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

AVRDC - The World Vegetabele Center, P.O. Box 42, Shanhua, Tainan 74199, Taiwan. Electronic address: .
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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Available from: Sanjeet Kumar
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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.
    Full-text · Article · Sep 2015 · Indian Journal of Agricultural Sciences
    • "Interestingly, in a similar study also using RAPD markers, Aladele et al. (2008) found that these two species were clearly separated. More recently, Schafleitner et al. (2013) used transcriptome data to develop SSR markers. Their study included three species, mainly A. esculentus from a vast geographical range alongside two samples of A. manihot and A. moschatus each. "
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    ABSTRACT: The genus Abelmoschus includes several crop plants which are especially important in SE Asia and several African countries. However, the systematic treatment of this genus is difficult, in part because hybridization between different forms seems to be frequent. In this study we present nuclear internal transcribed spacer ITS and chloroplast rpL16 sequences with the aim of reconstructing phylogenetic relationships within Abelmoschus, and its relationship with the genus Hibiscus and other related Malvaceae. Based on our analysis of nuclear ITS and chloroplast rpL16 sequence data, Abelmoschus is resolved as a monophyletic clade. Abelmoschus tetraphyllus is clearly separated from A. manihot but closely related to A. ficulneus and should not be treated as a subspecies of A. manihot. None of the wild species included in this study can be confirmed as an ancestor of A. esculentus or A. caillei. Neither A. esculentus nor A. caillei can be distinguished from each other by the markers used for this study, although the evidence does not exclude the possibility of a hybrid origin of A. caillei involving A. esculentus and an unknown species. The genetic diversity within A. esculentus and A. caillei is low if compared with A. manihot. The evidence presented here does not allow us to draw any conclusions about the geographic origin (Africa vs. Asia) of A. esculentus.
    No preview · Article · May 2015 · Genetic Resources and Crop Evolution
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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).
    Full-text · Article · May 2014 · Scientia Horticulturae
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