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

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Gene (Impact Factor: 2.14). 01/2013; 517(1). DOI: 10.1016/j.gene.2012.12.098
Source: PubMed


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 46 million 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.

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    • ". Abelmoschus accessions of different species, viz. A. esculentus, A. moschatus and A. manihot were located on distinct clusters and in accordance with Schafleitner et al. (2013) "
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    ABSTRACT: Genetic diversity analysis and germplasm characterization are essential steps in plant breeding and molecular markers are proved tool to accomplish. In spite of its high economic value of okra as fresh vegetable in tropical and subtropical regions of Asia and Africa, little attention has been paid to assess its genetic diversity at molecular level. In present study, genetic diversity analysis was performed on 24 Abelmoschus accessions using SSR markers. A total of 85 amplicons were detected from 18 SSR markers. Amplicon analysis revealed a very high level (93.72%) of polymorphism with a mean polymorphic information content (PIC) value of 0.53. Number of alleles scored per primer ranged from 2 to 15 with an average of 4.72 alleles per primer. The UPGMA cluster analysis grouped Abelmoschus genotypes into three main clusters at a cut off value of 0.62. In conclusion, SSR markers enabled discrimination among accessions and provide valuable information for future use in improvement of this genomic resource poor otherwise important vegetable crop.
    Indian Journal of Agricultural Sciences 09/2015; 85(9):99-104. · 0.14 Impact Factor
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    • "In okra, genetic diversity has been evaluated by phenotypic markers (Bisht et al., 1995; Düzyaman, 2005), but these are influenced by environmental factors and show continuous variation. To avoid these problems, molecular techniques have been used, including sequence related amplified polymorphism (SRAP) (Gulsen et al., 2007), random amplified polymorphic DNA (RAPD) markers (Martinello et al., 2003; Aladele et al., 2008), simple sequence repeats (SSRs) developed for Medicago truncatula (Sawadogo et al., 2009) and simple sequence repeats (SSRs) developed from okra transcriptome sequences (Schafleitner et al., 2013). "
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    ABSTRACT: Despite its high economic value in many countries (especially in developing regions of the tropics and sub-tropics), okra has received little attention with respect to its source of origin and genetic diversity, particularly at the molecular level. Phenotypic description (morphology, pod characteristics and seed germination) and AFLP (amplified fragment length polymorphism) analysis were performed on Greek and international genotypes. Whereas morphological descriptors did not separate the accessions according to their geographical origin, AFLP analysis revealed a low level (12%) of polymorphism and distinct geographical groupings. Greek germplasm separated into three distinct groups with no overlap between them on the basis of molecular markers. A higher degree of genetic heterogeneity was found (UPGMA analysis) among the accessions of the Boyiatiou group than in the Pylaias group, whereas the occurrence of some common phylogenetic characteristics made separation on the basis of morphology alone difficult. The results from AFLP markers indicate that Greek germplasm constitutes a significant pool of variation with respect to morphological parameters, pod characteristics and seed germinability. Moreover, differences in seed germination among phenotypes may relate to their geographical origin (mainland or islands).
    Scientia Horticulturae 05/2014; 171:58–70. DOI:10.1016/j.scienta.2014.03.029 · 1.37 Impact Factor
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    ABSTRACT: Okra (Abelmoschus esculentus L.) is not only a nutrient-rich vegetable but also an important medicinal herb. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 24 okra genotypes. In this study, the PCR products were separated by electrophoresis on 8% nondenaturing polyacrylamide gel and visualized by silver staining. The 22 ISSR primers produced 289 amplified DNA fragments, and 145 (50%) fragments were polymorphic. The 289 markers were used to construct the dendrogram based on the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. The dendrogram indicated that 24 okras were clustered into 4 geographically distinct groups. The average polymorphism information content (PIC) was 0.531929, which showed that the majority of primers were informative. The high values of allele frequency, genetic diversity, and heterozygosity showed that primer-sample combinations produced measurable fragments. The mean distances ranged from 0.045455 to 0.454545. The dendrogram indicated that the ISSR markers succeeded in distinguishing most of the 24 varieties in relation to their genetic backgrounds and geographical origins.
    Genetics and molecular research: GMR 05/2014; 13(2):3165-75. DOI:10.4238/2014.April.25.1 · 0.78 Impact Factor