Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification

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dc.creatorRavishankar, K.V.
dc.creatorVasudeva, R.
dc.creatorHemanth, B.
dc.creatorSandya, B.S.
dc.creatorSthapit, B.R.
dc.creatorPartasarathy, P.A.
dc.creatorRao, V.R.
dc.date2017
dc.date2017-08-23T12:59:33Z
dc.date2017-08-23T12:59:33Z
dc.date.accessioned2026-06-27T13:51:12Z
dc.descriptionGarcinia gummi-gutta (L.) Roxb. (Clusiaceae) is an endemic, semidomesticated, fruit-yielding tree species distributed in the Western Ghats of India and Sri Lanka. Various bioactive phytochemicals, such as garcinol, benzophenones and xanthones are isolated from G. gummi-gutta and have shown antibacterial, antiviral and antioxidant activities. We sequenced the total genomic DNA using Illumina Hiseq 2000 platform and examined 241,141,804 bp high quality data, assembled into 773,889 contigs. In these contigs, 27,313 simple-sequence repeats (SSRs) were identified, among which mononucleotide repeats were predominant (44.98%) followed by dinucleotide and trinucleotide repeats. Primers were designed for 9964 microsatellites among which 32 randomly selected SSR primer pairs were standardized for amplification. Polymerase chain reaction (PCR) amplification of genomic DNA in 30 G. gummi-gutta genotypes revealed polymorphic information content (PIC) across all 32 loci ranging from 0.867 to 0.951, with a mean value of 0.917. The observed and expected heterozygosity ranged from 0.00 to 0.63 and 0.896 to 0.974, respectively. Alleles per locus ranged from 12 to 27. This is the first report on the development of genomic SSR markers in G. gummi-gutta using next-generation sequencing technology. The genomic SSR markers developed in this study will be useful in identification, mapping, diversity and breeding studies.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/83205
dc.identifier.urihttp://hdl.handle.net/123456789/67801
dc.languageen
dc.publisherIndian Academy of Sciences
dc.rightsOpen Access
dc.sourceRavishankar, K.V.; Vasudeva, R.; Hemanth, B.; Sandya, B.S.; Sthapit, B.R.; Partasarathy, V.A.; Rao, V.R. (2017) Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification. Journal of Genetics 96(2) p.213-218. ISSN: 0022-1333
dc.subjectdna sequence
dc.subjectmicrosatellites
dc.subjectgenetic markers
dc.subjectgarcinia
dc.titleIsolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification
dc.typeJournal Article

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