LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement

Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SS...

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Autores principales:	Naveen Duhan, Rakesh Kaundal
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Fabaceae genetic linkage map genomics <i>in silico</i> data mining marker-assisted selection plant breeding and genetics Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/014c7876fa2e4d90a49476da0cb0fff9
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id	oai:doaj.org-article:014c7876fa2e4d90a49476da0cb0fff9
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spelling	oai:doaj.org-article:014c7876fa2e4d90a49476da0cb0fff92021-11-11T16:49:42ZLegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement10.3390/ijms2221113501422-00671661-6596https://doaj.org/article/014c7876fa2e4d90a49476da0cb0fff92021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11350https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform <i>in silico</i> validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that <i>legumeSSRdb</i> would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.Naveen DuhanRakesh KaundalMDPI AGarticleFabaceaegenetic linkage mapgenomics<i>in silico</i> data miningmarker-assisted selectionplant breeding and geneticsBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11350, p 11350 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Fabaceae genetic linkage map genomics <i>in silico</i> data mining marker-assisted selection plant breeding and genetics Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	Fabaceae genetic linkage map genomics <i>in silico</i> data mining marker-assisted selection plant breeding and genetics Biology (General) QH301-705.5 Chemistry QD1-999 Naveen Duhan Rakesh Kaundal LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement
description	Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform <i>in silico</i> validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that <i>legumeSSRdb</i> would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.
format	article
author	Naveen Duhan Rakesh Kaundal
author_facet	Naveen Duhan Rakesh Kaundal
author_sort	Naveen Duhan
title	LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement
title_short	LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement
title_full	LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement
title_fullStr	LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement
title_full_unstemmed	LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement
title_sort	legumessrdb: a comprehensive microsatellite marker database of legumes for germplasm characterization and crop improvement
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/014c7876fa2e4d90a49476da0cb0fff9
work_keys_str_mv	AT naveenduhan legumessrdbacomprehensivemicrosatellitemarkerdatabaseoflegumesforgermplasmcharacterizationandcropimprovement AT rakeshkaundal legumessrdbacomprehensivemicrosatellitemarkerdatabaseoflegumesforgermplasmcharacterizationandcropimprovement
_version_	1718432218671480832

LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement

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