Selection of Diploid and Tetraploid Banana Hybrids Resistant to Pseudocercospora fijiensis

Black Sigatoka, a disease caused by the fungus Pseudocercospora fijiensis, can lead to the complete loss of banana and plantain production in the absence of chemical control. The development of resistant cultivars is the focus of many banana breeding programs and is an alternative to the use of fungicides. In order to define a refined method of selection in genetic breeding programs, this study evaluated 23 improved diploids, seven tetraploids, and two commercial cultivars in the presence of P. fijiensis. Four selection criteria were considered: means of the disease severity index (ID) and area under the disease progress curve (AUDPC) estimated over the total period of the experiment, only in summer, only in winter, and the emission and harvesting of bunches. The selection of genotypes was more effective in the winter, and the evaluation of four leaves no. 3 emitted after six months of growth was efficient at differentiating the resistant and susceptible genotypes. For the improved diploids and tetraploid hybrids, DI varied from 0.0 to 48.8 and from 15.1 to 63.5, respectively, and the AACPD for the improved hybrids and tetraploid hybrids varied from 0.0 to 2439.5 and 1000.2 to 3717.7, respectively. The tetraploid hybrid of the Prata-type CNPMF0906 and the commercial cultivar, which is a hybrid of the BRS Princesa Silk type, showed quantitative resistance and can be used by banana producers. Results suggest that the guidelines adopted for the selection of genotypes resistant to black Sigatoka may include methodologies that reduce the evaluation time. In addition, new sources of resistance to the disease and the influence of its genetic inheritance in future crosses were found.

A polyketide synthase gene cluster required for pathogenicity of Pseudocercospora fijiensis on banana

Pseudocercospora fijiensis is the causal agent of the highly destructive black Sigatoka disease of banana. Previous research has focused on polyketide synthase gene clusters in the fungus, given the importance of polyketide pathways in related plant pathogenic fungi. A time course study of expression of the previously identified PKS7-1, PKS8-2, and PKS10-2 gene clusters showed high expression of all three PKS genes and the associated clustered genes in infected banana plants from 2 weeks post-inoculation through 9 weeks. Engineered transformants silenced for PKS8-2 and PKS10-2 were developed and tested for pathogenicity. Inoculation of banana plants with silencing transformants for PKS10-2 showed significant reduction in disease symptoms and severity that correlated with the degree of silencing in the conidia used for inoculation, supporting a critical role for PKS10-2 in disease development. Unlike PKS10-2, a clear role for PKS8-2 could not be determined. Two of four PKS8-2 silencing transformants showed reduced disease development, but disease did not correlate with the degree of PKS8-2 silencing in the transformants. Overall, the degree of silencing obtained for the PKS8-2 transformants was less than that obtained for the PKS10-2 transformants, which may have limited the utility of the silencing strategy to identify a role for PKS8-2 in disease. Orthologous PKS10-2 clusters had previously been identified in the related banana pathogens Pseudocercospora musae and Pseudocercospora eumusae. Genome analysis identified orthologous gene clusters to that of PKS10-2 in the newly sequenced genomes of Pseudocercospora fuligena and Pseudocercospora cruenta, pathogens of tomato and cowpea, respectively. Our results support an important role for the PKS10-2 polyketide pathway in pathogenicity of Pseudocercospora fijiensis, and suggest a possible role for this pathway in disease development by other Pseudocercospora species.

Genotype X Environment Response of ‘Matooke’ Hybrids (Naritas) to Pseudocercospora fijiensis, the Cause of Black Sigatoka in Banana

Growing bananas resistant to Pseudocercospora fijiensis, the cause of black Sigatoka, is the preferred disease control strategy for resource-poor farmers. Banana breeding programs in east Africa have developed 27 Matooke hybrids (commonly known as NARITAs) with higher yields than local landraces. To assess the response of NARITA hybrids to P. fijiensis, 22 hybrids were evaluated under natural field conditions in four locations—Kawanda and Mbarara in Uganda, and Maruku, and Mitarula in Tanzania—between 2016 and 2018 for three crop cycles. Black Sigatoka was visually assessed and the area under the disease progress curve calculated for each plant over time. Significant differences (p < 0.001) were observed between genotypes, environments, and their interaction. The highest contributor to black Sigatoka severity (39.1%) was the environment, followed by the genotype (37.5%) and the genotype Χ environment interaction (GEI) (23.4%). NARITA 2, 7, 14, 21 and 23 were resistant and the most stable hybrids across locations. If other attributes such as the yield and taste are acceptable to end-users, these hybrids can be released to farmers in the region to replace highly susceptible landraces. Mitarula was identified as an ideal site for evaluating banana against black Sigatoka and should be used as a representative location to minimize costs of disease evaluations.

The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies

Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease’s complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.

Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen

ABSTRACT Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance. IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.

Analysis of Pseudocercospora fijiensis genes upregulated during early interaction with Musa acuminata (var. Dwarf Cavendish)

Pseudocercospora fijiensis is a filamentous, hemi[B1] biotrophic fungus whose infection process in banana comprises biotrophic and necrotrophic phases; the biotrophic phase is the longer and less damaging of the two but is nonetheless a crucial stage of fungal establishment in the host. To discover the genes essential in this stage, we conducted an interaction experiment to isolate the transcriptome of the P. fijiensis and Musa acuminata interaction during the first 9 days of infection. Of more than 7000 P. fijiensis genes identified, the fifteen most highly expressed genes (RPKM>500) were analyzed. Specific non-canonical effector candidates were identified following in silico characterization which may be fundamental to pathogenicity. This report reveals essential details of a poorly-elucidated stage of the P. fijiensis-Musa sp. pathosystem.

First Draft Genome Sequence Resource of a Strain of Pseudocercospora fijiensis Isolated in North America

Black Sigatoka disease, caused by the fungus Pseudocercospora fijiensis, is one of the most devastating diseases of banana around the world. Fungicide applications are the primary tool used to manage black Sigatoka, but fungicide resistance in P. fijiensis, as in other fungal pathogens, is one of the major limitations in the efficient management and prevention of this disease. In the current study, we present the draft genome of P. fijiensis strain IIL-20, the first genomic sequence published from a strain of this fungus isolated in North America. Bioinformatic analysis showed putative genes involved in fungus virulence and fungicide resistance. These findings may lead us to a better understanding of the molecular pathogenesis of this fungal pathogen and also to the discovery of the mechanisms conferring fungicide resistance.