A Simplified Approach for Olive (&amp;lt;i&amp;gt;Olea europaea L.&amp;lt;/i&amp;gt;) Genotyping and Cultivars Traceability

Braglia, Luca; Manca, Antonella; Gianı̀, Silvia; Hatzopoulos, Polydefkis; Breviario, Diego

doi:10.4236/ajps.2017.813234

Cited by 5 publications

(4 citation statements)

References 22 publications

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“…Tubulin-based polymorphism (TBP) is a PCR-based, multilocus, codominant nuclear marker, targeting β-tubulin introns ( Bardini et al, 2004 ; Gavazzi et al, 2012 ), which has been widely tested for plant genotyping at the level of species and lower ranks, e.g., cultivar and ecotypes, in many different genera such as Vitis ( Gavazzi et al, 2016 ), Olea ( Braglia et al, 2017 ), Passiflora ( Braglia et al, 2014 ), and Triticum ( Silletti et al, 2019 ). Similar to AFLP and simple sequence repeats (SSR), polymorphic profiles are generated by amplicon length variation across clones, but differently to these markers, TBP is both fully transferable across species and a non-random marker, with defined genomic target loci that correspond to the members of the β-tubulin multigene family.…”

Section: Introductionmentioning

confidence: 99%

Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting

et al. 2021

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Duckweeds (Lemnaceae) are the smallest and fastest-growing angiosperms. This feature, together with high starch production and good nutritional properties, makes them suitable for several applications, including wastewater treatment, bioenergy production, or feed and food supplement. Due to their reduced morphology and great similarity between diverse species, taxonomic identification of duckweeds is a challenging issue even for experts. Among molecular genotyping methods, DNA barcoding is the most useful tool for species identification without a need for cluster analysis. The combination of two plastid barcoding loci is now considered the gold standard for duckweed classification. However, not all species can be defined with confidence by these markers, and a fast identification method able to solve doubtful cases is missing. Here we show the potential of tubulin-based polymorphism (TBP), a molecular marker based on the intron length polymorphisms of β-tubulin loci, in the genomic profiling of the genera Spirodela, Landoltia, and Lemna. Ninety-four clones were analyzed, including at least two representatives of each species of the three genera, with a special focus on the very heterogeneous species Lemna minor. We showed that a single PCR amplification with universal primers, followed by agarose gel analysis, was able to provide distinctive fingerprinting profiles for 10 out of 15 species. Cluster analysis of capillary electrophoresis–TBP data provided good separation for the remaining species, although the relationship between L. minor and Lemna japonica was not fully resolved. However, an accurate comparison of TBP profiles provided evidence for the unexpected existence of intraspecific hybrids between Lemna turionifera and L. minor, as further confirmed by amplified fragment length polymorphism and sequence analysis of a specific β-tubulin locus. Such hybrids could possibly correspond to L. japonica, as originally suggested by E. Landolt. The discovery of interspecific hybrids opens a new perspective to understand the speciation mechanisms in the family of duckweeds.

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Section: Introductionmentioning

confidence: 99%

Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting

et al. 2021

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“…Unweighted pair group method with arithmetic mean (UPGMA) dendrograms based on Nei and Li’ genetic distance calculated on the TBP data of 37 accessions of the genus Vitis , including different species, rootstocks, subspecies and cultivated clones, correctly grouped them in different clades and branches as similarly found with the use of internationally validated SSR markers [60]. Likewise, a consistent if not better classification, than that obtained with SSR markers, was also obtained by plant TBP genotyping of 15 different olive cultivars was obtained [61].…”

Section: Barcoding By Fragment Analysis: When Less Is Morementioning

confidence: 77%

Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices

Morello

Braglia

Gavazzi

et al. 2019

Genes

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The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.

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“…The same method, however, provided a useful resolution for the presumed Lemna minor clones, with 34 characters scored for the first intron and 36 genotypes identified among the 40 analysed clones [32]. Successful intraspecific genotyping was previously reported in crop species such as grape and olive [33,34]. However, because S. polyrhiza generally shows very little intraspecific variation [21,22], this species is a tough match for the TBP method and could be an exception rather than the common rule.…”

Section: Discussionmentioning

confidence: 95%

Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza

Bog

Braglia

Morello

et al. 2022

Plants

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The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for Spirodela polyrhiza, a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.

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A Simplified Approach for Olive (<i>Olea europaea L.</i>) Genotyping and Cultivars Traceability

Cited by 5 publications

References 22 publications

Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting

Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting

Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices

Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza

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