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A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions

Background: This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. A sample of 548 accessions of traditional upland rice landraces collected in Brazil...

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Main Authors: Pessoa Filho, Marco, Beló, André, Alcochete, António A. N., Rangel, Paulo H. N., Ferreira, Márcio Elias
Format: Artigo
Language: Inglês
Published: BioMed Central 2017
Subjects:
Microssatélites
Arroz
Germoplasma vegetal
Online Access: http://repositorio.unb.br/handle/10482/23866
https://dx.doi.org/10.1186/1471-2229-7-23
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spelling ir-10482-238662021-05-14T13:31:52Z A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions Pessoa Filho, Marco Beló, André Alcochete, António A. N. Rangel, Paulo H. N. Ferreira, Márcio Elias Microssatélites Arroz Germoplasma vegetal Background: This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. A sample of 548 accessions of traditional upland rice landraces collected in Brazil in the last 25 years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed. Results: The three panels yielded a combined matching probability of 6.4 × 10-21, polymorphism information content (PIC) of 0.637, and a combined power of exclusion greater than 99.99%. A few samples presented a genetic background of indica rice. The 16 SSR loci produced a total of 229 alleles. Gene diversity values averaged 0.667, and PIC values averaged 0.637. Genetic structure analysis of the collection using a Bayesian approach detected three possible major clusters, with an overall FST value of 0.177. Important inputs on the knowledge about upland rice germplasm differentiations which happened in Brazil in the last few centuries were also achieved and are discussed. Conclusion: The three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. The data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers. It contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm. 2017-07-20T16:13:43Z 2017-07-20T16:13:43Z 2007-05-21 Artigo PESSOA FILHO, Marco et al. A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions. BMC Plant Biology, v. 7, Article 23, 21 mai. 2007. Disponível em: <https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-7-23>. Acesso em: 19 jun. 2017. doi: https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-7-23. http://repositorio.unb.br/handle/10482/23866 https://dx.doi.org/10.1186/1471-2229-7-23 Inglês Acesso Aberto © 2007 Pessoa-Filho et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. application/pdf BioMed Central
institution REPOSITORIO UNB
collection REPOSITORIO UNB
language Inglês
topic Microssatélites
Arroz
Germoplasma vegetal
spellingShingle Microssatélites
Arroz
Germoplasma vegetal
Pessoa Filho, Marco
Beló, André
Alcochete, António A. N.
Rangel, Paulo H. N.
Ferreira, Márcio Elias
A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
description Background: This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. A sample of 548 accessions of traditional upland rice landraces collected in Brazil in the last 25 years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed. Results: The three panels yielded a combined matching probability of 6.4 × 10-21, polymorphism information content (PIC) of 0.637, and a combined power of exclusion greater than 99.99%. A few samples presented a genetic background of indica rice. The 16 SSR loci produced a total of 229 alleles. Gene diversity values averaged 0.667, and PIC values averaged 0.637. Genetic structure analysis of the collection using a Bayesian approach detected three possible major clusters, with an overall FST value of 0.177. Important inputs on the knowledge about upland rice germplasm differentiations which happened in Brazil in the last few centuries were also achieved and are discussed. Conclusion: The three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. The data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers. It contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm.
format Artigo
author Pessoa Filho, Marco
Beló, André
Alcochete, António A. N.
Rangel, Paulo H. N.
Ferreira, Márcio Elias
author_sort Pessoa Filho, Marco
title A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
title_short A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
title_full A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
title_fullStr A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
title_full_unstemmed A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
title_sort set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions
publisher BioMed Central
publishDate 2017
url http://repositorio.unb.br/handle/10482/23866
https://dx.doi.org/10.1186/1471-2229-7-23
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score 13.657419

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