Genomewide identification and development of microsatellite markers for <i>Marssonina brunnea</i> and their applications in two populations

Zhang, Y.; He, Wei; Yan, Donghui

doi:10.1111/efp.12433

Cited by 3 publications

(3 citation statements)

References 46 publications

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“…This finding is in agreement with the previous results obtained from U. maydis and R. cerealis (Li et al., 2017; Zhang et al., 2015). However, di‐nucleotide repeats were the most abundant in some other fungi, such as Marssonina brunnea and P. graminis (Karaoglu et al., 2013; Zhang et al., 2018). Hence, the SSR loci with di‐nucleotide and tri‐nucleotide repeats are often used for the development of SSR markers.…”

Section: Discussionmentioning

confidence: 99%

Development of genomic SSR markers and genetic diversity of Sphaerulina musiva in China

Ma,

Hu,

et al. 2023

Journal of Phytopathology

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Sphaerulina musiva is an important poplar pathogenic fungus that causes leaf spot and stem canker. SSR markers serve as excellent molecular markers for assessing genetic diversity in fungi. To date, few SSR markers have been developed and applied in S. musiva. In this study, genomic‐SSR markers were developed from the S. musiva genome, and applied to analyse the genetic diversity of S. musiva isolates from Henan province in China. A total of 9923 SSR loci were identified with a relative abundance of 343.15 SSR loci per Mb. Tri‐nucleotide repeats were the most abundant in five types of SSRs, and accounted for 56.82% of the total SSR loci. Twelve genomic‐SSR markers were successfully developed from tri‐nucleotide SSR loci. The number of alleles per locus ranged from 3 to 8 with an average of 4.08 alleles. The polymorphism information content of these loci ranged from 0.428 to 0.770, with an average of 0.553. Based on the SSR markers, a total of 48 haplotypes were identified from 48 S. musiva isolates. Forty‐eight isolates were divided into four main genetic groups at a genetic distance of 0.21. Genetic relationships of the isolates had no obvious correlation with geographic origin. It is the first time to develop genomic SSR markers in S. musiva. The developed SSR markers will be a useful tool to evaluate genetic diversity and population structure of S. musiva.

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Section: Discussionmentioning

confidence: 99%

Development of genomic SSR markers and genetic diversity of Sphaerulina musiva in China

Ma,

Hu,

et al. 2023

Journal of Phytopathology

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“…We initially screened 75 randomly selected microsatellite markers against three isolates of G. obscura , resulting in 100% amplification in at least one isolate. Whole‐genome sequencing approach to microsatellite marker development generally results in greater than 80% positive amplification (Cai et al, 2013; Mercière et al, 2015; Schoebel, Jung, et al, 2013; Si et al, 2019; Varady et al, 2019; Zhang et al, 2018). Polymorphic alleles are more difficult to predict and generally range from 10% to 70% of amplicons (Cai et al, 2013; Mercière et al, 2015; Schoebel, Jung, et al, 2013; Si et al, 2019; Zhang et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Whole‐genome sequencing approach to microsatellite marker development generally results in greater than 80% positive amplification (Cai et al, 2013; Mercière et al, 2015; Schoebel, Jung, et al, 2013; Si et al, 2019; Varady et al, 2019; Zhang et al, 2018). Polymorphic alleles are more difficult to predict and generally range from 10% to 70% of amplicons (Cai et al, 2013; Mercière et al, 2015; Schoebel, Jung, et al, 2013; Si et al, 2019; Zhang et al, 2018). Our results showed that 48% of the microsatellite markers produced polymorphic amplicons and could be of use in population genetic studies.…”

Section: Discussionmentioning

confidence: 99%

Characterization and microsatellite marker development for a common bark and ambrosia beetle associate, Geosmithia obscura

et al. 2022

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Symbioses between Geosmithia fungi and wood‐boring and bark beetles seldom result in disease induction within the plant host. Yet, exceptions exist such as Geosmithia morbida, the causal agent of Thousand Cankers Disease (TCD) of walnuts and wingnuts, and Geosmithia sp. 41, the causal agent of Foamy Bark Canker disease of oaks. Isolates of G. obscura were recovered from black walnut trees in eastern Tennessee and at least one isolate induced cankers following artificial inoculation. Due to the putative pathogenicity and lack of recovery of G. obscura from natural lesions, a molecular diagnostic screening tool was developed using microsatellite markers mined from the G. obscura genome. A total of 3256 candidate microsatellite markers were identified (2236, 789, 137 di‐, tri‐, and tetranucleotide motifs, respectively), with 2011, 703, 101 di‐, tri‐, and tetranucleotide motifs, respectively, containing markers with primers. From these, 75 microsatellite markers were randomly selected, screened, and optimized, resulting in 28 polymorphic markers that yielded single, consistently recovered bands, which were used in downstream analyses. Five of these microsatellite markers were found to be specific to G. obscura and did not cross‐amplify into other, closely related species. Although the remaining tested markers could be useful, they cross‐amplified within different Geosmithia species, making them not reliable for G. obscura detection. Five novel microsatellite markers (GOBS9, GOBS10, GOBS41, GOBS43, and GOBS50) were developed based on the G. obscura genome. These species‐specific microsatellite markers are available as a tool for use in molecular diagnostics and can assist future surveillance studies.

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Key Genes and Genetic Interactions of Plant-Pathogen Functional Modules in Poplar Infected by Marssonina brunnea

Chen

Zhang

Zhao

et al. 2020

MPMI

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Marssonina brunnea, the causative pathogen of Marssonina leaf spot of poplars (MLSP), devastates poplar plantations by forming black spots on leaves and defoliating trees. Although MLSP has been studied for over 30 years, the key genes that function during M. brunnea infection and their effects on plant growth are poorly understood. Here, we used multigene association studies to investigate the effects of key genes in the plant-pathogen interaction pathway, as revealed by transcriptome analysis, on photosynthesis and growth in a natural population of 435 Populus tomentosa individuals. By analyzing transcriptomic changes during three stages of infection, we detected 628 transcription factor genes among the 7,611 differentially expressed genes that might be associated with basal defense responses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that transcriptomic changes across different stages of infection lead to the reprogramming of metabolic processes possibly related to defense activation. We identified 29,399 common single-nucleotide polymorphisms (SNPs) within 221 full-length genes in plant-pathogen interaction pathways that were significantly associated with photosynthetic and growth traits. We also detected 4,460 significant epistatic pairs associated with stomatal conductance, tree diameter, and tree height. Epistasis analysis uncovered significant interactions between 2,561 SNP-SNP pairs from different functional modules in the plant-pathogen interaction pathway, revealing possible genetic interactions. This analysis revealed many key genes that function during M. brunnea infection and their potential roles in mediating photosynthesis and plant growth, shedding light on genetic interactions between functional modules in the plant-pathogen interaction pathway.

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Genomewide identification and development of microsatellite markers for Marssonina brunnea and their applications in two populations

Cited by 3 publications

References 46 publications

Development of genomic SSR markers and genetic diversity of Sphaerulina musiva in China

Development of genomic SSR markers and genetic diversity of Sphaerulina musiva in China

Characterization and microsatellite marker development for a common bark and ambrosia beetle associate, Geosmithia obscura

Key Genes and Genetic Interactions of Plant-Pathogen Functional Modules in Poplar Infected by Marssonina brunnea

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