Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map

Wang, Wei; Chen, Bingzhi; Zhang, Lei; Yan, Junjie; Lu, Yuanping; Zhang, Xiaoyin; Jiang, Yuji; Wu, Theodore Y.; Peer, Arend F. van; Li, Shaojie; Xie, Baogui

doi:10.3390/ijms160716669

Cited by 4 publications

(6 citation statements)

References 55 publications

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“…Recent identification of SV markers for PYd15 and PYd21 ( Wang et al 2015 ) enabled analysis of homo- and heterokaryosity with a higher resolution. Twenty-four different SV markers of 10 independent linkage groups were selected to analyze 105 SSIs of heterokaryon H1521, together with MAT-A loci specific primers for A1 and A2 mating types ( Table S4 ).…”

Section: Resultsmentioning

confidence: 99%

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Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Chen

Peer

Yan

et al. 2016

G3 Genes|Genomes|Genetics

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Volvariella volvacea is an important crop in Southeast Asia, but erratic fruiting presents a serious challenge for its production and breeding. Efforts to explain inconsistent fruiting have been complicated by the multinucleate nature, typical lack of clamp connections, and an incompletely identified sexual reproductive system. In this study, we addressed the life cycle of V. volvacea using whole genome sequencing, cloning of MAT loci, karyotyping of spores, and fruiting assays. Microscopy analysis of spores had previously indicated the possible coexistence of heterothallic and homothallic life cycles. Our analysis of the MAT loci showed that only MAT-A, and not MAT-B, controlled heterokaryotization. Thus, the heterothallic life cycle was bipolar. Karyotyping of single spore isolates (SSIs) using molecular markers supported the existence of heterokaryotic spores. However, most SSIs were clearly not heterokaryotic, yet contained structural variation (SV) markers relating to both alleles of both parents. Heterokaryons from crossed, self-sterile homokaryons could produce fruiting bodies, agreeing with bipolar heterothallism. Meanwhile, some SSIs with two different MAT-A loci also produced fruiting bodies, which supported secondary homothallism. Next, SSIs that clearly contained only one MAT-A locus (homothallism) were also able to fruit, demonstrating that self-fertile SSIs were not, per definition, secondary homothallic, and that a third life cycle or genetic mechanism must exist. Finally, recombination between SV markers was normal, yet 10 out of 24 SV markers showed 1:2 or 1:3 distributions in the spores, and large numbers of SSIs contained doubled SV markers. This indicated selfish genes, and possibly partial aneuploidy.

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Section: Resultsmentioning

confidence: 99%

“…Mating of homokaryons was confirmed by PCR on genomic DNA of crossed strains (see above) using MAT-A -specific markers ( Table S1B ). Sequence-characterized amplified regions (SCAR) and structural variation (SV) markers for analysis of single spore isolates were described by Wang et al (2015) .…”

Section: Methodsmentioning

confidence: 99%

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Chen

Peer

Yan

et al. 2016

G3 Genes|Genomes|Genetics

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“…Wang et al . (2015) developed 104 SV markers and constructed a linkage map for the basidiomycete Volvariella volvacea . In this study, we developed 195 SV markers for DXWR.…”

Section: Discussionmentioning

confidence: 99%

“…If the direction or distance is abnormal, then the region might has SVs. Abnormal pair-end alignments were further analysed by clustering and compared with previously defined SVs (Wang et al, 2015). The SVs were detected using the SOAPsv program as described by Li et al (2011), with support from at least three abnormal paired-end reads.…”

Section: Methodsmentioning

confidence: 99%

“…SV markers are genomic structural variation markers that represent deletions, insertions, duplications, inversions, and translocations of DNA segments in the genome (Xu et al ., 2011). SV markers can not only detect structural variations of up to several thousand nucleotide bases, but also have the advantages of co-dominance, repeatability, stability, and simplicity of use (Wang et al ., 2015). Although SVs had been studied in DXWR (Zhang et al ., 2016), the development of SV markers in this valuable genetic resource has not been reported.…”

Section: Introductionmentioning

confidence: 99%

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Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Zhang

Luo

et al. 2019

Plant Genet. Resour.

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Dongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

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Detection of Edible Mushroom Species by Using Molecular Markers

Khatun¹,

Islam²,

Gupta³

et al. 2017

Fungal Biology

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Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map

Cited by 4 publications

References 55 publications

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Detection of Edible Mushroom Species by Using Molecular Markers

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