Tag: tan spot

Scientists from IPBB evaluate wheat infected with tan spot and wheat rusts in Kazakhstan. (Photo: IPBB)

Genome-wide association study puts tan spot-resistant genes in the spotlight

Written by Madeline Dahm on July 29, 2021. Posted in Features.

Tan spot disease, caused by the fungus Pyrenophora tritici-repentis, may be less well-known than other pathogens of wheat such as rust and blast, but its potential to become a major threat to wheat-growing regions worldwide is a serious concern.

In Kazakhstan, one of the main wheat growing nations in Central Asia, farmers have struggled with tan spot epidemics since the 1980s. During epidemic years, Kazakh farmers have reported losing nearly half of their harvest to the disease.

A recent study published in Frontiers in Genetics has unlocked a promising new weapon against tan spot disease. Scientists at the Institute of Plant Biology and Biotechnology (IPBB) in Kazakhstan and the International Maize and Wheat Improvement Center (CIMMYT) conducted a genome-wide association study (GWAS) which found new sources of genetic resistance to tan spot disease.

“Bread wheat is the most important crop in Central Asia directly linked to food security. 45-60% of daily calories come from wheat,” said Alma Kokhmetova, Professor and Head of the Genetics and Breeding Laboratory at IPBB, who partnered with CIMMYT on this project.

Evaluation of tan spot disease resistance in a greenhouse. (Photo: IPBB)

Creative approaches to challenging, global issues

Global agriculture is repeatedly tested and threatened by emerging pests and diseases.

Fungicides and pesticides are not a one-stop, sustainable solution to controlling outbreaks. In addition to being unaffordable to much of the world’s smallholder population, they have also been found to have some negative environmental and health side effects. But crop breeders will argue that there is a more efficient path to resilience: through genetics.

For example, some wheat varieties are naturally resistant to diseases such as tan spot — it is in their DNA. If breeders can figure out what genes hold the code to tan spot disease resistance, in this case, they can cross and breed future varieties to be naturally immune to the disease. It is a much cleaner, cheaper and greener solution than dousing the world’s crops in fungus- and bug-killing chemicals.

A figure from the genome-wide association study shows novel genomic associations — especially here on chromosome 6A — that display resistance to both races of the tan spot fungus. (Figure: CIMMYT and IPBB)

Finding the needle in the haystack

Working together, CIMMYT and IPBB were able to find some important and novel genetic associations with resistance to tan spot for the two main races of the disease, race 1 and race 5, which are the most prevalent in Kazakhstan. The research centers assembled a panel with 191 samples of wheat having different levels of resistance from Kazakhstan, Russia and CIMMYT, through the International Winter Wheat Yield Partnership (IWWYP).

In order to conduct the genome-wide association study, the scientists used a genotyping platform called DArTseq to sequence the entries in the panel, a device that CIMMYT houses in its global headquarters in Mexico. The DArTseq method sequences the genome representations on the Next Generation Sequencing platforms and generates high-density single nucleotide polymorphisms (SNPs) data in a cost-effective manner.

Using the SNPs generated by DArTSeq and the phenotypic scoring of resistance to tan spot at the seedling and adult plant stages in Kazakhstan, the scientists were able to mark genomic regions associated with resistance to the disease. Novel regions on chromosomes 3BS, 5DL and 6AL were all found to have some promising traits of resistance, especially 6AL, which appears to be superior in protecting plants from both of the races of the pathogen.

Tan spot, caused by Pyrenophora tritici-repentis on susceptible wheat cultivar Steklovidnaya 24. (Photo: IPBB)

Tan spot-resistant wheat cultivar Tyngysh. (Photo: IPBB)

The next steps

This discovery of a new source of genetic resistance to tan spot is exciting to breeders, researchers, donors, national agricultural systems, seed companies and, ultimately, farmers both in and outside of Kazakhstan. Essentially, any country that struggles with race 1 and race 5 of tan spot disease will benefit from this discovery.

“For breeding purposes, 25 lines with the best allele combinations of novel and known genes identified in this study are currently being used in different crossing programs in Kazakhstan,” said Deepmala Sehgal, CIMMYT wheat geneticist. The next stage of this project will also be a collaborative effort with CIMMYT, where the results will be validated in other in genetic backgrounds.

“Once the results are validated, their sequence information will be updated in a genotyping platform called Intertek, which has been designed to assist breeders in genotyping their germplasm with gene-based markers,” added Sehgal

More impact together

“Thanks to the exchange of wheat materials between CIMMYT, Turkey and ICARDA (IWWIP), we have selected and produced disease-resistant advanced wheat lines. These wheat entries now are being evaluated in the different stages of the breeding process,” said Kokhmetova.

The early success of this study and partnership between CIMMYT and IPBB has led to another round of funding approved by the Kazakhstan government to bring this research to the next stage. Additionally, more projects that seek to find sources of genetic resistance to leaf rust and yellow rusts have recently been approved.

“Due to this previous successful collaboration done between IPBB and CIMMYT, two more projects have been funded to our national agricultural research system partner Professor Alma,” said Sehgal.

Although the story of tan spot-resistant wheat is still unfolding, major strides will continue to follow in the footsteps of this exceptional discovery.

Cover photo: Scientists from IPBB evaluate wheat infected with tan spot and wheat rusts in Kazakhstan. (Photo: IPBB)

Researcher Tamaya Peressini performs disease evaluations 10 days post infection at CIMMYT’s glasshouse facilities.

University of Queensland student researches tan spot resistance in wheat at CIMMYT

Written by on January 21, 2019. Posted in Features.

This story, part of a series on the international agricultural research projects of recipients of the Crawford Fund’s International Agricultural Student Award, was originally posted on the Crawford Fund blog.

In 2018, Tamaya Peressini, from the Queensland Alliance for Agriculture and Food Innovation (QAAFI), a research institute of the University of Queensland (UQ), travelled to CIMMYT in Mexico as part of her Honours thesis research, focused on a disease called tan spot in wheat.

Tan spot is caused by the pathogen Pyrenophora triciti-repentis (Ptr) and her project aimed to evaluate the resistance of tan spot in wheat to global races to this pathogen.

“The germplasm I’m studying for my thesis carries what is known as adult plant resistance (or APR) to tan spot, which has demonstrated to be a durable source of resistance in other wheat pathosystems such as powdery mildew,” Peressini said.

Tan spot is prevalent worldwide, and in Australia causes the most yield loss out of the foliar wheat diseases. In Australia, there is only one identified pathogen race that is prevalent, called Ptr Race 1. For Ptr Race 1, the susceptibility gene Tsn1 in wheat is the main factor that results in successful infection in Ptr strains that carry Toxin A. However, globally it is a more difficult problem, as there are seven other pathogen races that consist of different combinations of necrotrophic toxins. Hence, developing cultivars that are multi-race resistant to Ptr presents a significant challenge to breeders, as multiple resistant genes would be required for resistance to other pathogens.

“At CIMMYT, I evaluated the durability of APR I identified in plant material in Australia by inoculating with a local strain of Ptr and also with a pathogen that shares ToxA: Staganospora nodorum,” Peressini explained.

“The benefit of studying this at CIMMYT was that I had access to different strains of the pathogen which carry different virulence factors of disease, I was exposed to international agricultural research and, importantly, I was able to create research collaborations that would allow the APR detected in this population to have the potential to reach developing countries to assist in developing durably resistant wheat cultivars for worldwide deployment.”

Recent work in Dr Lee Hickey’s laboratory in Queensland has identified several landraces from the Vavilov wheat collection that exhibited a novel resistance to tan spot known as adult plant resistance (APR). APR has proven to be a durable and broad-spectrum source of resistance in wheat crops, namely with the Lr34 gene which confers resistance to powdery mildew and leaf stem rust of wheat.

“My research is focused on evaluating this type of resistance and identifying whether it is resistant to multiple pathogen species and other races of Ptr. This is important to the Queensland region, as the northern wheat belt is significantly affected by tan spot disease. Introducing durable resistance genes to varieties in this region would be an effective pre-breeding strategy because it would help develop crop varieties that would have enhanced resistance to tan spot should more strains reach Australia. Furthermore, it may provide durable resistance to other necrotrophic pathogens of wheat,” Peressini said.

The plant material Peressini studied in her honors thesis was a recombinant inbred line (RIL) population, with the parental lines being the APR landrace — carries Tsn1 — and the susceptible Australian cultivar Banks — also carries Tsn1. To evaluate the durability of resistance in this population to other strains of Ptr, this material along with the parental lines of the population and additional land races from the Vavilov wheat collection were sent to CIMMYT for Tamaya to perform a disease assay.

“At CIMMYT I evaluated the durability of APR identified in plant material in Australia by inoculating with a local strain of Ptr and also with a pathogen that shares ToxA: Staganospora nodorum. After infection, my plant material was kept in 100 per cent humidity for 24 hours (12 hours light and 12 hours dark) and then transferred back to regular glasshouse conditions. At 10 days post infection I evaluated the resistance in the plant material.”

From the evaluation, the APR RIL line demonstrated significant resistance compared to the rest of the Australian plant material against both pathogens. The results are highly promising, as they demonstrate the durability of the APR for both pre-breeding and multi-pathogen resistance breeding. Furthermore, this plant material is now available for experimental purposes at CIMMYT, where further trials can validate how durable the resistance is to other necrotrophic pathogens and also be deployed worldwide and be tested against even more strains of Ptr.

“During my visit at CIMMYT I was able to immerse myself in the Spanish language and take part in professional seminars, tours, lab work and field work around the site. A highlight for me was learning to prepare and perform toxin infiltrations for an experiment comparing the virulence of different strains of spot blotch,” Peressini said.

Peressini had a chance to visit the pyramids of Teotihuacán and other Mexican landmarks. — *During her stay in Mexico, Peressini had a chance to visit the pyramids of Teotihuacán and other cultural landmarks.*

“I also formed valuable friendships and research partnerships from every corner of the globe and had valuable exposure to the important research underway at CIMMT and insight to the issues that are affecting maize and wheat growers globally. Of course, there was also the chance to travel on weekends, where I was able to experience the lively Mexican culture and historical sites – another fantastic highlight to the trip!”

“I would like to thank CIMMYT and Dr Pawan Singh for hosting me and giving the opportunity to learn, grow and experience the fantastic research that is performed at CIMMYT and opportunities to experience parts of Mexico. The researchers and lab technicians were all so friendly and accommodating. I would also like to thank my supervisor Dr Lee Hickey for introducing this project collaboration with CIMMYT. Lastly, I would like to thank the Crawford Fund Queensland Committee for funding this visit; not only was I able to immerse myself in world class plant pathology research, I have been given valuable exposure to international agricultural research that will give my research career a boost in the right direction,” Peressini concluded.