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

Abstract

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.

Population and genome-wide association studies of Sclerotinia sclerotiorum isolates collected from diverse host plants throughout the United States

“…Variation in S. sclerotiorum isolate aggressiveness has been reported previously on numerous crop hosts, including sunflower ( Ekins et al, 2007 ; Otto-Hanson et al, 2011 ; Taylor et al, 2015 ; Denton-Giles et al, 2018 ; Yu et al, 2020 ; Rather et al, 2022 ). We observed only a modest correlation between isolate aggressiveness on the two sunflower inbred lines, consistent with observations of genotype-isolate interactions for S. sclerotiorum isolates evaluated on crop hosts such as soybean, canola, and sunflower ( Davar et al, 2011 ; Ge et al, 2012 ; Willbur et al, 2017 ; Buchwaldt et al, 2022 ). Resistance to S. sclerotiorum is quantitative rather than governed by single, dominant resistance genes characteristic of gene-for-gene interactions commonly observed in plant interactions with biotrophic pathogens.…”

Molecular Characterization of Ciborinia camelliae Kohn Shows Intraspecific Variability and Suggests Transcontinental Movement of the Pathogen

“…This was further confirmed by the complete MLST sequence and UP-PCR profile identity of French and New Zealand isolates, as reported in Figure 4 [47][48][49]. Studies on the diversity within the Sclerotiniacae family showed that variability among strains can be very high [50], but it can also be very limited in space and time [51], suggesting the need to better decipher the different genetic backgrounds of Sclerotiniaceae undergoing fast genetic changes, or on the contrary, high genetic stability.…”

Cryptic recombination and transposition drive structural variation to shape genomic plasticity and life history traits in a host generalist fungal plant pathogen

“…Clonality was most prevalent among the Australian strains, whereas European and North American strains were mostly genotypically distinct (Figure 1). This was expected because most of the European and North American strains were previously shown to be distinct lineages using markers [48,49], whereas 99 of the Australian strains were collected from five sites (two of which were in the same locality) in Western Australia with no prior genotyping [50,51].…”