Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series

Persistent Link:
http://hdl.handle.net/10150/610083
Title:
Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series
Author:
Blair, Matthew; Hurtado, Natalia; Chavarro, Carolina; Munoz-Torres, Monica; Giraldo, Martha; Pedraza, Fabio; Tomkins, Jeff; Wing, Rod
Affiliation:
CIAT - International Center for Tropical Agriculture, Biotechnology Unit and Bean Project, AA6713, Cali, Valle, Colombia; Clemson University Genomics Institute, Clemson, South Carolina, USA; Department of Biology, Georgetown University, Washington DC, USA; Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA; Sun Seeds, Fargo ND, USA; Arizona Genomics Institute, Tuscon, Arizona, USA
Issue Date:
2011
Publisher:
BioMed Central
Citation:
Blair et al. BMC Plant Biology 2011, 11:50 http://www.biomedcentral.com/1471-2229/11/50
Journal:
BMC Plant Biology
Rights:
© 2011 Blair 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)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants.RESULTS:A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers.CONCLUSIONS:The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva Granada and Mesoamerica subgroup 1 (black beans) both with regards to gene expression and as sources of markers. However, we found few differences between SSR type and frequency between the G19833 leaf and DOR364 root tissue-derived ESTs. Overall, our work adds to the analysis of microsatellite frequency evaluation for common bean and provides a new set of 120 BMc markers which combined with the 248 previously developed BMc markers brings the total in this series to 368 markers. Once we include BMd markers, which are derived from GenBank sequences, the current total of gene-based markers from our laboratory surpasses 500 markers. These markers are basic for studies of the transcriptome of common bean and can form anchor points for genetic mapping studies in the future.
EISSN:
1471-2229
DOI:
10.1186/1471-2229-11-50
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2229/11/50

Full metadata record

DC FieldValue Language
dc.contributor.authorBlair, Matthewen
dc.contributor.authorHurtado, Nataliaen
dc.contributor.authorChavarro, Carolinaen
dc.contributor.authorMunoz-Torres, Monicaen
dc.contributor.authorGiraldo, Marthaen
dc.contributor.authorPedraza, Fabioen
dc.contributor.authorTomkins, Jeffen
dc.contributor.authorWing, Roden
dc.date.accessioned2016-05-20T08:58:10Z-
dc.date.available2016-05-20T08:58:10Z-
dc.date.issued2011en
dc.identifier.citationBlair et al. BMC Plant Biology 2011, 11:50 http://www.biomedcentral.com/1471-2229/11/50en
dc.identifier.doi10.1186/1471-2229-11-50en
dc.identifier.urihttp://hdl.handle.net/10150/610083-
dc.description.abstractBACKGROUND:Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants.RESULTS:A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellitesen
dc.description.abstractthe majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers.CONCLUSIONS:The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva Granada and Mesoamerica subgroup 1 (black beans) both with regards to gene expression and as sources of markers. However, we found few differences between SSR type and frequency between the G19833 leaf and DOR364 root tissue-derived ESTs. Overall, our work adds to the analysis of microsatellite frequency evaluation for common bean and provides a new set of 120 BMc markers which combined with the 248 previously developed BMc markers brings the total in this series to 368 markers. Once we include BMd markers, which are derived from GenBank sequences, the current total of gene-based markers from our laboratory surpasses 500 markers. These markers are basic for studies of the transcriptome of common bean and can form anchor points for genetic mapping studies in the future.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2229/11/50en
dc.rights© 2011 Blair 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)en
dc.titleGene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc seriesen
dc.typeArticleen
dc.identifier.eissn1471-2229en
dc.contributor.departmentCIAT - International Center for Tropical Agriculture, Biotechnology Unit and Bean Project, AA6713, Cali, Valle, Colombiaen
dc.contributor.departmentClemson University Genomics Institute, Clemson, South Carolina, USAen
dc.contributor.departmentDepartment of Biology, Georgetown University, Washington DC, USAen
dc.contributor.departmentDepartment of Plant Pathology, Kansas State University, Manhattan, Kansas, USAen
dc.contributor.departmentSun Seeds, Fargo ND, USAen
dc.contributor.departmentArizona Genomics Institute, Tuscon, Arizona, USAen
dc.identifier.journalBMC Plant Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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