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Development of a panel of unigene derived polymorphic EST-SSR markers in lentil using public database information

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Title Development of a panel of unigene derived polymorphic EST-SSR markers in lentil using public database information
 
Creator Sen Gupta, Debjyoti
 
Contributor Cheng, Peng
Sablok, Gaurav
Thavarajah, Dil
Thavarajah, Pushparajah
Coyne, Clarice J
Agrawal, Shiv Kumar
Baum, Michael
McGee, Rebecca
 
Subject unigene sequences
est database
est–ssrs
 
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.
 
Date 2016-10-01
2017-03-05T07:16:58Z
2017-03-05T07:16:58Z
 
Type Journal Article
 
Identifier http://www.sciencedirect.com/science/article/pii/S2214514116300666
https://mel.cgiar.org/reporting/download/hash/TEkgJYPZ
Debjyoti Sen Gupta, Peng Cheng, Gaurav Sablok, Dil Thavarajah, Pushparajah Thavarajah, Clarice J Coyne, Shiv Kumar Agrawal, Michael Baum, Rebecca McGee. (1/10/2016). Development of a panel of unigene derived polymorphic EST-SSR markers in lentil using public database information. The Crop Journal, 4 (5), pp. 425-433.
https://hdl.handle.net/20.500.11766/6148
Open access
 
Language en
 
Rights CC-BY-NC-ND-4.0
 
Format PDF
 
Publisher Crop Science Society of China and Institute of Crop Science, CAAS
 
Source The Crop Journal;4,(2016) Pagination 425-433