The okra (Abelmoschus esculentus) transcriptome as a source for gene sequence information and molecular markers for diversity analysis

A combined leaf and pod transcriptome of okra (Abelmoschus esculentus (L.) Moench) has been produced by RNA sequencing and short read assembly. More than 150,000 unigenes were obtained, comprising some 46million base pairs of sequence information. More than 55% of the unigenes were annotated through...

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Bibliographic Details
Published in:Gene 2013-03, Vol.517 (1), p.27-36
Main Authors: Schafleitner, Roland, Kumar, Sanjeet, Lin, Chen-yu, Hegde, Satish Gajanana, Ebert, Andreas
Format: Article
Language:English
Subjects:
Abelmoschus - genetics
Abelmoschus esculentus
breeding
DNA, Plant - genetics
Genes, Plant
genetic markers
Genome, Plant
genomics
genotype
germplasm
leaves
Microsatellite marker
microsatellite repeats
Microsatellite Repeats - genetics
Next-generation sequencing
okra
Plant Leaves - genetics
Polymorphism, Genetic
provenance
RNA
sequence analysis
Sequence Analysis, RNA
Transcriptome
unigenes
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Summary:A combined leaf and pod transcriptome of okra (Abelmoschus esculentus (L.) Moench) has been produced by RNA sequencing and short read assembly. More than 150,000 unigenes were obtained, comprising some 46million base pairs of sequence information. More than 55% of the unigenes were annotated through sequence comparison with databases. The okra transcriptome sequences were mined for simple sequence repeat (SSR) markers. From 935 non-redundant SSR motifs identified in the unigene set, 199 were chosen for testing in a germplasm set, resulting in 161 polymorphic SSR markers. From this set, 19 markers were selected for a diversity analysis on 65 okra accessions comprising three different species, revealing 58 different genotypes and resulted in clustering of the accessions according to species and geographic origin. The okra gene sequence information and the marker resource are made available to the research community for functional genomics and breeding research. ► RNA sequencing led to an okra transcriptome comprising >150,000 unigenes. ► Unigene annotation was accomplished by sequence comparison with databases. ► 935 non-redundant SSR markers were identified in the unigene set. ► From 199 selected SSR markers 161 were validated in a germplasm panel. ► The SSR markers were applied for a diversity analysis on an okra germplasm sample.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2012.12.098