Genetic changes in grapevine genomes after stress induced by in vitro cultivation, thermotherapy and virus infection, as revealed by AFLP

Baránek, Miroslav; Raddová, Jana; Křižan, B.; Pidra, M.

doi:10.1590/s1415-47572009005000079

Cited by 14 publications

(8 citation statements)

References 21 publications

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“…AFLP analysis was performed as described in Vos et al (1995) with modification (Baránek et al, 2009). Genomic DNA (0.30 μg) was digested with restriction enzymes EcoRI and MseI (10 units each) at 37°C for 6 h in 1 × NEB buffer, and EcoRI and MseI adapters were ligated to both ends of the restriction fragments with 1 unit of T4 DNA ligase at 16°C overnight.…”

Section: Aflp Protocolmentioning

confidence: 99%

Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

Oduwaye¹,

BarÃ¡nek²,

ÄŒechovÃ³

et al. 2014

J. Plant Breed. Crop Sci.

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The present study reported the effectiveness of two PCR-based molecular techniques, inters simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs), for genetic assessment of amaranth. The polymorphic loci ranged from 110 among A. caudatus to 228 among A. cruentus and 16 among A. tricolor to 56 among A. hypochondriacus for AFLP primer combinations and ISSR primers, respectively. Among the two marker systems used, ISSR fingerprinting detected the highest number of alleles per locus (1.83) compared to AFLPs (1.63). However, the assay efficiency index for AFLP was 14.49, more than five-fold higher than ISSR (1.75). The study also revealed that ISSR primers with di-nucleotide repeats gave a good fingerprint, indicating that di-nucleotide repeats are more frequent in amaranth genome. The reproducibility of the two marker systems was confirmed by the narrow gene diversity (0.03 ± 0.11 to 0.07 ± 0.17) observed between the controls. Bayesian consensus and neighbor-joining trees were constructed to describe the cluster arrangement among the Amaranthus spp. The cluster pattern was similar for both markers, though the cluster order in the trees was slightly different. The results of this study confirm the usefulness of AFLPs and ISSRs for the genetic assessment of amaranth.

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Section: Aflp Protocolmentioning

confidence: 99%

Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

Oduwaye¹,

BarÃ¡nek²,

ÄŒechovÃ³

et al. 2014

J. Plant Breed. Crop Sci.

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“…Müller Thurgau and Riesling, respectively. From distributions not classified into some easy and known scenario of methylation, the following ones were the most frequent: 111101 ( Baranek et al 2009), it is evident that coefficient values were lower in the case of MSAP. However, the level of similarity remained relatively high in spite of the fact that DNA methylation belongs to the most significant agent within epigenetic control of plant stress response (Boyko and Kovalchuk 2008).…”

Section: Statistical Evaluation Of Alterations In Cytosine Methylatiomentioning

confidence: 99%

DNA-methylation changes in grapevine somaclones following in vitro culture and thermotherapy

Baránek

Křižan

Ondrušíková

et al. 2009

Plant Cell Tiss Organ Cult

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The methylation-sensitive amplified polymorphism (MSAP) technique using HpaII and MspI isoschizomers was used to analyse DNA-methylation alterations in stressed grapevine plants. The stress used was in vitro propagation via nodal segments and in vitro thermotherapy for virus elimination. A set of pertinent grapevine plants derived from two cultivars (18 plants each for Müller Thurgau and Riesling) was used as stressed variants for analyses. A total of 695 and 700 MSAP bands were recognised and evaluated as present/absent for all analysed variants derived from both cvs. Müller Thurgau and Riesling. Average computed similarity of MSAP banding between analysed variants (Dice/Nei and Li coefficient) was 0.935 for both cultivars. Clustering of variants within resulting dendrograms showed significant differences between woody cuttings despite originating from the one plant. Further, there was a strong 'donor' effect of maternal plants on future arrays of DNA methylation in their regenerants. The 'donor' effect even seemed to prevail in the effect of stress on final DNA-methylation state in stressed regenerants. Additional MSAP evaluation suggests that thermotherapy induced an additional array of methylation changes when compared with stress caused by in vitro cultivation. From the viewpoint of whether methylation of CCGG loci increased/decreased due to stress, the results showed moderate prevalence for decreasing CCGG loci methylation.

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“…The availability of such a broad-spectrum detection technique provides powerful support to certification processes, which are supposed to guarantee the clean health status of propagation materials [6]. …”

Section: Introductionmentioning

confidence: 99%

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

et al. 2016

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Comprehensive next generation sequencing virus detection was used to detect the whole spectrum of viruses and viroids in selected grapevines from the Czech Republic. The novel NGS approach was based on sequencing libraries of small RNA isolated from grapevine vascular tissues. Eight previously partially-characterized grapevines of diverse varieties were selected and subjected to analysis: Chardonnay, Laurot, Guzal Kara, and rootstock Kober 125AA from the Moravia wine-producing region; plus Müller-Thurgau and Pinot Noir from the Bohemia wine-producing region, both in the Czech Republic. Using next generation sequencing of small RNA, the presence of 8 viruses and 2 viroids were detected in a set of eight grapevines; therefore, confirming the high effectiveness of the technique in plant virology and producing results supporting previous data on multiple infected grapevines in Czech vineyards. Among the pathogens detected, the Grapevine rupestris vein feathering virus and Grapevine yellow speckle viroid 1 were recorded in the Czech Republic for the first time.

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Genetic changes in grapevine genomes after stress induced by in vitro cultivation, thermotherapy and virus infection, as revealed by AFLP

Cited by 14 publications

References 21 publications

Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

Reliability and comparison of the polymorphism revealed in amaranth by amplified fragment length polymorphisms (AFLPs) and inters simple sequence repeats (ISSRs)

DNA-methylation changes in grapevine somaclones following in vitro culture and thermotherapy

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

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