Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification
The fruit-bearing medicinal tree, Garcinia morella, grows in the tropical rain forests of India’s Western Ghats, Indo-Chinese Himalayan regions and Sri Lanka. Its fruit rinds are used as a garnish and in seasoning during food preparation. In order to genetically exploit it and assess diversity, dev...
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| Format: | Article |
| Language: | English |
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Society for Promotion of Horticulture - Indian Institute of Horticultural Research
2023-12-01
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| Series: | Journal of Horticultural Sciences |
| Online Access: | https://jhs.iihr.res.in/index.php/jhs/article/view/2173 |
| _version_ | 1797220658858426368 |
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| author | K V Ravishankar R Vasudeva B Hemanth D Narendrababu P Nischita B S Sandya B R Sthapit V A Parthasarathy V Ramanatha Rao |
| author_facet | K V Ravishankar R Vasudeva B Hemanth D Narendrababu P Nischita B S Sandya B R Sthapit V A Parthasarathy V Ramanatha Rao |
| author_sort | K V Ravishankar |
| collection | DOAJ |
| description |
The fruit-bearing medicinal tree, Garcinia morella, grows in the tropical rain forests of India’s Western Ghats, Indo-Chinese Himalayan regions and Sri Lanka. Its fruit rinds are used as a garnish and in seasoning during food preparation. In order to genetically exploit it and assess diversity, development of microsatellite markers was attempted. We partially sequenced genomic DNA using the Illumina Hiseq 2000 platform and examined sequence data for microsatellite loci. We obtained high-quality 10653 Mbp data and was assembled into 1613263 contigs. A total of 121199 SSRs were discovered, Di nucleotide repeats were predominant (42.5%), followed by mono and tri nucleotide repeats (30.4 and 7.9%, respectively). We were able to design primers for 52901 microsatellites. Genetic analysis of 48 SSR loci, showed PIC values ranging from 0.067 to 0.939 with a mean value of 0.7547. The allele per locus ranged from 2 to 24 with a mean of 13. These microsatellite markers can be employed for genetic diversity analysis, molecular characterization and mapping different traits.
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| first_indexed | 2024-04-24T12:53:03Z |
| format | Article |
| id | doaj.art-40810e799b8b481c89f5f9c70f44ab8c |
| institution | Directory Open Access Journal |
| issn | 0973-354X 2582-4899 |
| language | English |
| last_indexed | 2024-04-24T12:53:03Z |
| publishDate | 2023-12-01 |
| publisher | Society for Promotion of Horticulture - Indian Institute of Horticultural Research |
| record_format | Article |
| series | Journal of Horticultural Sciences |
| spelling | doaj.art-40810e799b8b481c89f5f9c70f44ab8c2024-04-05T18:20:11ZengSociety for Promotion of Horticulture - Indian Institute of Horticultural ResearchJournal of Horticultural Sciences0973-354X2582-48992023-12-0118210.24154/jhs.v18i2.2173Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplificationK V Ravishankar0R Vasudeva1B Hemanth2D Narendrababu3P Nischita4B S Sandya5B R Sthapit6V A Parthasarathy7V Ramanatha Rao8ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru - 560089, Karnataka, IndiaCollege of Forestry, University of Agricultural Sciences, Dharwad Sirsi - 581401, Karnataka, IndiaICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru - 560089, Karnataka, IndiaICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru - 560089, Karnataka, IndiaICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru - 560089, Karnataka, IndiaICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru - 560089, Karnataka, IndiaRegional Project Coordinator (UNEP-GEF), Bioversity International, Pokhara, NepalNational Project Coordinator (UNEP-GEF), ICAR-Indian Institute of Horticultural Research, Bengaluru - 560089, IndiaBioversity International, Rome The fruit-bearing medicinal tree, Garcinia morella, grows in the tropical rain forests of India’s Western Ghats, Indo-Chinese Himalayan regions and Sri Lanka. Its fruit rinds are used as a garnish and in seasoning during food preparation. In order to genetically exploit it and assess diversity, development of microsatellite markers was attempted. We partially sequenced genomic DNA using the Illumina Hiseq 2000 platform and examined sequence data for microsatellite loci. We obtained high-quality 10653 Mbp data and was assembled into 1613263 contigs. A total of 121199 SSRs were discovered, Di nucleotide repeats were predominant (42.5%), followed by mono and tri nucleotide repeats (30.4 and 7.9%, respectively). We were able to design primers for 52901 microsatellites. Genetic analysis of 48 SSR loci, showed PIC values ranging from 0.067 to 0.939 with a mean value of 0.7547. The allele per locus ranged from 2 to 24 with a mean of 13. These microsatellite markers can be employed for genetic diversity analysis, molecular characterization and mapping different traits. https://jhs.iihr.res.in/index.php/jhs/article/view/2173 |
| spellingShingle | K V Ravishankar R Vasudeva B Hemanth D Narendrababu P Nischita B S Sandya B R Sthapit V A Parthasarathy V Ramanatha Rao Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification Journal of Horticultural Sciences |
| title | Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification |
| title_full | Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification |
| title_fullStr | Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification |
| title_full_unstemmed | Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification |
| title_short | Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification |
| title_sort | isolation and characterization of microsatellite markers from garcinia morella using next generation sequencing technology and cross species amplification |
| url | https://jhs.iihr.res.in/index.php/jhs/article/view/2173 |
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