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Articles containing the keyword 'molecular markers'.

Category: Research article

article id 1691, category Research article
Enéas Ricardo Konzen, Raquel Peron, Márcio Akira Ito, Gilvano Ebling Brondani, Siu Mui Tsai. (2017). Molecular identification of bamboo genera and species based on RAPD-RFLP markers. Silva Fennica vol. 51 no. 4 article id 1691. https://doi.org/10.14214/sf.1691
Highlights: We investigated the potential of RAPD-RFLP (Random Amplified Polymorphic DNA, Restriction Fragment Length Polymorphism) in detecting genetic relationships among bamboo genera and species; RFLP profiles resolved in acrylamide gels revealed high number of markers, which accurately differentiated species and genera, based on cophenetic correlation coefficients; We recommend RAPD-RFLP for analyses of genetic diversity and divergence among bamboo genera, species and varieties.

Bamboo species have a very significant ecological and economic impact. Determining morphological and genetic differences among bamboo genera and species are crucial to explore desirable traits for breeding purposes. Several advances have been made in the taxonomy of bamboos by using molecular fingerprinting tools and next generation sequencing technologies. Nevertheless, classical molecular markers such as RAPD (Random Amplified Polymorphic DNA), AFLP (Amplified Fragment Length Polymorphism) and ISSR (Inter Simple Sequence Repeats) also provide an accurate discrimination among genera and species. Moreover, the RAPD-RFLP (Random Amplified Polymorphic DNA, Restriction Fragment Length Polymorphism) method, in which amplification products from RAPD are digested with restriction enzymes, is a reliable, fast and cost-effective method for fingerprinting. RAPD-RFLP has been scarcely used in the literature and no report regarding bamboo taxonomy is available with this method. Here we explored the molecular (RAPD, RAPD-RFLP) variation among genera (Bambusa, Dendrocalamus, Guadua and Phyllostachys) and species of bamboo cultivated in Brazil. Both molecular markers allowed clear distinction among the genera studied. Moreover, high cophenetic correlation values in UPGMA clusters indicated their potential for discriminating bamboo species. The digestion of RAPD products (RFLP) resulted in high number of polymorphic bands and produced very characteristic profiles for each genus with three enzyme combinations (HindIII/HaeIII, HinfI/RsaI, and single digestion with MspI). We recommend RAPD-RFLP as a reproducible and informative method for screening differences among genera, species and varieties of bamboos. Providing a cost-effective and accurate method for species identification and characterization is straightforward for bamboo conservation, management and breeding.

  • Konzen, Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Centenário Av., 303, Piracicaba, SP, P.O. Box 96, Brazil; Forest Sciences, Federal University of Lavras (UFLA), Lavras, MG, P.O. Box 3037, Brazil ORCID ID:E-mail: erkonzen@gmail.com (email)
  • Peron, Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Centenário Av., 303, Piracicaba, SP, P.O. Box 96, Brazil ORCID ID:E-mail: rperon@purdue.edu
  • Ito, Embrapa Western Agriculture, Brazilian Agricultural Research Corporation (EMBRAPA), BR 163 Rd., km 253, Dourados, MS, P.O. Box 449, Brazil ORCID ID:E-mail: marcio.ito@embrapa.br
  • Brondani, Forest Sciences, Federal University of Lavras (UFLA), Lavras, MG, P.O. Box 3037, Brazil ORCID ID:E-mail: gebrondani@gmail.com
  • Tsai, Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Centenário Av., 303, Piracicaba, SP, P.O. Box 96, Brazil ORCID ID:E-mail: tsai@cena.usp.br
article id 29, category Research article
Piotr Androsiuk, Roman Zielinski, Kornelia Polok. (2011). B-SAP markers derived from the bacterial KatG gene differentiate populations of Pinus sylvestris and provide new insights into their postglacial history. Silva Fennica vol. 45 no. 1 article id 29. https://doi.org/10.14214/sf.29
The aim of the studies was to evaluate the efficiency of the KatG gene based B-SAP markers as a tool to distinguish morphologically diversified and geographically distant Scots pine populations and to track the routes of migrations. The 19 populations growing in the IUFRO 1982 provenance experiment and representing the natural distribution of the species in Europe were scored using 103 B-SAP loci. Among them 26% loci were polymorphic. The level of polymorphism was associated with the location of primers on the KatG template. The diversity was low, He = 0.086, and deposited mostly among populations. Seven unique markers were found that identified populations and likely they were associated with morphology. The overall genetic identity was relatively low, I = 0.933 (D = 0.069). The block of six B-SAP markers discriminated populations into two groups in agreement with their geographic origin and thereby further described as the North and the South. The North group was uniform with genetic diversity, He = 0.026 and the overall genetic distance D = 0.022. Presumably, it migrated from refugia in the Alps via France, northern Germany and Denmark, to Scandinavia and Russia. The South group was heterogeneous with He = 0.063 and D = 0.047. This group migrated from the Carpathians via Slovakia to Germany and Poland. The Balkans and Asian refugia did not take part in recolonization of Europe. The block of six B-SAP/KatG markers can be recommended for tracking postglacial history of Scots pine.
  • Androsiuk, University of Warmia and Mazury in Olsztyn, Department of Genetics, Plac Lodzki 3, 10-967 Olsztyn, Poland ORCID ID:E-mail:
  • Zielinski, University of Warmia and Mazury in Olsztyn, Department of Genetics, Plac Lodzki 3, 10-967 Olsztyn, Poland ORCID ID:E-mail:
  • Polok, University of Warmia and Mazury in Olsztyn, Department of Genetics, Plac Lodzki 3, 10-967 Olsztyn, Poland ORCID ID:E-mail: kpolok@moskit.uwm.edu.pl (email)
article id 476, category Research article
Ignazio Monteleone, Diana Ferrazzini, Piero Belletti. (2006). Effectiveness of neutral RAPD markers to detect genetic divergence between the subspecies uncinata and mugo of Pinus mugo Turra. Silva Fennica vol. 40 no. 3 article id 476. https://doi.org/10.14214/sf.476
Fifteen populations of Pinus mugo subsp. mugo (shrub) and Pinus mugo subsp. uncinata (erect), located in the Alps, were investigated through genetic variation scored at 64 polymorphic RAPD loci. In addition, morphological traits of the female cones were analysed. According to AMOVA most of the genetic variation was found within populations (83.39%), and only 1.25% of it between subspecies. Populations differed in terms of their internal genetic variation, with Nei’s gene diversity ranging from 0.227 to 0.397. Morphological data showed differences between subspecies, although none of the populations showed full accordance with expectations. Significant correlation was found between matrices for geographical and morphological distances, while genetic distances were not correlated with any other aspect. The efficacy of morphological and RAPD markers in discriminating between subspecies, and the contribution of the results in relation to the preservation of biodiversity, are discussed.
  • Monteleone, DI.VA.P.R.A., Plant Genetics and Breeding, University of Turin, via Leonardo da Vinci 44, I-10095 Grugliasco, Italy ORCID ID:E-mail:
  • Ferrazzini, DI.VA.P.R.A., Plant Genetics and Breeding, University of Turin, via Leonardo da Vinci 44, I-10095 Grugliasco, Italy ORCID ID:E-mail:
  • Belletti, DI.VA.P.R.A., Plant Genetics and Breeding, University of Turin, via Leonardo da Vinci 44, I-10095 Grugliasco, Italy ORCID ID:E-mail: piero.belletti@unito.it (email)

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