Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information
Lentil (Lens culinaris Medik.), a diploid (2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2016-10-01
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| Series: | Crop Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214514116300666 |
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| author | Debjyoti Sen Gupta Peng Cheng Gaurav Sablok Dil Thavarajah Pushparajah Thavarajah Clarice J. Coyne Shiv Kumar Michael Baum Rebecca J. McGee |
| author_facet | Debjyoti Sen Gupta Peng Cheng Gaurav Sablok Dil Thavarajah Pushparajah Thavarajah Clarice J. Coyne Shiv Kumar Michael Baum Rebecca J. McGee |
| author_sort | Debjyoti Sen Gupta |
| collection | DOAJ |
| description | Lentil (Lens culinaris Medik.), a diploid (2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information (ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information (NCBI) database to develop unigene-based simple sequence repeat (SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches (using E-value 1 × 10−5) against the public UniProt (http://www.uniprot.org/) and NCBI (http://www.ncbi.nlh.nih.gov/) databases were performed. Further functional annotation was performed using PLAZA (version 3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding. |
| first_indexed | 2024-12-22T21:52:48Z |
| format | Article |
| id | doaj.art-f7d2cc207e044e77aef24c04c257f962 |
| institution | Directory Open Access Journal |
| issn | 2214-5141 |
| language | English |
| last_indexed | 2024-12-22T21:52:48Z |
| publishDate | 2016-10-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Crop Journal |
| spelling | doaj.art-f7d2cc207e044e77aef24c04c257f9622022-12-21T18:11:20ZengKeAi Communications Co., Ltd.Crop Journal2214-51412016-10-014542543310.1016/j.cj.2016.06.012Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database informationDebjyoti Sen Gupta0Peng Cheng1Gaurav Sablok2Dil Thavarajah3Pushparajah Thavarajah4Clarice J. Coyne5Shiv Kumar6Michael Baum7Rebecca J. McGee8Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USADivision of Plant Sciences, University of Missouri, Columbia, MO 65211-7140, USADepartment of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento, ItalyAgricultural and Environmental Sciences, Clemson University, Clemson, SC 29634, USAInternational College Beijing, China Agricultural University, Beijing, ChinaUSDA-ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA 99164, USABIGM Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Instituts, Rabat, MoroccoBIGM Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, LebanonUSDA-ARS, Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, WA 99164, USALentil (Lens culinaris Medik.), a diploid (2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information (ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information (NCBI) database to develop unigene-based simple sequence repeat (SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches (using E-value 1 × 10−5) against the public UniProt (http://www.uniprot.org/) and NCBI (http://www.ncbi.nlh.nih.gov/) databases were performed. Further functional annotation was performed using PLAZA (version 3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.http://www.sciencedirect.com/science/article/pii/S2214514116300666Lens culinarisEST–SSRsFunctional annotationUnigene sequencesEST databaseGenetic resources |
| spellingShingle | Debjyoti Sen Gupta Peng Cheng Gaurav Sablok Dil Thavarajah Pushparajah Thavarajah Clarice J. Coyne Shiv Kumar Michael Baum Rebecca J. McGee Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information Crop Journal Lens culinaris EST–SSRs Functional annotation Unigene sequences EST database Genetic resources |
| title | Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information |
| title_full | Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information |
| title_fullStr | Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information |
| title_full_unstemmed | Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information |
| title_short | Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information |
| title_sort | development of a panel of unigene derived polymorphic est ssr markers in lentil using public database information |
| topic | Lens culinaris EST–SSRs Functional annotation Unigene sequences EST database Genetic resources |
| url | http://www.sciencedirect.com/science/article/pii/S2214514116300666 |
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