Asian soybean rust genome directs new management strategies

Phakopsora pachyrhizi, the fungus that causes Asian soybean rust, has one of the largest genomes among plant pathogens (1,057 Gb), a size similar to that of the soybean genome, its main host. In addition, it is enriched with repetitive sequences (transposable elements or transposons), capable of “jumping” or changing position in the genome, a characteristic that can confer adaptability and thus “dodge” control actions.

These were some of the discoveries obtained from the sequencing and assembly of three genomes of the microorganism (Phakopsora pachyrhizi), carried out between 2019 and 2021 by the ASR Genome Consortium, an international research group.

These results were presented this month at the IX Brazilian Soy Congress, in Foz do Iguaçu (PR), by Embrapa Soja (PR) researcher Francismar Marcelino-Guimarães. “We saw, for example, that part of these elements are active in the fungus genome during its interaction with soybeans, which can contribute to its genetic variability and, consequently, to its adaptability to control measures”, emphasizes the scientist.

The consortium’s data are publicly available to the scientific community on the internet (mycocosm.jgi.doe.gov/Phapa1). “The availability of the fungus’ reference genome is essential for advancing our knowledge of its biology and the factors involved in its adaptability, with the aim of accelerating the development of new strategies to control Asian rust,” adds Guimarães.

Furthermore, the researcher reports that the P.pachyrhizi has a spore with two nuclei and a high difference (polymorphism), in addition to low communication between them. “This characteristic allows this fungus to maintain variations or alternative copies of genes, which can also constitute an important source of variation”, says the researcher.

She says that the reference genome has enabled comparisons between the set of genes of P.pachyrhizi with that of other fungal species. Additionally, studies have identified unique gene families in P.pachyrhizi, some with high numbers and others with low numbers, when compared to other species. According to the researcher, these are genes involved in the production of energy and the transport of nutrients in the plant, which may indicate flexibility in its metabolism and adaptations to its parasitism. 

“Understanding the lifestyle of this parasite, at a molecular level, is important, for example, to identify the genes that can act in the parasitism of the soybean plant and, therefore, that are essential for the acquisition of nutrients and the survival of the fungus”, he explains. 

“Such genes are important targets for the development of control strategies, such as gene silencing or RNA interference, which can compromise vital processes of the species and reduce the aggressiveness of the fungus,” he highlights.

Joint results

Embrapa Soja, in partnership with the Federal University of Viçosa (UFV), is seeking to decipher the fungus' attack mechanisms, identifying which soybean targets are being manipulated by the pathogen. “We discovered that the fungus acts on a soy protein involved in the plant’s defense response and that the presence of the fungus inhibits the activity of this protein”, he explains.

Another important discovery came from the analysis of variations in soybean DNA in this gene targeted by the fungus, which showed a polymorphism that separates soybean cultivars that contain resistance genes to this fungus from those that are susceptible to it.

“This variation reveals a potential DNA-based marker that can aid in the development of soybean cultivars by combining these basal defense genes with resistance genes (Rpp genes),” he emphasizes. Embrapa has already been using Rpp resistance genes in its genetic improvement program to develop soybean cultivars using Shield technology.

Another line of research by Embrapa, in partnership with Bayer, has been exploring the variability existing in natural populations of the fungus, which is widely found in Brazil and the American continent. 

“Resequencing and comparing DNA sequences between different isolates collected in Brazil and in countries on other continents, and over a broad time scale, have revealed regions of the genome with different levels of differentiation. This has allowed, for example, the identification of new mutations in one of the main target genes of fungicides, which may be associated with the efficiency of these molecules. This information may help guide new studies to improve the chemical management of soybean rust,” he explains.  

Asian soybean rust: management strategies

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

Management strategies are centered on practices such as: sanitary void, which is a period of at least 90 days without live soybean plants in the field, to reduce the fungus inoculum (see table below about sanitary void); the use of early cycle cultivars and sowing at the beginning of the season is recommended as a disease escape strategy, the adoption of resistant cultivars, respect for the sowing calendar (see information on scheduling in the table) and the use of fungicides.

Currently, the fungus P.pachyrhizi presents mutations that confer resistance to the three main groups of site-specific fungicides and new mutations can be selected over time. “The fungus that causes the disease is capable of adapting to some of the control strategies, either by losing sensitivity to fungicides or by “breaking” the genetic resistance of soybean cultivars,” explains researcher Cláudia Godoy, from Embrapa Soja.

Therefore, Embrapa's recommendation is for producers to adopt available management strategies in order to preserve available fungicides and cultivars. “All strategies, when used together, have allowed adequate management of the disease. Some regions that use early cultivars to produce a second crop with corn or cotton have experienced escape or late incidence of Asian rust and other diseases that have predominated in the crop. In regions that sow later, cultivars with resistance genes and fungicides have provided good control, even with all the resistance problems that have been occurring”, explains Godoy.

In 2021, the Ministry of Agriculture, Livestock and Supply (Mapa) published Ordinance No. 388, of August 31, 2021, which establishes the sanitary gap, as a measure to control the fungus that causes Asian soybean rust and the sowing calendar, as a phytosanitary measure to rationalize the number of fungicide applications.

Soy void and its importance

In June and July, the health vacuum begins in the three largest Brazilian soybean producers: Paraná (June 10), Mato Grosso (June 15) and Rio Grande do Sul (July 13).

The sanitary break is the defined and continuous period in which no live soybean plants can be kept in a given area. This period must be at least 90 days without the crop and without volunteer plants in the field.

“The objective is to reduce the fungus population in the environment during the off-season and thus delay the occurrence of the disease during the harvest,” explains researcher Claudine Seixas, from Embrapa Soja.

Every year, the sanitary vacuum periods are established by the Secretariat of Agricultural Defense based on suggestions from state Plant Health Defense agencies. For 2022, the periods were established by SDA Ordinance No. 516, of February 1, 2022.

Soybean sowing calendar

Another important management strategy for Asian rust is the establishment of a sowing calendar, which aims to reduce the number of fungicide applications throughout the harvest and thereby reduce the selection pressure for fungus resistance to fungicides.

According to Seixas, late soybean sowings can be infected by the fungus, at the beginning of the harvest (vegetative stages), which requires the application of fungicide to be brought forward and promotes a greater number of applications. “The greater the number of applications, the greater the exposure of fungicides and the greater the chance of accelerating the process of selecting populations resistant to these products”, he explains.