Browsing by Author "Cordero, Cecilia"

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    Efficient protocols for the extraction of microbial DNA from the rhizosphere of hydrophilic forests in Chile
    (PONTIFICIA UNIV CATOLICA CHILE, FAC AGRONOMIA INGENIERIA FORESTAL, 2012) Caceres, Pablo; Cordero, Cecilia; Gonzalez, Gloria; Quiroz, Karla; Bobadilla, Juan C.; Bravo, Carmen; Caligari, Peter D. S.; Carrasco, Basilio; Garcia Gonzales, Rolando
    P. Caceres, C. Cordero, G. Gonzalez, K. Quiroz, J.C. Bobadilla, C. Bravo, P.D.S. Caligari, B. Carrasco, and R. Garcia-Gonzales. 2012. Efficient protocols for the extraction of microbial DNA from the rhizosphere of hydrophilic forests in Chile. Cien. Inv. Agr. 38(3): 585-592. A lysis buffer-based protocol (Protocol BA), a modified lysis buffer-based protocol (Protocol BA Mod) and a commercial extraction kit (Protocol PS Kit) (Power Soil, Mo bio Laboratories, CA USA) were each evaluated for their ability to produce high-quality DNA with yields sufficient to allow its use in biodiversity studies. Similarly, the effect of liquid nitrogen on the process of cell disruption in all of the protocols that were studied. DNA yields ranged from 12.4 ng g(-1) of processed soil to 9620 ng g(-1) using the modified lysis buffer and commercial extraction kit, respectively. The quality of the DNA was determined by the ability of the DNA to produce efficient and reproducible polymerase chain reaction (PCR) products, using primers for universal 16S and 18S ribosomal RNA regions from bacteria and fungi, respectively. High-quality DNA was obtained to run PCRs in all protocols, but the efficiency of the method depended on the dilution of the DNA prior to performing the PCR. The three extraction methods generated PCR products with 90% efficiency. The DNA produced with the commercial kit was able to produce the highest PCR efficiency (95%) when the 10(-1) dilution was used. The method based on the use of lysis buffer produced the highest efficiency (90%) using a 10(-2) dilution. Meanwhile, the modified lysis buffer-based protocol generated the highest efficiency of PCR products using the 10(-3) dilution factor with 95% of efficiency. For the first time, reliable and efficient DNA isolation from the rhizosphere of hydrolic forest is documented, enabling a wide range of applications for this technique.
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    MOLECULAR TOOLS FOR RAPID AND ACCURATE DETECTION OF BLACK TRUFFLE (Tuber melanosporum Vitt.) IN INOCULATED NURSERY PLANTS AND COMMERCIAL PLANTATIONS IN CHILE
    (2011) Cordero, Cecilia; Caceres, Pablo; Gonzalez, Gloria; Quiroz, Karla; Bravo, Carmen; Ramirez, Ricardo; Caligari, Peter D. S.; Carrasco, Basilio; Garcia-Gonzales, Rolando
    Truffle (Tuber melanosporum Vitt.) culture is an agroforestry sector in Chile of increasing interest due to the high prices that truffles fetch in the national market and the recent evidence that its commercial production is possible in Chilean climatic and soil conditions. In this study, the efficiency of three methods of DNA extraction from a mix of 5 g of soil and roots from both nursery and field plants of Quercus ilex L. mycorrhized with T. melanosporum were evaluated, and a simple and reproducible protocol was established. Detection of T. melanosporum was performed by the technique of cleaved amplified polymorphic sequence (CAPS) from amplicons generated with the primers ADL1 (5'-GTAACGATAAAGGCCATCTATAGG-3') and ADL3 (5'-CGTTTTTCCTGAACTCTTCATCAC-3'), where a restriction fragment of 160 bp specific for T. melanosporum was generated, which allows the discrimination of this species from the rest of the species belonging to the Tuber sp. genus. Direct detection of T. melanosporum in one step was also obtained by polymerase chain reaction (PCR) from total DNA isolated from mycorrhized roots and with the primers ITSML (5'-TGGCCATGTGTCAGATTTAGTA-3') and ITSLNG (5'-TGATATGCTTAAGTTCAGCGGG-3'), generating a single amplicon of 440 bp. The molecular detection of T. melanosporum by the methods presented here will allow the rapid and accurate detection of mycorrhization of trees, both under nursery and field conditions. This technology will also provide more security to farmers by controlling the quality of the mycorrhized trees they will plant and also by following the mycorrhization status of established orchards.
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    Phylogeographical Analysis of Neotropical Rhagoletis (Diptera: Tephritidae): Did the Andes Uplift Contribute to Current Morphological Differences?
    (2008) Ramirez, Claudio C.; Salazar, Marcela; Eduardo Palma, R.; Cordero, Cecilia; Meza-Basso, Luis
    Neotropical Rhagoletis species are arranged in four groups: nova, psalida, striatella and ferruginea, which include 18 species. On both sides of the Andes, the evolution of morphological differences among these groups has been suggested to be related to the Andes uplift process. In order to test this hypothesis, a phylogenetic analysis of morphological and molecular data was performed. The results suggest that: 1) Neotropical species of Rhagoletis constitute a separate group from Paleartic and North American species, with the only exception being a member of the striatella group having a certain association with the northern species. 2) Neotropical species seem to form a monophyletic clade, although statistical support for this is weak. 3) The split of South American Rhagoletis from other groups was dated at 4.333 million years ago, which is before the emergence of a continuous landbridge between Central and South America. 4) Within species distributed in South America, morphological and molecular data were coincident, placing species of the ferruginea group separate from the other Neotropical Rhagoletis. 5) The divergence of the ferruginea group from the other groups was dated at 3.882 million years ago, which is before the last uplift of the Andes. These results suggest that diversification of the ferruginea, psalida and nova groups, on each side of the Andes, was the result of a vicariant separation followed by dispersal and isolation processes. Thus, these results support the hypothesis that the Andes uplift has played an important role in Neotropical Rhagoletis diversification.