Genetic variation and structure of <i>Sclerotinia sclerotiorum </i>populations from soybean in Brazil

Pannullo, Anthony G.; Kamvar, Zhian N.; Miorini, T; Steadman, James R.; Everhart, Sydney E.

doi:10.7287/peerj.preprints.26600

Cited by 3 publications

(5 citation statements)

References 7 publications

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“…The values for polymorphic information content (PIC) and genomic diversity (H) for each SSR marker were highly correlated (r = 0.99) and ranged from 0.126 to 0.949 and 0.136 to 0.959, respectively ( Table 2). The PIC value was above 0.5 for 81% (26) of the AAFC markers. The following markers on 12 chromosomes were particularly informative since they each amplified a highly polymorphic locus shared by many isolates: AAFC-2d on chromosome 1, AAFC-22c on chromosome 2, AAFC-3c on chromosome 4, AAFC-7b on chromosome 5, AAFC-9b on chromosome 6, AAFC-6f on chromosome 7, AAFC-11a on chromosome 9, AAFC-20b on chromosome 11, AAFC-33d on chromosome 12, AAFC-12a on chromosome 13, AAFC-25d on chromosome 14, AAFC-15e on chromosome 15, and AAFC-4d on contig R. .…”

Section: Simple Sequence Repeat Polymorphismsmentioning

confidence: 81%

“…In contrast, there were no similarity between SSR haplotype among the remaining incompatible isolates, which had numerous private alleles. [24], 11 SSR [25,26], 12 SSR [27], and 13 SSR [28]. Understandably, using only 6 to 13 SSR markers limits the number of polymorphic alleles that can be detected, and consequently, pathogen populations are seen to comprise isolates with the same haplotype.…”

Section: Discussionmentioning

confidence: 99%

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Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

Buchwaldt

Garg

Puri

et al. 2020

Preprint

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The ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity and aggressiveness were determined in a population of 127 isolates from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was an unique haplotype. Analysis of molecular variation showed 97% was due to isolate and 3% to geographical location. Testing of mycelium compatibility identified clones of mutually compatible isolates, and stings of pairwise compatible isolates not seen before. Importantly, mutually compatible isolates had similar SSR haplotype, in contrast to high diversity among incompatible isolates. Isolates from the Province of Manitoba had higher allelic richness and higher mycelium compatibility (61%) than Alberta (35%) and Saskatchewan (39%). All compatible Manitoba isolates were interconnected in clones and strings, which can be explained by wetter growing seasons and more susceptible crops species both favouring more mycelium interaction and life cycles. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus and restricted outcrossing due to mycelium incompatibility, and only one meiosis per lifecycle. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides, not withstanding the high mutation rate of SSRs compared to genes. It seems accumulation of these polymorphisms lead to increasing mycelium incompatibility in a population over time. A phylogenetic tree grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Results were significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs. Since the S. sclerotiorum life cycle is universal, conclusions on sources of genomic diversity extrapolates to populations in other geographical areas and host crops.Author summarySclerotinia sclerotiorum populations from various plant species and geographical areas have been studied extensively using mycelium compatibility tests and genotyping with a shared set of 6-13 SSR markers published in 2001. Most conclude the pathogen is clonally propagated with some degree of outcrossing. In the present study, a population of S. sclerotiorum isolates from 1.5 million km2 area in western Canada were tested for mycelium compatibility, and genotyped with 9 published and 30 newly developed SSR markers targeting all chromosomes in the dikaryot genome (8+8). A new way of visualizing mycelium compatibility results revealed clones of mutual compatible isolates, as well as long and short strings of pairwise compatible isolates. Importantly, clonal isolates had similar SSR haplotype, while incompatible isolates were highly dissimilar; a relationship difficult to discern previously. Analysis of population structure found a lack of linkage disequilibrium ruling out random recombination. Outcrossing, a result of alignment of non-sister chromosomes during meiosis, is unlikely in S. sclerotiorum, since mycelium incompatibility prevents karyogamy, and compatibility only occur between isolates with similar genomic composition. Instead, genomic diversity comprise transfer of nuclei through hyphal anastomosis, allelic modifications during cell division and point mutation. Genomic polymorphisms accumulate over time likely result in gradual divergence of individuals, which seems to resemble the ‘ring-species’ concept. We are currently studying whether nuclei in microconidia might also contribute to diversity. A phylogenetic analysis grouped isolates into 17 sub-populations. One isolate from each sub-population showed different level of aggressiveness when inoculated onto B. napus lines previously determined to have quantitative resistance to a single isolate. Seed of these lines and S. sclerotiorum isolates have been transferred to plant breeders, and can be requested from the corresponding author for breeding purposes. Quantitative resistance is likely to hold up over time, since the rate of genomic change is relatively slow in S. sclerotiorum.

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Section: Simple Sequence Repeat Polymorphismsmentioning

confidence: 81%

Section: Discussionmentioning

confidence: 99%

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

Buchwaldt

Garg

Puri

et al. 2020

Preprint

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“…Like us, these researchers used different sub-sets of markers published by Sirjusingh and Kohn in 2001 [ 4 ] to genotype S . sclerotiorum isolates from various plant species and geographic locations such as 6 SSR [ 20 ], 8 SSR [ 6 , 21 – 23 ], 10 SSR [ 24 ], 11 SSR [ 25 , 26 ], 12 SSR [ 27 ], and 13 SSR [ 28 ]. Understandably, using only 6 to 13 SSR markers limits the number of polymorphic alleles that can be detected, and consequently, pathogen populations are seen to comprise isolates with the same haplotype.…”

Section: Discussionmentioning

confidence: 99%

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

et al. 2022

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The ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity was determined in a population of 127 isolates obtained from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was a unique haplotype. Analysis of molecular variance showed 97% was due to isolate and 3% due to geographical location. Testing of mycelium compatibility among 133 isolates identified clones of mutually compatible isolates with 86–95% similar SSR haplotype, whereas incompatible isolates were highly diverse. In the Province of Manitoba, 61% of isolates were compatible forming clones and stings of pairwise compatible isolates not described before. In contrast, only 35% of isolates were compatible in Alberta without forming clones and strings, while 39% were compatible in Saskatchewan with a single clone, but no strings. These difference can be explained by wetter growing seasons and more susceptible crop species in Manitoba favouring frequent mycelium interaction and more life cycles over time, which might also explain similar differences observed in other geographical areas and host crops. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus, restricted outcrossing due to mycelium incompatibility, and only a single annual opportunity for genomic recombination during meiosis in the ascospore stage between non-sister chromatids in the rare event nuclei from different isolates come together. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides that accumulate and likely increase mycelium incompatibility in a population over time. A phylogenetic tree based on SSR haplotype grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Analysis of variance was significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs.

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“…Microsatellite markers (e.g. SSR) have been used in population studies for the evaluation of outcrossing potential in S. sclerotiorum and their relation with mycelial compatibility groups (MCGs) (Atallah et al 2004;Attanayake et al 2019;Pannullo et al 2019), a kind of marker that have been thoroughly discussed in a recent review (Kamvar and Everhart 2019). Sympatric isolates originated from different hosts have shown significant phenotypic variability (Mert-Türk et al 2007;Attanayake et al 2013).…”

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confidence: 99%

“…On the other hand, uniformity has been identified in other locations such as in a study of potato-infecting isolates in the United States (Atallah et al 2004). Both large and small variability in S. sclerotiorum populations in common bean have been reported in Brazil (Gomes et al 2011;Abreu and Souza 2015;Lehner et al 2015;Pannullo et al 2019) with the predominance of only a few haplotypes in the Brazilian populations (Lehner et al 2019). The virulence of S. sclerotiorum isolates towards different hosts has also been a topic of investigation in several studies (Atallah et al 2004;Kull et al 2004;Sexton and Howlett 2004;Otto-Hanson et al 2011;Lehner et al 2015Lehner et al , 2019.…”

mentioning

confidence: 99%

Phenotypic and genotypic characterization of single isolate-derived monoascospore strains of Sclerotinia sclerotiorum from common bean

Abreu

Leite

Ferreira

et al. 2019

Trop. plant pathol.

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White mold is a highly destructive disease caused by Sclerotinia sclerotiorum, a polyphagous fungus that infects several hosts including common bean grown that is widely cultivated in Brazil. The pathogenic populations are known to exhibit genetic variability but studies rarely used single ascospore-derived strains. In this study, 12 monoascospore strains originated from a same isolate (UFLA 54), but from different apothecia, were compared among them and with the mother strain with regards: days to first sclerotium formation, mycelial growth rate mycelial compatibility groups, microsatellite markers and mating type locus (MAT1-1 and MAT1-2). Their pathogenicity was assessed on three common bean lines. Cluster analysis of growth rates data separated UFLA 54 from all monoascospore strains, which shared same alleles in the microsatellite locus. Inversion of MAT1-1 region was found for both UFLA 54 and half of monoascospore strains. Aggressiveness of the monoascospore strains was not consistent across common bean lines. Our study reveals significant variability of S. sclerotiorum at the single isolate level. Keywords Phaseolus vulgaris. White mold. Aggressiveness. Morphological traits White mold is a fungal disease caused by Sclerotinia sclerotiorum (Lib.) de Bary, a necrotrophic and homothallic fungus capable of infecting several hosts and causing severe epidemics in important field crops including soybean, common bean and sunflower. White mold epidemics are reported worldwide, including Brazil, with yield losses estimated at 19% to 70% depending on the geographic region and year (

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Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

Cited by 3 publications

References 7 publications

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

Phenotypic and genotypic characterization of single isolate-derived monoascospore strains of Sclerotinia sclerotiorum from common bean

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