Asian soybean rust genome directs new management strategies

Phakopsora pachyrhizi, the fungus that causes Asian soybean rust, has one of the largest genomes found in plant pathogens (1,057 Gb), similar in size to soybeans, their main host. Moreover, it is enriched with repetitive sequences (transposable elements or transposons) that can “jump” or move from one position in the genome to another, a characteristic that can gives it adaptability to skirt control. These were some of the discoveries obtained as the internationalr research group ASR Genome Consortium sequenced and assembled three genomes of the microorganism (Phakopsora pachyrhizi) between 2019 and 2021.

The results were presented this month at the IX Brazilian Soybean Congress, in Foz do Iguaçu, PR, by the Embrapa Soybeans researcher Francismar Marcelino-Guimarães. “As an example, we observed that those elements are active in the fungus' genome during its interaction with the soybean plant, which can contribute to its genetic variability and thus to its adaptability to control measures”, the scientist asserts.

The consortium data are publicly available for the scientific community online. “The availability of fungus reference genome is essential for advances in knowledge of the biology and the factors involved in the adaptability of this fungus, with the aim to accelerate the development of new strategies to control Asian rust”, Guimarães adds.

Moreover, the researcher reports that P. pachyrhizi has a spore with two nuclei and high difference (polymorphism), with low communication between them. “This trait helps the fungus have variations or alternative gene copies, which can also constitute an important source of variation”, the researcher states.

Guimarães states that the reference genome has enabled comparisons between the genes sets of P. pachyrhizi and of other fungus species. Additionally, the studies identified exclusive gene families in P. pachyrhizi, some with a high number and others with a reduced number, when compared with other species. According to the researcher, these are genes involved in energy production and plant nutrient transportation, which can indicate flexibility in metabolism and adaptations to parasitism. “To understand the parasite's lifestyle on a molecular level, it is important, for example, to identify the genes that can be active in the soybean plant parasitism and are thus essential for the fungus' nutrient acquisition and survival”, she explains. "Such genes are important for the development of control strategies like gene silencing or RNA interference, which can compromise vital processes and reduce the aggressiveness of the fungus”.

Joint results

Embrapa Soybeans, in partnership with the Federal University of Viçosa (UFV), has been making efforts to decipher the fungus' mechanisms of attack by identifying which soybean targets the pathogen manipulates. "We discovered that the fungus works on a soybean protein involved in the plant's defense response and that the presence of the fungus inhibits the activity of this protein", she explains.

Another important discovery came from the analysis of variations of the fungus' target gene in the soybean DNA, which showed a polymorphism that separates soybean cultivars that contain genes of resistance to this fungus from those that are susceptible to it. “This variation reveals a potential DNA-based marker, which can help in the development of soybean cultivars by combining such basal defense genes with resistance ones (Rpp genes)”, Guimarães asserts. Embrapa has already been using Rpp genes in breeding programs to develop soybean cultivars through the Shield technology.

Another line of research at Embrapa, in partnership with Bayer, has been exploring the existing variability in the natural populations of the fungus, which is widely found in Brazil and the American continent. “The re-sequencing and the comparison of the DNA sequences of different isolates collected in Brazil and in other continents on a broad time scale, have revealed genome regions with different differentiation indexes. This allowed, for instance, the identification of new mutations in one of the main fungicide target genes, which could be associated with the efficiency of those molecules. Such information can help directing new studies to develop the chemical management of Asian soybean rust”, she explains.

Asian soybean rust: management strategies

Since its introduction in Brazil, in 2001, Asian soybean rust, caused by Phakopsora pachyrhizi, is the most severe disease of the crop, as it can lead to losses of up to 80% if it is not controlled. According to surveys by the Antirust Consortium, expenses with Asian soybean rust exceed US$ 2 billion, per harvest, considering the acquisition of fungicides and productivity losses resulting from the disease.

Management strategies center on practices like: sanitary break, which is the period of at least 90 days without live soybean plants in the fields, to reduce fungus innoculation; the use of early-cycle cultivars and sowing at recommended times as a strategy to escape the disease; the adoption of resistant cultivars, compliance with the Brazilian sowing calendar, and the use of fungicides.

Currently, the P. pachyrhizi fungus shows mutations that give it resistance to the three main groups of site-specific fungicides, and new mutations can be selected in the course of time. “The disease-causing fungus can adapt to some of the control strategies, either through the loss of sensitivity to the fungicides or by 'breaking' the genetic resistance of the soybean cultivars”, explains the researcher Cláudia Godoy, from Embrapa Soybeans.

Therefore, Embrapa's recommendation is that farmers adopt the management strategies available with the aim to preserve the fungicides and cultivars available. “All the strategies combined have allowed suitable disease management. Some regions that use early-cycle soybean cultivars to have a second corn or cotton crop in the same harvest year have escaped or shown delayed incidence of Asian rust, and other diseases have prevailed in the crop. In regions where soybeans are sown later, the cultivars with resistance genes and fungicides have provided adequate control, despite the ongoing resistance issue”, Godoy explains.