Brazil
June 6, 2023
>> Genoma do fungo causador da ferrugem da soja revela pistas para seu controle
The work provides some clues about the fungus' high variability, which makes it quickly adapt and circumvent different control measures - Photo: Elizeo Garrcia
- Genome helps to understand how the fungus quickly adapts to adverse conditions, which hinders its control.
- The study found that over 90% of the genome is composed of repetitive DNA sequences that can change their position in the genome. This finding would be the most likely cause of the fungus' high variability.
- The respective paper was published in the international journal Nature Communications.
- The study also found expansions in gene families responsible for energy production and nutrient transportation, which could help to define biotechnological solutions for fungal control.
- Research has already been testing the silencing of a few of the fungus' essential genes, a strategy that can reduce the severity of the disease.
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Embrapa and other members of the International Asian Soybean Rust Genome Consortium celebrate the advances achieved by sequencing and assembling the genome of three samples (two isolates obtained in Brazil and one from Uruguay) of the fungus P. pachyrhizi, which causes Asian soybean rust. The work provides some clues about one of the most challenging characteristics of the microorganism: its high variability, which makes it quickly adapt and circumvent different control measures. The study was published in the journal Nature Communications.
Asian soybean rust is one of the crop's main phytosanitary challenges because the fungus can adapt to control strategies, either by losing sensitivity to fungicides or by "breaking" the genetic resistance present in soybean cultivars. “The availability of a reference genome for the fungus is essential for advances in knowledge of the biology and the factors involved in the fungus' adaptability, with the aim of accelerating the development of new control strategies,” states the Embrapa Soybeans researcher Francismar C. Marcelino-Guimarães, one of the authors of the paper.
The researcher explains that detailed knowledge about the operation of the fungus' reference genome is essential to understand the factors that are involved in its adaptability and that thus contribute to hindering its control. “Based on the genome, we found that about 93% is composed of repetitive DNA sequences called transposons, DNA fragments that can 'jump' or change places in the genome, which can contribute to its high variability,” the researcher explains. “Interestingly, we were able to observe that some of such transposons become active in the fungus and jump in the genome during an infection, especially in the first hours of contact with the host. They become active 24 to 48 hours after the infection alongside other genes that are essential for infection success known as effectors, which work by suppressing the plant's defense responses", she details
In the study, it was also possible to identify the fungus' full set of effectors, which was shared by the three samples of the fungus, including those that were active or expressed at the crucial moments of infection. Some of these effectors have been characterized by Embrapa Soybeans, showing their action or attack against the host during the parasitism. “Understanding the pathogen's attack strategies is crucial for the development of control strategies,” the researcher asserts.
Guimarães also revealed that based on the genome available, comparative genomics studies with other fungal species also showed adaptive particularities stemming from the contraction or expansion of gene families. “By comparing the genome of the soybean rust pathogen with those of 14 fungal species, we identified that gene loss is more frequent in P. pachyrhizi. This trait explains its high dependence on the plant tissue of the living host and, in some biological processes, the pathogen is completetely reliant on the host”, she reports, as she explains that learning the processes and key elements involved in parasitism is essential to develop host plants that are less attractive or more tolerant to the fungus.
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The importance of the sanitary break
Management strategies are centered on practices such as the sanitary break, a period when the field rests without live soybean plants for at least 90 days. The practice reduces fungal inoculums. In Brazil, the sanitary break starts in June in several soybean producing states. The full calendar is here.
In addition, other strategies to evade the disease are: the use of early cycle cultivars and sowing at the beginning of the recommended season; the adoption of resistant cultivars; observance of the sowing calendar; and the use of fungicides. .
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According to the researcher, they also observed the occurrence of expanded gene families – involved in energy production and nutrient transportation –, which may point to a certain flexibility in their metabolism and in nutrient acquisition. “Understanding the parasite's lifestyle at a molecular level is important to identify the genes that are essential during soybean parasitism and that are thus essential for nutrient acquisition and fungal survival,” she explains.
Such genes can be used for the development of control strategies (e.g. via gene editing or transgenics) as they can compromise vital processes such as parasitism. “Studies conducted at Embrapa have also tested the effectiveness of silencing some of the fungus' essential genes, a strategy with potential to reduce the severity of the disease,” she observes.
The analysis of the genome also revealed a high level of differences (heterozygosity) between the two nuclei that constitute the fungus' genome. “This characteristic indicates an absence of recombination between them, backing the fungus' propagation or asexual reproduction in South America.
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Learn more
DNA - The key to understanding the behavior and evolution of the species lies in the genome: an organism's set of genetic information. The genome has the mission of coordinating how cells operate - building, rebuilding and managing the activity of individual ones. On the other hand, genes represent functional sections of this genome, which are relevant to biological activity.
Asian soybean rust - Asian soybean rust has been the most severe disease to affect soybean cultivation since its identification in the 2000s. The disease can lead to losses of up to 80% if left uncontrolled, while management costs for Brazilian farmers exceed US$2 billion per crop year. The fungus can adapt to control strategies, either by losing sensitivity to fungicides or by "breaking" the genetic resistance present in soybean cultivars, so that the number of practical solutions to control the disease is still limited.
International Asian Soybean Rust Genome Consortium - Between the years 2019 and 2021, the international research initiative ASR Genome Consortium made the sequencing and assembly of the reference genome of three isolates of P. pachyrhizi publicly available (the data are publicly available to the scientific community on this link).
The international consortium is composed of 12 public and private institutions: Embrapa, the German universities of Hohenheim and RWTH Aachen, France's National Institute of Agronomic Research (INRA) and the University of Lorraine, in addition to the Joint Genome Institute (JGI) in the USA, the 2Blades Foundation, Bayer, Keygene, the Sainsbury Laboratory (UK), Syngenta and the Federal University of Viçosa (Brazil).
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