Genetic diversity assessment of bittersweet (Solanum dulcamara, Solanaceae) germplasm using conserved DNA-derived polymorphism and intron-targeting markers

Poczai, Péter; Varga, Ildikó; Bell, Neil; Hyvönen, Jaakko

doi:10.1111/j.1744-7348.2011.00482.x

Cited by 28 publications

(23 citation statements)

References 47 publications

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“…The technique is based on single long primer amplification with a high annealing temperature, which improves reproducibility. However, there have also been attempts to combine primers in CDDP reactions to amplify polymorphic regions representing DNA stretches between two identical or very similar conserved primer binding sites [80]. The reproducibility of the technique has proved to be high compared to traditional AADs.…”

Section: Gene-targeted and Functional Markers (Gtms And Fms)mentioning

confidence: 99%

Advances in plant gene-targeted and functional markers: a review

et al. 2013

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Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.

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Section: Gene-targeted and Functional Markers (Gtms And Fms)mentioning

confidence: 99%

Advances in plant gene-targeted and functional markers: a review

et al. 2013

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“…Current efforts in tomato breeding program focused on discovering and utilizing the gene for the trait most important for human being by exploring tomato germplasms (Bai & Lindhout, 2007). Knowledge on germplasm diversity is very important for conservation purposes and plant breeding activities in order to develop varieties and to improve production and productivity (Poczai, Varga, Bell, & Hyvönen, 2011;Herison, Handajaningsih, Fahrurrozi, & Rustikawati, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Analysis in 27 Tomato Accessions Using Morphological and Molecular Markers

Herison

Sutjahjo

Sulastrini³

et al. 2018

Agrivita.J.Agr.Sci

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Genetic diversity is the most important aspect in tomato breeding activities. Better assessment on the diversity of the collected accessions will come up with better result of the cultivar development. This study aimed at analyzing the genetic diversity of 27 tomato accessions by morphological and molecular markers. Twenty seven accessions collected from various regions of Indonesia were planted in the field and evaluated for their morphological traits, and RAPD analyzed for their molecular markers. The UPGMA clustering analyzes, elaborating the combination of morphological and molecular data, indicated that the tomato accessions could be grouped into 5 major groups with 70 % genetic similarity levels. Current study indicated that although many accessions came from different locations, they congregated into the same group. Cherry, Kudamati 1 and Lombok 3 were the farthest genetic distant accessions to the others. Those three genotypes will be the most valuable accessions, when they were crossed with other accessions, for designing a prospective breeding program in the future.

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“…It was also used to evaluate the genetic diversity existed in Solanum dulcamara [22]. The short conserved sequences found in plant genome in multiple copies are targeted by primers designed to bind to these genes and generate polymorphic banding patterns.…”

Section: Conserved Dna Derived Polymorphism (Cddp)mentioning

confidence: 99%

The Use of Molecular Marker Methods in Plants: A Review

2017

IJCRR

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Different DNA markers have been utilized in the last few decades as important molecular tools in plants for genetic relation studies among individuals, hybrid and varietal identification, phylogenetic relationship among species, gene mapping and tracking quantitative trait loci. These markers can be broadly classified into hybridization and PCR based markers. Restriction fragment length polymorphism (RFLP) represents the hybridization based marker; while PCR dependent includes more reliable and advanced polymorphic markers like amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSR), single nucleotide polymorphism (SNP), sequence related amplified polymorphism (SRAP), start codon targeted (SCoT) and interprimer binding site (iPBS) among others. Functional markers (FMs) have also been developed from functionally characterised sequence motifs which are superior to random markers due to their complete linkage to trait locus alleles. With the advent of next generation sequencing (NGS) technology, excellent opportunities are offered for generating ample structural and functional genomic information in many important crops. The novel approach of genotyping-by-sequencing (GBS) employs NGS protocols for discovering and genotyping SNPs in many important crop genomes and populations. The present review focuses on the description of varied molecular markers, their methodologies, strengths and limitations as well as applications in plant breeding and genetic research.

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Genetic diversity assessment of bittersweet (Solanum dulcamara, Solanaceae) germplasm using conserved DNA-derived polymorphism and intron-targeting markers

Cited by 28 publications

References 47 publications

Advances in plant gene-targeted and functional markers: a review

Advances in plant gene-targeted and functional markers: a review

Genetic Diversity Analysis in 27 Tomato Accessions Using Morphological and Molecular Markers

The Use of Molecular Marker Methods in Plants: A Review

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