A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber

A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber

Background: Agave tequilana has a great economic importance in Mexico in order to produce alcoholic beverages and bioenergy. However, in this species the structure and organization of the rDNAs in the genome are limited, and it represents an obstacle both in their genetic research and improvement as well. rDNA copy number variations per eukaryotic genome have been considered as a source of genetic rearrangements. In this study, the copy number of 18S and 5S rDNAs in the A. tequilana genome was estimated, and an absolute quantitative qPCR assay and genome size was used. In addition, an association between the rDNAs copy number and physical mapping was performed to confirm our results. Results: The analysis were successfully applied to determine copy number of 18S and 5S rDNAs in A. tequilana genome, showing high reproducibility with coefficient of variation (CV) values of 0.014-0.0129%, respectively. A variation of 51 times in the copy number the 18s regarding 5s rDNA was found, thus contributing to genome size of 1.47 and 8.38 x 10-3%, respectively. Similarly, data show a linear relationship (R [2] = 0.992) between rDNA copy number and the detected signals for each of the loci by FISH. The comparison of the rDNA copy number of agave showed differential relationship with other organisms and it may be due to evolutionary ecology.Conclusions: Results show that the proposed method a) can correctly detect the rDNA copy number, b) could be used as species-specific markers and c) might help in understanding the genetic diversity, genome organization and evolution of this species.

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Main Authors: Rubio-Piña,Jorge, Quiroz-Moreno,Adriana, Sánchez-Teyer,L. Felipe
Format: Digital revista
Language:English
Published: Pontificia Universidad Católica de Valparaíso 2016
Online Access:http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000400002
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spelling oai:scielo:S0717-345820160004000022016-09-13A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila WeberRubio-Piña,JorgeQuiroz-Moreno,AdrianaSánchez-Teyer,L. Felipe Agave tequilana Copy number Fluorescent in situ hybridization Ribosomal DNA Quantitative PCR Background: Agave tequilana has a great economic importance in Mexico in order to produce alcoholic beverages and bioenergy. However, in this species the structure and organization of the rDNAs in the genome are limited, and it represents an obstacle both in their genetic research and improvement as well. rDNA copy number variations per eukaryotic genome have been considered as a source of genetic rearrangements. In this study, the copy number of 18S and 5S rDNAs in the A. tequilana genome was estimated, and an absolute quantitative qPCR assay and genome size was used. In addition, an association between the rDNAs copy number and physical mapping was performed to confirm our results. Results: The analysis were successfully applied to determine copy number of 18S and 5S rDNAs in A. tequilana genome, showing high reproducibility with coefficient of variation (CV) values of 0.014-0.0129%, respectively. A variation of 51 times in the copy number the 18s regarding 5s rDNA was found, thus contributing to genome size of 1.47 and 8.38 x 10-3%, respectively. Similarly, data show a linear relationship (R [2] = 0.992) between rDNA copy number and the detected signals for each of the loci by FISH. The comparison of the rDNA copy number of agave showed differential relationship with other organisms and it may be due to evolutionary ecology.Conclusions: Results show that the proposed method a) can correctly detect the rDNA copy number, b) could be used as species-specific markers and c) might help in understanding the genetic diversity, genome organization and evolution of this species.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.19 n.4 20162016-07-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000400002en10.1016/j.ejbt.2016.05.002
institution SCIELO
collection OJS
country Chile
countrycode CL
component Revista
access En linea
databasecode rev-scielo-cl
tag revista
region America del Sur
libraryname SciELO
language English
format Digital
author Rubio-Piña,Jorge
Quiroz-Moreno,Adriana
Sánchez-Teyer,L. Felipe
spellingShingle Rubio-Piña,Jorge
Quiroz-Moreno,Adriana
Sánchez-Teyer,L. Felipe
A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber
author_facet Rubio-Piña,Jorge
Quiroz-Moreno,Adriana
Sánchez-Teyer,L. Felipe
author_sort Rubio-Piña,Jorge
title A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber
title_short A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber
title_full A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber
title_fullStr A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber
title_full_unstemmed A quantitative PCR approach for determining the ribosomal DNA copy number in the genome of Agave tequila Weber
title_sort quantitative pcr approach for determining the ribosomal dna copy number in the genome of agave tequila weber
description Background: Agave tequilana has a great economic importance in Mexico in order to produce alcoholic beverages and bioenergy. However, in this species the structure and organization of the rDNAs in the genome are limited, and it represents an obstacle both in their genetic research and improvement as well. rDNA copy number variations per eukaryotic genome have been considered as a source of genetic rearrangements. In this study, the copy number of 18S and 5S rDNAs in the A. tequilana genome was estimated, and an absolute quantitative qPCR assay and genome size was used. In addition, an association between the rDNAs copy number and physical mapping was performed to confirm our results. Results: The analysis were successfully applied to determine copy number of 18S and 5S rDNAs in A. tequilana genome, showing high reproducibility with coefficient of variation (CV) values of 0.014-0.0129%, respectively. A variation of 51 times in the copy number the 18s regarding 5s rDNA was found, thus contributing to genome size of 1.47 and 8.38 x 10-3%, respectively. Similarly, data show a linear relationship (R [2] = 0.992) between rDNA copy number and the detected signals for each of the loci by FISH. The comparison of the rDNA copy number of agave showed differential relationship with other organisms and it may be due to evolutionary ecology.Conclusions: Results show that the proposed method a) can correctly detect the rDNA copy number, b) could be used as species-specific markers and c) might help in understanding the genetic diversity, genome organization and evolution of this species.
publisher Pontificia Universidad Católica de Valparaíso
publishDate 2016
url http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000400002
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