Visual Clustering Analysis of some traditional Mango (Mangifera indica L.) varieties of Murshidabad District, West Bengal using Clust Vis web tool
A clustergram or a heatmap is one of several techniques that directly visualize data without the need for dimensionality reduction. Heatmap is a representation of data in the form of a map or diagram in which data values are represented as colours. Cluster heatmaps have high data density, allowing them to compact large amounts of information into a small space. “ClustVis”, is a web tool for visualizing clustering of multivariate data using Principal Component Analysis and Heatmap. Using this web tool, genetic relationships among the traditional mango (Mangifera indica L.) varieties can be visualized. In this investigation ten (10) indigenous mango varieties were selected. These were elite varieties of Murshidabad viz. Anaras, Bhabani, Champa, Dilpasand, Kalabati, Kohinoor, Kohitoor, Molamjam. The morphological and biological characters were analyzed using this tool. Analysis and assessment of the current status of mango genetic resources will be important for ascertaining the relationship among traditional varieties. This data may be used for appropriate conservation and sustainable utilization measures. This information may also be needed to carry out breeding programs to develop improved cultivars for sustainable livelihoods of local communities.
Bruneau, P.,Pinheiro, P. Broeksema, B. Otjacques, B. (2015). Cluster sculptor, an interactive visual clustering system. Neurocomputing, 150: 627–644,
Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998).Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences 95, 14863–14868.
Dash, R. C. and Hota, B. N. 1977. Some indigenous mango varieties of Orissa. Orissa J. Hort., 5: 35-52.
De, Mitu, Das, Jhilik, Saha, Meghna, Pal, Ankush and Dey, Santi Ranjan. (2014). Documentation and Characterization of the Indigenous Mango (Mangifera indica L.) varieties of Malda and Murshidabad districts of West Bengal. J. Environ. & Sociobiol. (ISSN 0973-0834): 11(2), Dec: 187-198pp.
Galvez-Lopez D., Salvador-Figueroa M., Adriano-Anaya L. and Mayek-Perez N. (2010). Morphological Characterization of Native Mangoes from Chiapas, Mexico. Subtropical Plant Science, 62: pp 18-26.
Guijarro-Real, Carla, Jaime Prohens, Adrián Rodríguez-Burruezo, and Ana Fita. (2020). "Morphological Diversity and Bioactive Compounds in Wall Rocket (Diplotaxis erucoides (L.) DC.)" Agronomy 10, no. 2: 306.
Hastie, T., Tibshirani, R., Friedman, J. And Franklin, J. (2005). The elements of statistical learning: data mining, inference and prediction. The Mathematical Intelligencer, 27(2):83–85.
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. (2012). Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods.; 9(5):473–6.
Ionov, Yurij; Rogovskyy, Artem S. (2020): Principal Component Analysis plot (A) and heatmap (B) generated, via the ClustVis, by the whole-unique-sequence-based analysis (WUSA). PLOS ONE. https://doi.org/10.1371/journal.pone.0226378.g004
International Plant Genetic Resourcces Institute IPGRI (2006). Descriptors for mango (Mangifera indica L). International Plant Genetic Resources Institute, Rome, Italy.
Liu, Yiming & Zhang, Xunzhong & Tran, Hong & Shan, Liang & Kim, Jeongwoon & Childs, Kevin & Ervin, Erik & Frazier, Taylor & Zhao, Bingyu. (2015). Assessment of drought tolerance of 49 switchgrass (Panicum virgatum) genotypes using physiological and morphological parameters. Biotechnology for Biofuels, 8(1), 1-18.
Majumder, D. N. 2013. Genetic Diversity in Mango (Mangifera Indica L.) through multivariate analysis. Bangladesh J. Agril. Res., 38(2): 343-353.
Majumder, D. N. (2013). Genetic Diversity in Mango (Mangifera Indica L.) through multivariate analysis. Bangladesh J. Agril. Res., 38(2): 343-353.
Majumder Dan, Hassan L, Rahim MA Kabir MA (2011). Studies on physio-morphology, floral biology and fruit characteristics of mango. J Bangladesh Agri Univ. 9 (2):187-199.
Metsalu, T and Vilo,J. (2015). ClustVis: a web tool for visualising clustering of multivariate data using PCA and Hetmap. Nucleic Acid Research. 43: Web Server issue.
Mukherjee, S.K. 1953. The mango-its botany cultivation, uses and future improvements, especially as observed in India. Econ. Bot. 7: 130–162.
Nam, E. J., Han, Y., Mueller, K., Zelenyuk, A. and Imre, D. (2007). Cluster Sculptor: A visual analytics tool for high-dimensional data. In Proc. IEEE VAST’07.
Njuguna J.K., Wepukhulu S.B. and Wanjala S. (2009). Mango cultivar evaluation programme in Kenya. Acta Horticulturae, 820: pp 133-135.
Pavlopoulos, G. A., Wegener, A.-L. & Schneider, R. (2008). A survey of visualization tools for biological network analysis. Biodata mining 1, 12.
Shen, Feng & Li, Yanxia & Zhang, Min & Awasthi, Mukesh & Ali, Amjad & li, Ronghua & Wang, Quan & Zhang, Zengqiang. (2016). Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA. Scientific Reports. 6. 39148.
Sokal, R and Michener, C. 1958. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 1409–1438..
Subedi A., Bajracharya J., Joshi B.K., Regmi H.N., Gupta S.R. and Hari B.C.K. 2005. Characterization and genetic diversity of mango (Mangifera indica L.) in Nepal. In: Sthapit BR, Upadhyay MP, Shrestha PK, Jarvis DI (eds.). On-farm conservation of agricultural biodiversity in Nepal. Volume I. Assessing the amount and distribution of genetic diversity on-farm. Proceedings of the Second National Workshop, 25- 27 Aug 2004, Nagarkot, Nepal. International Plant Genetic Resources Institute, Rome, Italy, pp. 167-175.
Toubiana D, Cabrera R, Salas E, et al. (2020). Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor. The Plant Journal : for Cell and Molecular Biology. Sep;103(6): 2193-2210.
Uddin MZ, Rahim MA, Barman JC Wadud MA. (2006). A study on the physical characteristics of some mango germplasm grown in Mymensingh condition. Int J Sustain Crop Prod. 1(2): 33-38
Wilkinson L, Friendly M. (2009). The history of the cluster heat map. The American Statistician; 63(2):179–84.
Zhao, Shilin & Guo, Yan & Sheng, Quanhu & Shyr, Yu. (2014). Advanced Heat Map and Clustering Analysis Using Heatmap3. BioMed research international. 986048. 10.1155/2014/9860
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