Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines

In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs); 262 random amplified polymorphic DNAs (RAPDs); 185 restriction fragment length polymorphisms (RFLPs); and 68 simple sequence repeats (SSR). For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV) revealed a skewed distribution. The dominant markers (AFLP and RAPD) had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for the RAPD markers, all the markers correlated genetic distance with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.

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Main Authors: Garcia,Antonio A. F., Benchimol,Luciana L., Barbosa,Antônia M. M., Geraldi,Isaias O., Souza Jr.,Cláudio L., Souza,Anete P. de
Format: Digital revista
Language:English
Published: Sociedade Brasileira de Genética 2004
Online Access:http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400019
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spelling oai:scielo:S1415-475720040004000192005-01-14Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred linesGarcia,Antonio A. F.Benchimol,Luciana L.Barbosa,Antônia M. M.Geraldi,Isaias O.Souza Jr.,Cláudio L.Souza,Anete P. de diversity studies genetic distances maize molecular markers In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs); 262 random amplified polymorphic DNAs (RAPDs); 185 restriction fragment length polymorphisms (RFLPs); and 68 simple sequence repeats (SSR). For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV) revealed a skewed distribution. The dominant markers (AFLP and RAPD) had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for the RAPD markers, all the markers correlated genetic distance with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.info:eu-repo/semantics/openAccessSociedade Brasileira de GenéticaGenetics and Molecular Biology v.27 n.4 20042004-01-01info:eu-repo/semantics/articletext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400019en10.1590/S1415-47572004000400019
institution SCIELO
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country Brasil
countrycode BR
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libraryname SciELO
language English
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author Garcia,Antonio A. F.
Benchimol,Luciana L.
Barbosa,Antônia M. M.
Geraldi,Isaias O.
Souza Jr.,Cláudio L.
Souza,Anete P. de
spellingShingle Garcia,Antonio A. F.
Benchimol,Luciana L.
Barbosa,Antônia M. M.
Geraldi,Isaias O.
Souza Jr.,Cláudio L.
Souza,Anete P. de
Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines
author_facet Garcia,Antonio A. F.
Benchimol,Luciana L.
Barbosa,Antônia M. M.
Geraldi,Isaias O.
Souza Jr.,Cláudio L.
Souza,Anete P. de
author_sort Garcia,Antonio A. F.
title Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines
title_short Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines
title_full Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines
title_fullStr Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines
title_full_unstemmed Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines
title_sort comparison of rapd, rflp, aflp and ssr markers for diversity studies in tropical maize inbred lines
description In order to compare their relative efficiencies as markers and to find the most suitable marker for maize diversity studies we evaluated 18 inbred tropical maize lines using a number of different loci as markers. The loci used were: 774 amplified fragment length polymorphisms (AFLPs); 262 random amplified polymorphic DNAs (RAPDs); 185 restriction fragment length polymorphisms (RFLPs); and 68 simple sequence repeats (SSR). For estimating genetic distance the AFLP and RFLP markers gave the most correlated results, with a correlation coefficient of r = 0.87. Bootstrap analysis were used to evaluate the number of loci for the markers and the coefficients of variation (CV) revealed a skewed distribution. The dominant markers (AFLP and RAPD) had small CV values indicating a skewed distribution while the codominant markers gave high CV values. The use of maximum values of genetic distance CVs within each sample size was efficient in determining the number of loci needed to obtain a maximum CV of 10%. The number of RFLP and AFLP loci used was enough to give CV values of below 5%, while the SSRs and RAPD loci gave higher CV values. Except for the RAPD markers, all the markers correlated genetic distance with single cross performance and heterosis which showed that they could be useful in predicting single cross performance and heterosis in intrapopulation crosses for broad-based populations. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationships among tropical maize inbred lines with high accuracy.
publisher Sociedade Brasileira de Genética
publishDate 2004
url http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400019
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