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.; Parthasarathy, V. A.; Rao, V. Ramanatha

doi:10.1007/s12041-017-0756-0

Cited by 13 publications

(4 citation statements)

References 20 publications

(18 reference statements)

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“…However, it is unknown if selection is involved in the distribution of SSR types in genomic DNA (Celik et al, 2014). A similar trend was observed in other Garcinia species, G. indica (Ravishankar et al, 2021) and G. gummigutta (Ravishankar et al, 2017).…”

Section: G Indica G Gummiguttasupporting

confidence: 53%

Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification

K V,

et al. 2024

J. Hortic. Sci.

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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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Section: G Indica G Gummiguttasupporting

confidence: 53%

Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification

K V,

et al. 2024

J. Hortic. Sci.

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“…[25] High variability among these quantitative characteristics strengthens the economic importance. [26] Likewise, in the present study twelve quantitative morphological markers were observed to estimate phenotypic diversity.N. sativa plant usually exhibited mixed (self / cross) pollination types but it is predicted that cross pollination may prove more fruitful with reference to genetic variation.…”

Section: Petal Colorsupporting

confidence: 52%

Morphological Variability Assessment of Worldwide Germplasm of Pharmaceutically Important Plant Nigella Sativa L.

Aftab¹,

Yousaf²,

Rasheed³

et al. 2022

JJPS

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N. sativa is an important industrial crop globally but neglected crop in Pakistan, hence imported. It has been used for revitalizing body system in almost all ancient civilizations. In the present investigation worldwide accessions of N. sativa were cultivated for three years to select the most diverse accessions for cultivation and future breeding purpose in Pakistan. More diverse and acclimatized accessions with enhanced morphological traits were observed. Seed length, seed width, plant height, number of flowers and number of follicles showed maximum considerable variation in three years. Morphological variations observed and collected for all three years were not consistent among all accessions, due to some environmental fluctuations while some of the accessions like ACC 20662, ACC W626529, ACC 20878, ACC 21545, ACC 21428and ACC 20990 showed consistency at some extent among results of different morphological markers (number of flowers, number of stamens, number of follicles, follicle length, follicle width and seed per follicle). 50% accessions germinated in 26-35 days consecutively three years and showed optimum growth. The maximum height was noticed as 108cm in two accessions ACC 20878 and ACC 20780. The maximum frequency of flower initiation days was noted 101-110 days. The maximum frequency distribution for number of branches was noted in frequency class 11-15 during all three years. The maximum frequency of flower initiation days was noted 101-110 days for 2015-16 and 2017-18. The data recorded in 2017-18 depicted the maximum number of flowers as 15 (ACC 20780 and ACC 20878). The rate of follicle production per plant was 10 among accessions (ACC W626529, ACC 20545 and ACC 21295). The largest frequency class for stamens number was 21-25 stamens, whereas the plants with frequency class 31-35 stamens were least frequent. The flower color varied in the recombinant plants (RC) as Purple White whereas in the parents it was White (Jordan) and Bluish white (Ukraine). In general the accessions belonging to Gujranwala, Jordan, Lahore, Haripur, Attock and Sargodha were found morphologically more significant and diverse.

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“…In cross species amplification, out of 48 SSR primers, 6 amplified in G. morella , accounting 12.5 per cent transferability and 9 amplified in G. gummigutta accounting 18.8 percent transferability (ESM2). This relatively low cross-species transferability compar ed to what has been observed in G. gummigutta species (Ravishankar et al, 2017).…”

Section: Short Communicationmentioning

confidence: 50%

Isolation and characterization of microsatellite markers from Garcinia indica and cross species amplification

et al. 2021

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Garcinia indica popularly known as ‘Kokum’ or Murugalu”, is a medium-sized evergreen tree found in the western-ghats of India. This tree species is highly exploited to produce anti-obesity drugs and culinary purposes. Its population is threatened by overexploitation and loss of habitat. The development of microsatellite markers would help in understanding the genetic structure and further to develop appropriate conservation strategies. In this study, using next generation sequencing platform Illumina Hiseq 2000, we have sequenced the partial genome of G. indica and identified 3725 microsatellites. Forty-eight microsatellite markers were analyzed using 30 accessions. Polymorphism information content (PIC) values ranged from 0.718 to 0.968 with a mean value of 0.922. Allele per locus ranged from 3 to 33 per locus. The probability of identity values ranged from 0.00329 to 0.30489. Cross-species amplification SSR primers in the related species showed a moderate transferability from 12.5 % (for G. morella) to 18.7%(for G. gummigutta)

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

Cited by 13 publications

References 20 publications

Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification

Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification

Morphological Variability Assessment of Worldwide Germplasm of Pharmaceutically Important Plant Nigella Sativa L.

Isolation and characterization of microsatellite markers from Garcinia indica and cross species amplification

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