastly, they found a high ratio of selection response by selecting for grain yield in the SEs of Obregón than directly in the target sites.

“The results of this study make it evident that the rigorous multi-year yield testing in Obregón environments has helped to develop wheat lines that have wide-adaptability across diverse geographical locations and resilience to environmental variations,” said Philomin Juliana, CIMMYT associate scientist and lead author of the article.

“This is particularly important for smallholder farmers in developing countries growing wheat on less than 2 hectares who cannot afford crop losses due to year-to-year environmental changes.”

In addition to these comparisons, the scientists conducted genomic prediction for grain yield in the target sites, based on the performance of the same lines in the SEs of Obregón. They found high year-to-year variations in grain yield predictabilities, highlighting the importance of multi-environment testing across time and space to stave off the environment-induced uncertainties in wheat yields.

“While our results demonstrate the challenges involved in genomic prediction of grain yield in future unknown environments, it also opens up new horizons for further exciting research on designing genomic selection-driven breeding for wheat grain yield,” said Juliana.

This type of quantitative genetics analysis using multi-year and multi-site grain yield data is one of the first steps to assessing the effectiveness of CIMMYT’s current grain yield testing and making recommendations for improvement—a key objective of the new Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project, which aims to accelerate the breeding progress by optimizing current breeding schemes.

This work was made possible by the generous support of the Delivering Genetic Gain in Wheat (DGGW) project funded by the Bill & Melinda Gates Foundation and the UK Foreign, Commonwealth & Development Office (FCDO) and managed by Cornell University; the U.S. Agency for International Development’s Feed the Future initiative; and several collaborating national partners who generated the grain yield data.

Read the full article: Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields

This story was originally posted on the website of the CGIAR Research Program on Wheat (wheat.org).

Cover photo: Wheat fields at CIMMYT’s Campo Experimental Norman E. Borlaug (CENEB) in Ciudad Obregón, Mexico. (Photo: CIMMYT)