Identification and Validation of Microsatellite Markers in Rhododendron campanulatum D. Don through cross transferability
DOI:
https://doi.org/10.36808/if/2022/v148i8/156732Keywords:
Conservation, population genetic analysis, microsatellite markers, SSRs, cross transferability, genetic diversityAbstract
The genetic diversity maintained by Forest Genetic Resources (FGRs) bestow them the capability for survival, adaptation and evolution in response to the changing climatic conditions. Population genetic studies based on DNA based marker may aid in understanding the actual level of diversity and its distribution within and among the populations, gene flow, allele fixation, structuring etc. that could be wisely used in their conservation and management. Rhododendron campanulatum is a medicinally, horticulturally and ecologically important tree species growing at tree line throughout the Himalayas. In the present study, efforts were carried out to identify simple sequence repeat (SSR) markers in R. campanulatum through cross species amplification. In total, 15 SSR markers developed in R. arboreum (Choudhary et al., 2014) were tested for cross transferability and polymorphism in R. campanulatum. Of these, 12 primer pairs were positively amplified but only 5 (SSR-7, SSR-8, SSR-11, SSR-25 and SSR-29) showed polymorphism across the populations. Mean Polymorphic Information Content (PIC), expected heterozygosity (H ) and observed heterozygosity (H ) of these markers were e o recorded as 0.609, 0.360 and 0.343, respectively. Other measures such as genetic differentiation (F ) and gene flow (N ) were recorded as 0.467 and ST m 0.486, respectively. Population of Valley of Flowers had the highest percentage of polymorphic loci (100.0%). Analysis of molecular variance (AMOVA) revealed about 25% among the populations and 75% within population. The markers identified in the study could be highly useful for detailed population genetic analysis of this species.References
Abdurakhmonov I.Y. (2016). Introduction to Microsatellites: Basics, Trends and Highlights. In: Abdurakhmonov IY (ed) Microsatellite Markers, Intech Open. http://dx.doi.org/ 10.5772/66446
Annual Report 2018-19. Botanical Survey of India (BSI), Ministry of Environment, Forest & Climate Change, Govt. of India, Kolkata, p72.
BSIENVIS (2018). Floral Statistics of India. http://bsienvis.nic.in/ Database/Floral_Statistics_of_India_2018 _26352.aspx. Accesed 12 July, 2020.
CCDB (2020). Chromosome Count Database. http://ccdb.tau.ac.il/search/Rhododendron%20campanulatum /. Accesed 27 February, 2020.
Charrier O., Dupont P., Pornon A. and Escaravage N. (2014). Microsatellite Marker Analysis Reveals the Complex Phylogeographic History of Rhododendron ferrugineum (Ericaceae) in the Pyrenees. Plos One, 9(3): 1-9. e92976. doi:10.1371/journal.pone.0092976
Chhetri P.K., Chhetri B. and Badola H.K. (2018). Rhododendron diversity along the Kusong- Panch Pokhari transect in Khangchendzonga Biosphere Reserve, the eastern Himalaya: a conservation perspective, Journal of Threatened Taxa, 10(1): 11192-11200.
Choudhary S., Thakur S., Saini R.G. and Bhardwaj P. (2014). Development and characterization of genomic microsatellite markers in Rhododendron arboreum, Conservation Genetics Resources, 6(4): 937–940.
Dayanandan S., Bawa K.S. and Kesseli R. (1997). Conservation of Microsatellites among Tropical Trees (Leguminosae), American Journal of Botany, 84(12): 16581663.
DTE (2019). Rhododendron, Fragrance of life. https://www.downtoearth.org.in/news/economy/fragrance-oflife51635. Accesed 29 August, 2019.
Duran C., Appleby N., Edwards D. and Batley J. (2009). Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation, Current Bioinformatics, 4: 16-27.
ENVIS (2020). Plant Details for a Rhododendron campanulatum DON. http://envis.frlht.org/plantdetails/ 32841e2001bbb69ec02654d368f861f7/4391b7e506fba83a83 db93a7df955ae3, Accesed 29 April, 2020.
Gibbs D., Chamberlain D. and Argent G. (2011). The Red List of Rhododendrons. Botanic Gardens Conservation International, Richmond, UK, 128 p. https://portals.iucn.org/library/sites/ library/files/documents/RL-2011-002.pdf
Iqbal K. and Negi A.K. (2017). Rhododendrons in Uttarakhand: Diversity and Conservation, International Journal of Environment, 6(1): 31-45.
JKF (2020). Glossary of Some Plant Species. Billawar Forest Division. http://jkforest.gov.in/pdf/flora_combined.pdf. Accesed 20 February, 2020.
Jones J.R., Ranney T.G. and Lynch N.P. (2007). Ploidy Levels and Relative Genome Sizes of Diverse Species, Hybrids, and Cultivars of Rhododendron, Journal American Rhododendron Society, 61(4): 220-227.
Kumar D. and Meena R.K. (2020). Importances of Abiotic Stresses and their Mitigation in Forestry Tree Species. Abstract in the Section of Agriculture and Forestry Sciences, Proceedings of 107th Indian Science Congress, Bangalore, 2: 336-7.
Kumar M., Paul Y. and Anand V.K. (2009). An Ethnobotanical Study of Medicinal Plants used by the Locals in Kishtwar, Jammu and Kashmir, India, Ethnobotanical Leaflets, 13: 124056.
Kumar P., Gupta V.K., Misra A.K., Modi D.R. and Pandey B.K. (2009). Potential of Molecular Markers in Plant Biotechnology, Plant Omics Journal, 2(4): 141-162.
Kurashige Y., Etoh J., Handa T., Takayanagi K. and Yukawa T. (2001). Sectional relationships in the genus Rhododendron (Ericaceae): evidence from matK and trnK intron sequences, Plant Systematics and Evolution, 228:1-14 https://doi.org/10.1007/s006060170033
Mainali K., Shrestha B.B., Sharma R.K., Adhikari A., Gurarie E., Singer M. and Parmesan C. (2020). Contrasting responses to climate change at Himalayan treelines revealed by population demographics of two dominant species, Ecology and Evolution, 00:1–14.
Nilkanta H., Amom T., Tikendra L., Rahaman H. and Nongdam P. (2017). ISSR Marker Based Population Genetic Study of Melocanna baccifera (Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India, Hindawi Scientifica, 2017: 1-9. https://doi.org/10.1155/2017/3757238
PFAF (2020). Rhododendron campanulatum - D.Don. https://pfaf.org/user/Plant.aspx?LatinName=Rhododendron+c ampanulatum. Accesed 20 February, 2020.
Pradhan B.K., Subba S., Dahal S., Chewang D. and Tamang M. (2015). Rapid Biodiversity Survey Report - II. Sikkim Biodiversity Conservation and Forest Management Project (SBFP), FEWMD. Government of Sikkim, Deorali, Gangtok, East Sikkim.
Pragya (2020). Rhododendron campanulatum . https://www.himalayanvoices.org/sites/default/files/Rhododen dron%20campanulatum.pdf. Accesed 24 December, 2019.
Rana P., Koirala M., Bhuju D.R. and Boonchird C. (2016). Population Structure of Rhododendron campanulatum D. Don and Associated Tree Species along the Elevational Gradient of Manaslu Conservation Area, Nepal, Journal of Institute of Science and Technology, 21(1): 95-102.
RHS (2019). Bell Rhododendron. https://www.rhs.org.uk/ Plants/100435/Rhododendron-campanulatum/Details, Accesed 24 December, 2019.
Roy J.D. (2015). Study on Adaptogenic Activity in Vivo and in Vitro of Rhododendron arboreum from N. E India and its Molecular Characterization. Ph.D. thesis, Gauhati University, Gauhati. https://shodhganga.inflibnet.ac.in/bitstream/10603/73389/10/10_chapter%202.pdf
SDG (2020). Review of Literature, Rhododendron. https://shodhganga.inflibnet.ac.in/bitstream/10603/236890/7/07_chapter%202.pdf. Accesed 07 February, 2020.
Sekar K.C. and Srivastava S.K. (2010). Rhododendrons in Indian Himalayan Region: Diversity and Conservation, American Journal of Plant Sciences, 1: 131-137.
Sharma G., Singh A., Majeed A., Ali V. and Bharadwaj P. (2017). Development and Characterization of UGMS markers for Genetic Diversity Analysis in Rhododendron arboreum. Proceedings of International Conference on Recent Innovations in Science, Agriculture, Engineering and Management, Bhatinda, Punjab, India, pp. 1057-1070.
Sharma H., Bhandawat A. and Rawat S. (2020a). Crosstransferability of SSR markers developed in Rhododendron species of Himalaya, Molecular Biology Reports. https://doi.org/10.1007/s11033-020-05606-0
Sharma H., Kumar P., Singh A., Aggarwal K., Roy J., Sharma V. and Rawat S. (2020b). Development of polymorphic EST-SSR markers and their applicability in genetic diversity evaluation in Rhododendron arboreum, Molecular Biology Reports. https://doi.org/10.1007/s11033-020-05300-1
Shilpa, Sagar A. and Rani N. (2016). Seasonal Fluctuations among the Fungal Associates of Rhododendron campanulatum D. Don, International Journal of Current Microbiology and Applied Science, 5(1): 679-685.
Singh G., Rawat G.S. and Verma D. (2010). Comparative study of fuelwood consumption by villagers and seasonal "Dhaba owners" in the tourist affected regions of Garhwal Himalaya, India, Energy Policy, 38(4): 1895-1899.
Singh P., Arya V., Negi G.C.S. and Singh S.P. (2018). Expansion of Rhododendron campanulatum krummholz in the treeline ecotone in Tungnath, Garhwal Himalaya, Tropical Ecology, 59(2): 287–295.
Singh S.P. (2018). Research on Indian Himalayan Treeline Ecotone: an overview, Tropical Ecology, 59(2): 163–176.
SQX (2020). Principal Coordinates Analysis. https://www.sequentix.de/gelquest/help/principal_coordinates
_analysis.htm. Accesed 26 June, 2020.
Vetaas O.R. (2002). Realized and potential climate niches: a comparison of four Rhododendron tree species, Journal of Biogeography, 29: 545–554.
Vieira M.L.C., Santini L., Diniz A.L. and Munhoz C.D.F. (2016). Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology, 39(3): 312-328.
Wang S., Li Z., Guo X., Fang Y., Jun Xiang J. and Jin W. (2018). Comparative analysis of microsatellite, SNP, and In Del markers in four Rhododendron species based on RNA-seq, Breeding Science, 68: 536–544.
Zhang Y., Zhang X., Wang Y.H. and Shen S.K. (2017). De Novo Assembly of Transcriptome and Development of Novel ESTSSR Markers in Rhododendron rex Lévl. through Illumina Sequencing, Frontiers in Plant Sciences, 8: 1664. doi: 10.3389/fpls
Zhao B. and Zheng Z.S. (2015).Genetic relationship among nine Rhododendron species in Qinling mountains, China using amplified fragment length polymorphism markers, Pakistan Journal of Botany, 47(3): 1069-1074.
Downloads
Downloads
Published
How to Cite
Issue
Section
License
Unless otherwise stated, copyright or similar rights in all materials presented on the site, including graphical images, are owned by Indian Forester.
