Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification
Garcinia 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 antibacte...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Indian Academy of Sciences
2017
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| Acceso en línea: | https://hdl.handle.net/10568/83205 |
| _version_ | 1855528972041846784 |
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| author | Ravishankar, K.V. Vasudeva, R. Hemanth, B. Sandya, B.S. Sthapit, B.R. Partasarathy, P.A. Rao, V.R. |
| author_browse | Hemanth, B. Partasarathy, P.A. Rao, V.R. Ravishankar, K.V. Sandya, B.S. Sthapit, B.R. Vasudeva, R. |
| author_facet | Ravishankar, K.V. Vasudeva, R. Hemanth, B. Sandya, B.S. Sthapit, B.R. Partasarathy, P.A. Rao, V.R. |
| author_sort | Ravishankar, K.V. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Garcinia 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. |
| format | Journal Article |
| id | CGSpace83205 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Indian Academy of Sciences |
| publisherStr | Indian Academy of Sciences |
| record_format | dspace |
| spelling | CGSpace832052025-11-12T05:43:31Z Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification Ravishankar, K.V. Vasudeva, R. Hemanth, B. Sandya, B.S. Sthapit, B.R. Partasarathy, P.A. Rao, V.R. dna sequence microsatellites genetic markers garcinia Garcinia 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. 2017 2017-08-23T12:59:33Z 2017-08-23T12:59:33Z Journal Article https://hdl.handle.net/10568/83205 en Open Access application/pdf Indian Academy of Sciences Ravishankar, 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 |
| spellingShingle | dna sequence microsatellites genetic markers garcinia Ravishankar, K.V. Vasudeva, R. Hemanth, B. Sandya, B.S. Sthapit, B.R. Partasarathy, P.A. Rao, V.R. Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification |
| title | Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification |
| title_full | Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification |
| title_fullStr | Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification |
| title_full_unstemmed | Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification |
| title_short | Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification |
| title_sort | isolation and characterization of microsatellite markers in garcinia gummi gutta by next generation sequencing and cross species amplification |
| topic | dna sequence microsatellites genetic markers garcinia |
| url | https://hdl.handle.net/10568/83205 |
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