Frequency and distribution of microsatellites from ESTs of citrus

Frequency and distribution of microsatellites from ESTs of citrus

Nearly 65,000 citrus EST (Expressed Sequence Tags) have been investigated using the CitEST project database. Microsatellites were investigated in the unigene sequences from Citrus spp. and Poncirus trifoliata. From these sequences, approximately 35% of the non-redundant ESTs contained SSRs. The frequencies of different SSR motifs were similar between Citrus spp and trifoliate orange. In general, mononucleotide repeats appeared to be the most abundant SSRs in the CitEST database, but we also identify di-, tri-, tetra-, penta- and hexanucleotide repeats. The AG/CT and AAG/CTT were the most common dinucleotide and trinucleotide motifs, with frequencies of 54.4% and 25.2%, respectively. Primer sequences flanking SSR motifs were successfully designed and synthesized. After in silico polymorphism analysis, a subset of sixty-eight primers was validated in different Citrus spp. and Poncirus trifoliata. PCR-amplification revealed polymorphism in citrus with all tested primer pairs and showed the potential of these markers for linkage mapping. Our study showed that the CitEST database can be exploited for the development of SSR markers that can amplify Citrus spp. and related genus for comparative mapping and other genetic analyses.

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Main Authors: Palmieri,Darío Abel, Novelli,Valdenice Moreira, Bastianel,Marinês, Cristofani-Yaly,Mariângela, Astúa-Monge,Gustavo, Carlos,Eduardo Fermino, Oliveira,Antonio Carlos de, Machado,Marcos Antonio
Format: Digital revista
Language:English
Published: Sociedade Brasileira de Genética 2007
Online Access:http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500029
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spelling oai:scielo:S1415-475720070005000292007-11-06Frequency and distribution of microsatellites from ESTs of citrusPalmieri,Darío AbelNovelli,Valdenice MoreiraBastianel,MarinêsCristofani-Yaly,MariângelaAstúa-Monge,GustavoCarlos,Eduardo FerminoOliveira,Antonio Carlos deMachado,Marcos Antonio Citrus spp. Poncirus trifoliata ESTs microsatellites in silico polymorphism Nearly 65,000 citrus EST (Expressed Sequence Tags) have been investigated using the CitEST project database. Microsatellites were investigated in the unigene sequences from Citrus spp. and Poncirus trifoliata. From these sequences, approximately 35% of the non-redundant ESTs contained SSRs. The frequencies of different SSR motifs were similar between Citrus spp and trifoliate orange. In general, mononucleotide repeats appeared to be the most abundant SSRs in the CitEST database, but we also identify di-, tri-, tetra-, penta- and hexanucleotide repeats. The AG/CT and AAG/CTT were the most common dinucleotide and trinucleotide motifs, with frequencies of 54.4% and 25.2%, respectively. Primer sequences flanking SSR motifs were successfully designed and synthesized. After in silico polymorphism analysis, a subset of sixty-eight primers was validated in different Citrus spp. and Poncirus trifoliata. PCR-amplification revealed polymorphism in citrus with all tested primer pairs and showed the potential of these markers for linkage mapping. Our study showed that the CitEST database can be exploited for the development of SSR markers that can amplify Citrus spp. and related genus for comparative mapping and other genetic analyses.info:eu-repo/semantics/openAccessSociedade Brasileira de GenéticaGenetics and Molecular Biology v.30 n.3 suppl.0 20072007-01-01info:eu-repo/semantics/articletext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500029en10.1590/S1415-47572007000500029
institution SCIELO
collection OJS
country Brasil
countrycode BR
component Revista
access En linea
databasecode rev-scielo-br
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region America del Sur
libraryname SciELO
language English
format Digital
author Palmieri,Darío Abel
Novelli,Valdenice Moreira
Bastianel,Marinês
Cristofani-Yaly,Mariângela
Astúa-Monge,Gustavo
Carlos,Eduardo Fermino
Oliveira,Antonio Carlos de
Machado,Marcos Antonio
spellingShingle Palmieri,Darío Abel
Novelli,Valdenice Moreira
Bastianel,Marinês
Cristofani-Yaly,Mariângela
Astúa-Monge,Gustavo
Carlos,Eduardo Fermino
Oliveira,Antonio Carlos de
Machado,Marcos Antonio
Frequency and distribution of microsatellites from ESTs of citrus
author_facet Palmieri,Darío Abel
Novelli,Valdenice Moreira
Bastianel,Marinês
Cristofani-Yaly,Mariângela
Astúa-Monge,Gustavo
Carlos,Eduardo Fermino
Oliveira,Antonio Carlos de
Machado,Marcos Antonio
author_sort Palmieri,Darío Abel
title Frequency and distribution of microsatellites from ESTs of citrus
title_short Frequency and distribution of microsatellites from ESTs of citrus
title_full Frequency and distribution of microsatellites from ESTs of citrus
title_fullStr Frequency and distribution of microsatellites from ESTs of citrus
title_full_unstemmed Frequency and distribution of microsatellites from ESTs of citrus
title_sort frequency and distribution of microsatellites from ests of citrus
description Nearly 65,000 citrus EST (Expressed Sequence Tags) have been investigated using the CitEST project database. Microsatellites were investigated in the unigene sequences from Citrus spp. and Poncirus trifoliata. From these sequences, approximately 35% of the non-redundant ESTs contained SSRs. The frequencies of different SSR motifs were similar between Citrus spp and trifoliate orange. In general, mononucleotide repeats appeared to be the most abundant SSRs in the CitEST database, but we also identify di-, tri-, tetra-, penta- and hexanucleotide repeats. The AG/CT and AAG/CTT were the most common dinucleotide and trinucleotide motifs, with frequencies of 54.4% and 25.2%, respectively. Primer sequences flanking SSR motifs were successfully designed and synthesized. After in silico polymorphism analysis, a subset of sixty-eight primers was validated in different Citrus spp. and Poncirus trifoliata. PCR-amplification revealed polymorphism in citrus with all tested primer pairs and showed the potential of these markers for linkage mapping. Our study showed that the CitEST database can be exploited for the development of SSR markers that can amplify Citrus spp. and related genus for comparative mapping and other genetic analyses.
publisher Sociedade Brasileira de Genética
publishDate 2007
url http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500029
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