Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.

Simple sequence repeats (SSR) or micro-satellites are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. De novo generation of micro-satellite markers through laboratory-based screening of SSR-enriched genomic libraries is highly time c...

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Autores principales:	Mahalakshmi,Viswanathan, Aparna,P., Ramadevi,S., Ortiz,Rodomiro
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2002
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582002000300007
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spelling	oai:scielo:S0717-345820020003000072003-08-18Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.Mahalakshmi,ViswanathanAparna,P.Ramadevi,S.Ortiz,Rodomiro Simple sequence repeats (SSR) or micro-satellites are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. De novo generation of micro-satellite markers through laboratory-based screening of SSR-enriched genomic libraries is highly time consuming and expensive. An alternative is to screen the public databases of related model species where abundant sequence data is already available. All the genomic sequences of Medicago from the public domain database were searched and analysed of di, tri, and tetra nucleotide repeats. Of the total of about 156,000 sequences which were searched, 7325 sequences were found to contain repeat motif and may yield SSR which will yield product sizes of around 200 bp. Of these the most abundantly found repeats were the tri-nucleotide (5210) group. Except for a very small proportion (436), these link to the gene annotation database at TIGR (<A HREF="http://www.tigr.org/">http://www.tigr.org</A>). To facilitate further exploration of this resource, a dynamic database with options to search and link to other resources is available at (<A HREF="http://www.icrisat.org/text/research/grep/homepage/genomics/medssrs1.asp">http://www.icrisat.org/text/research/grep/homepage/genomics/medssrs1.asp</A>) and on CDs from <A HREF="mailto:V.Mahalakshmi@cgiar.org">V.Mahalakshmi@cgiar.org</A>.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.5 n.3 20022002-12-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582002000300007en
institution	Scielo Chile
collection	Scielo Chile
language	English
description	Simple sequence repeats (SSR) or micro-satellites are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. De novo generation of micro-satellite markers through laboratory-based screening of SSR-enriched genomic libraries is highly time consuming and expensive. An alternative is to screen the public databases of related model species where abundant sequence data is already available. All the genomic sequences of Medicago from the public domain database were searched and analysed of di, tri, and tetra nucleotide repeats. Of the total of about 156,000 sequences which were searched, 7325 sequences were found to contain repeat motif and may yield SSR which will yield product sizes of around 200 bp. Of these the most abundantly found repeats were the tri-nucleotide (5210) group. Except for a very small proportion (436), these link to the gene annotation database at TIGR (<A HREF="http://www.tigr.org/">http://www.tigr.org</A>). To facilitate further exploration of this resource, a dynamic database with options to search and link to other resources is available at (<A HREF="http://www.icrisat.org/text/research/grep/homepage/genomics/medssrs1.asp">http://www.icrisat.org/text/research/grep/homepage/genomics/medssrs1.asp</A>) and on CDs from <A HREF="mailto:V.Mahalakshmi@cgiar.org">V.Mahalakshmi@cgiar.org</A>.
author	Mahalakshmi,Viswanathan Aparna,P. Ramadevi,S. Ortiz,Rodomiro
spellingShingle	Mahalakshmi,Viswanathan Aparna,P. Ramadevi,S. Ortiz,Rodomiro Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.
author_facet	Mahalakshmi,Viswanathan Aparna,P. Ramadevi,S. Ortiz,Rodomiro
author_sort	Mahalakshmi,Viswanathan
title	Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.
title_short	Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.
title_full	Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.
title_fullStr	Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.
title_full_unstemmed	Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.
title_sort	genomic sequence derived simple sequence repeats markers a case study with medicago spp.
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2002
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582002000300007
work_keys_str_mv	AT mahalakshmiviswanathan genomicsequencederivedsimplesequencerepeatsmarkersacasestudywithmedicagospp AT aparnap genomicsequencederivedsimplesequencerepeatsmarkersacasestudywithmedicagospp AT ramadevis genomicsequencederivedsimplesequencerepeatsmarkersacasestudywithmedicagospp AT ortizrodomiro genomicsequencederivedsimplesequencerepeatsmarkersacasestudywithmedicagospp
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Genomic sequence derived simple sequence repeats markers A case study with Medicago spp.

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