Identification of novel microsatellite markers in okra (Abelmoschus esculentus (L.) Moench) through next-generation sequencing and their utilization in analysis of genetic relatedness studies and cross-species transferability

Ravishankar, K. V.; Muthaiah, Gayathri; Pitchaimuthu, M.; Gundale, Santhosh-kumar

doi:10.1007/s12041-018-0893-0

Cited by 17 publications

(14 citation statements)

References 20 publications

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“…These differences might reflect the variability in the SSR search criteria, size of sequence data, and the species used. In this work, it was found that di-nucleotide repeats were the most frequent SSRs, in accord with that reported in Pareuchiloglanis sinensis (Chen and He 2018), okra (Ravishankar et al 2018), and Chlorostoma rustica (Wang et al 2018). However, in some species such as Pogostemon cablin, trinucleotide repeats were the most frequent SSRs (Ouyang et al 2018).…”

Section: Discussionsupporting

confidence: 90%

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Ding

Kumpeangkeaw

et al. 2019

Physiol Mol Biol Plants

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Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, * 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) [ 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri-(14.9%), tetra-(4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM B 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.Lili Fu and Zehong Ding have contributed equally to this work.

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Section: Discussionsupporting

confidence: 90%

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Ding

Kumpeangkeaw

et al. 2019

Physiol Mol Biol Plants

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“…Previous studies reported that seed shape and trichome structure had major taxonomic importance and proved to be valuable characters for separating taxa of Abelmoschus [5]. SSR markers (mainly in A. esculentus) were also developed from transcriptome data and genomic DNA to investigate genetic relatedness and cross-species transferability [7,19]. Pfeil et al analyzed the phylogeny of Hibiscus and the Tribe Hibisceae using chloroplast DNA sequences of ndhF and rp116 intron, and found two tested Abelmoschus species were embedded within Hibiscus [33].…”

Section: Taxonomic Discrepancies and Hotspots In Abelmoschusmentioning

confidence: 99%

“…Most members of this genus are economically important plants, and used in agriculture, food and medicines. A. esculentus (okra) and A. caillei are widely cultivated as vegetables due to their tender pods [6][7][8]. A. manihot is a popular green leafy vegetable and its flowers have been applied in clinical treatment of burns, chronic kidney disease and oral ulcers owing to the flavonoids [9,10].…”

Section: Introductionmentioning

confidence: 99%

“…Fluorochrome-binding pattern of nine Abelmoschus species showed polyploidy was an important factor in the chromosome number variation and evolution in this genus [4]. Some researchers also used molecular markers to analyze genetic relationships of Abelmoschus, but most studied focused on genetic diversity within A. esculentus and A. manihot [2,7,9,18,19], molecular markers were relatively lacking in other species. Thus, new molecular tools were necessary to study the accurate phylogeny in Abelmoschus.…”

Section: Introductionmentioning

confidence: 99%

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Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

Liu

et al. 2020

PLoS ONE

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Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

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“…Analysis of genetic diversity and inter-relationship among species of a particular genus is a key to nding the success of any breeding program (Poehlman and Sleper 1995). Unknown genome size, variation in ploidy level and chromosome number in okra make it more challenging for the breeder for the genetic improvement of this crop (Ravishankar et al 2018). There are only a few studies reported where molecular markers like random ampli ed polymorphic DNA (RAPD), a sequence related ampli ed polymorphism (SRAP) and simple sequence repeat (SSR) were used to assess the genetic diversity in okra (Lata et al 2021).In contrast to RAPD, CBDP markers developed from the CAAT box of plant promoters are more reproducible for assessing genetic diversity (Singh et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Exploring Genetic Variability In Okra (Abelmoschus Sp.) Accessions Using Promoter Targeted CAAT Box-Derived Polymorphism (CBDP) And Start Codon Targeted (Scot) Markers

Lata

Yadav

et al. 2022

Preprint

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Okra is a warm season vegetable with excellent nutritional, medicinal and industrial potential. Though it is an important vegetable crop but genetic maps and linkage groups are not defined due to the presence of a few polymorphic molecular markers. In this study, we have used CAAT box-derived polymorphism (CBDP) and start codon targeted (ScoT) markers to determine the genetic diversity and population structure of the wild and cultivated population of okra, a genetically orphan crop. Twenty-five CBDP and thirty-six ScoT markers were used on eighty-nine okra accessions to generate polymorphic bands and to analyze the genetic diversity. Out of the 61 primers used, 27 (20-CBDP and 7-ScoT) primers were amplified with clearly visible polymorphic bands. The band size range of CBDP primers was 350-1500bp and for ScoT primers, it was 200-3000bp.Nei’sgenetic diversity was 1.7 for CBDP and 0.13 for ScoT. AMOVA of both markers combined showed 17% and 83% variation among and within-population, respectively. A UPGMA hierarchical dendrogram based on Jaccard’s similarity was drawn for CBDP and ScoT clustered all the accessions into many clades, with significant clustering of cultivated accessions on one clade and wild populations on the other. Bayesian model STRUCTURE analysis of Abelomoschus populations based on CBDP and ScoT markers gave two (K =2) and four (K = 4) genetic structures, respectively, with small admixture. In all the parameters studied, CBDP markers outperformed the ScoT markers.

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Identification of novel microsatellite markers in okra (Abelmoschus esculentus (L.) Moench) through next-generation sequencing and their utilization in analysis of genetic relatedness studies and cross-species transferability

Cited by 17 publications

References 20 publications

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

Exploring Genetic Variability In Okra (Abelmoschus Sp.) Accessions Using Promoter Targeted CAAT Box-Derived Polymorphism (CBDP) And Start Codon Targeted (Scot) Markers

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