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
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Abelmoschus esculentusL. (Malvaceae), populary known as okra, is one of the important pod vegetable crops in tropics and subtropics. To develop the microsatellite markers, we have partially sequenced genomic DNA using Roche 454 Titanium pyrosequencing technology. A total of 979,806 bp data from 61,722 reads were obtained. These reads were assembled into 3735 contigs of which 2708 had microsatellites. Primers were designed for 402 microsatellites, from which 50 randomly selected SSR primers were standardized for amplification of okra DNA. Genetic analysis was done by employing 29 genotypes. Polymorphic information content (PIC) across all 50 loci ranged from 0.000 to 0.865 with a mean value of 0.519. The observed and expected heterozygosity ranged from 0.000 to 0.750 and 0.000 to 0.972, respectively. Alleles per locus ranged from 1 to 27. This is the first report on the development of genomic SSR markers in okra using next-generation sequencing technology. We have also...
Keywordsmicrosatellite markers transferability polymorphic information content Abelmaschus esculentus
Authors acknowledge the financial support through institute project from ICAR-Indian Institute of Horticultural Research, Bengaluru.
- Aladele S. E., Ariyo O. J. and Lapena R. 2008 Genetic relationships among West African okra (Abelmoschuscaillei) and Asian genotypes (Abelmoschu sesculentus) using RAPD. Afr. J. Biotechnol. 7, 1426–1431.Google Scholar
- Buschiazzo E. and Gemmell N. 2006 The rise fall and renaissance of microsatellites in eukaryotic genomes. BioEssays. 28, 1040–1050.Google Scholar
- Chakravarthi B. K. and Naravaneni R. 2006 SSR Marker based DNA fingerprinting and diversity study in rice (Oriza sativa L.). Afr. J. Biotechnol. 5, 684–688.Google Scholar
- Fan Q., Chen S., Li M., He S., Zhou R. and Liao W. 2013 Development and characterization of microsatellite markers from the transcriptome of Firmiana danxiaensis (Malvaceaes.l.). Appl. Plant Sci. 28, 12–16.Google Scholar
- Gilles A., Meglé Cz E., Pech N., Ferreira S., Malausa T., and Martin J. F. 2011 Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12, 245.Google Scholar
- Huang and Anup M. 1999 CAP3: A DNA sequence assembly programe. Genome Res. 9, 868–877.Google Scholar
- Muhammad S., Bahaeldeen B. M., Muhammad A. A., Agung N. P., Kamran S. B., Ahmad A. S. and Tayyab H. 2013 Genetic diversity assessment of cotton (Gossypium hirsutum L.) genotypes from pakistan using simple sequence repeat markers. Aust. J. Crop Sci. 7, 261–267.Google Scholar
- Nwangburuka C. C., Kehinde O. B., Ojo D. K., Denton O. A. and Popoola A. R. 2011 Morphological classification of genetic diversity in cultivated okra, Abelmoschu sesculentus (L.) Moench using principal component analysis (PCA) and single linkage cluster analysis (SLCA). Afr. J. Biotechnol. 10, 54.Google Scholar
- Perrier X., Flori A. and Bonnot F. 2003 Data analysis methods. Enfield. Sci. Publish. Montpellier. 43–76.Google Scholar
- Phuekvilai P. and Wolff K. 2013 Characterization of microsatellite loci in Tiliap latyphyllos (Malvaceae) and cross-amplification in related species. Appl. Plant Sci. 1. https://doi.org/10.3732/apps.1200386.
- Prakash K., Pitchaimuthu M. and Ravishankar K. V. 2011 Assessment of genetic relatedness among okra genotypes (Abelmoschu sesculentus L. Moench) using RAPD markers. Electron. J. Plant Breed. 2, 80–86.Google Scholar
- Ramya P. and Bhat K. V. 2012 Analysis of phylogenetic relationships in Abelmoschus species (Malvaceae) using ribosomal and chloroplast intergenic spacers. Indian J. Genet. Plant Breed. 72, 445–453.Google Scholar
- Sawadogo M., Ouedraogojt B. D., Ouedraogo M., Gowdabs B. C. and Timko M. 2009 The use of cross species SSR primers to study genetic diversity of okra from Burkina Faso. Afr. J. Biotechnol. 8, 2476–2482.Google Scholar
- Sonah H., Deshmukh R. K., Sharma A., Singh V. P., Gupta D. K., Gacche R. N. et al. 2011 Genome wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 10, 137.Google Scholar
- Sunday E., Aladele O. J. Ariyo L. and Robert D. L. 2008 Genetic relationship among West African Okra (Abelmo schuscaillei) and Asian genotypes (Abelmo schusesculentus) using RAPD. Afri. J. Biotechnol. 7, 1426–1431.Google Scholar
- Suping F., Helin T., You C., Jingyi W., Yeyuan C., Guangming S. et al. 2013 Development of pineapple microsatellite markers and germplasm genetic diversity analysis. Biomed. Res. Int. 1–11. https://doi.org/10.1155/2013/317912.
- Untergasser A., Cutcutache J., Koressaar T., Ye J., Faircloth B. C., Remm M. and Rozen S. G 2012 Rozen.Primer3 - new capabilities and interfaces. Nucleic. Acids. Res. 40, 15.Google Scholar
- Wang S., Xiaokun L., Jianwei L., Juan H., Gang C., Xinxin X. et al. 2013 Effects of controlled-release urea application on the growth, yield and nitrogen recovery efficiency of cotton. Agric. Sci. 4, 3–38.Google Scholar