Journal of Bioscience and Agriculture Research |
|
RESEARCH ARTICLE:
Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta
Hasan Mehraj (1,2) and Kazuhiko Shimasaki (2)
1The United Graduate School of Agricultural Sciences, Ehime University, Ehime 790-8556, Japan
2Lab of Vegetable and Floricultural Science, Faculty of Agriculture, Kochi University, B200 Monobe, Nankoku, Kochi 783-8502, Japan
J. bios. agric. res. | Volume 12, Issue 02, pp. 1029-1035 | Available online: 25 February 2016.
Crossref: https://doi.org/10.18801/jbar.120217.125
Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta
Hasan Mehraj (1,2) and Kazuhiko Shimasaki (2)
1The United Graduate School of Agricultural Sciences, Ehime University, Ehime 790-8556, Japan
2Lab of Vegetable and Floricultural Science, Faculty of Agriculture, Kochi University, B200 Monobe, Nankoku, Kochi 783-8502, Japan
J. bios. agric. res. | Volume 12, Issue 02, pp. 1029-1035 | Available online: 25 February 2016.
Crossref: https://doi.org/10.18801/jbar.120217.125
FULL TEXT PDF:
| 125_jbar_hierarchical_cluster_euclidean_distance_and_principal_component_analysis_based_on_phenotypic_characters_of_hosta.pdf |
Title: Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta
Abstract: Hosta is a widely grown ornamental plants and sometimes used as vegetables. Hybridization of hostas is frequently done by home gardener. We conducted an experiment using twelve hosta taxa (coded from T1-T12) to analyze the morphological traits based hierarchical cluster, euclidean distance and PCA with a view to provide necessary information to the hosta breeders. We used complete randomized design with five replicates for the data collection of morphological traits. H. sieboldiana and H. montana had similar morphological characters while H. longipes var. gracillima, H. kiyosumiensis were mostly similar morphological characters as well. From the dissimilarity analysis, it was found that the dissimilarity distance between H. alismifolia and H. montana was maximum (452.2) which was closely followed by H. longissima and H. montana (447.6) where as minimum dissimilarity distance between H. sieboldii and H. nakaiana (36.2). PCA indicated that two important components accounted for 97.76% of the total variation among traits in of hosta taxa. The first and second component contributed 81.92% and 15.84% of the total variation, respectively. Leaf area was found as a unique morphological trait. H. sieboldiana, H. montana and H. longipes var. gracillima shared the common components; as well as H. alismifolia with H. longissima, H. sieboldii with H. nakaiana and H. tardiva with H. longipes var. caduca comprised common components. Overall, results revealed importance morphological components in breeding ability in hosta taxa.
Key Words: Plantain lily, Giboshi, Taxa, Dendrogram, Proximity distance matrix and PCA
Abstract: Hosta is a widely grown ornamental plants and sometimes used as vegetables. Hybridization of hostas is frequently done by home gardener. We conducted an experiment using twelve hosta taxa (coded from T1-T12) to analyze the morphological traits based hierarchical cluster, euclidean distance and PCA with a view to provide necessary information to the hosta breeders. We used complete randomized design with five replicates for the data collection of morphological traits. H. sieboldiana and H. montana had similar morphological characters while H. longipes var. gracillima, H. kiyosumiensis were mostly similar morphological characters as well. From the dissimilarity analysis, it was found that the dissimilarity distance between H. alismifolia and H. montana was maximum (452.2) which was closely followed by H. longissima and H. montana (447.6) where as minimum dissimilarity distance between H. sieboldii and H. nakaiana (36.2). PCA indicated that two important components accounted for 97.76% of the total variation among traits in of hosta taxa. The first and second component contributed 81.92% and 15.84% of the total variation, respectively. Leaf area was found as a unique morphological trait. H. sieboldiana, H. montana and H. longipes var. gracillima shared the common components; as well as H. alismifolia with H. longissima, H. sieboldii with H. nakaiana and H. tardiva with H. longipes var. caduca comprised common components. Overall, results revealed importance morphological components in breeding ability in hosta taxa.
Key Words: Plantain lily, Giboshi, Taxa, Dendrogram, Proximity distance matrix and PCA
HOW TO CITE THIS ARTICLE?
APA (American Psychological Association)
Mehraj, H. and Shimasaki, K. (2017). Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta. Journal of Bioscience and Agriculture Research,12(02), 1029-1035.
MLA (Modern Language Association)
Mehraj, H. and Shimasaki, K. “Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta”. Journal of Bioscience and Agriculture Research, 12.02(2017), 1029-1035.
Chicago and orTurabian
Mehraj, H. and Shimasaki, K. “Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta”. Journal of Bioscience and Agriculture Research, 11. no. 01(2016), 1029-1035.
APA (American Psychological Association)
Mehraj, H. and Shimasaki, K. (2017). Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta. Journal of Bioscience and Agriculture Research,12(02), 1029-1035.
MLA (Modern Language Association)
Mehraj, H. and Shimasaki, K. “Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta”. Journal of Bioscience and Agriculture Research, 12.02(2017), 1029-1035.
Chicago and orTurabian
Mehraj, H. and Shimasaki, K. “Hierarchical cluster, euclidean distance and principal component analysis based on phenotypic characters of hosta”. Journal of Bioscience and Agriculture Research, 11. no. 01(2016), 1029-1035.
- Addinsoft (2016). XLSTAT v. 2016. Data analysis and statistics software for Microsoft Excel. Addinsoft, New York, USA.
- Arivalagan, M., Bhardwaj, R., Gangopadhyay, K. K., Prasad, T. V. and Sarkar, S. K. (2013). Mineral composition and their genetic variability analysis in egg plant (Solanum melongena L.) germplasm. Journal of Applied Botany and Food Quality, 86, 99-103.
- Ashfaq, M., Khan, A. S., Khan, S. H. U. and Ahmad, R. (2012). Association of various morphological traits with yield and genetic divergence in rice (Oryza Sativa L.). International Journal of Agriculture and Biology, 14, 55-62.
- Bailey, L. H. (1930). Hosta: The plantain lilies. Gentes Hebarum, 2, 119-142.
- Bose, L. K. and Pradhan, S. K. (2005). Genetic divergence in deepwater rice genotypes. Journal of Central European Agriculture, 6(4), 635–640.
- Cheema, A. A., Rashid, M., Ashraf, M. and Qamar, Z. (2004). Genetic divergence in rice collection. Pakistan Journal of Botany, 36(3), 557–565.
- Chung, M. G. (1990). A Biosystematic study on the genus Hosta (Liliaceae/Funkiaceae) in Korea and Tsushima Island of Japan. Ph. D. Dissertation, University of Georgia, Athens.
- Chung, M. G. and Kim, J. W. (1991). The genus Hosta Tratt. (Liliaceae) in Korea. Sida, Contributions To Botany, 14(3), 411-420.
- Fujita, N. (1976). The genus Hosta (Liliaceae) in Japan. Actaphytotaxonomicaet Geobotanica, 27(3-4), 66–96 (in Japanese).
- Gana, A. S. (2006). Variability studies of the response of rice varieties to biotic and abiotic stresses. Ph.D Thesis, University of Ilorin.
- Gana, A. S., Shaba, S. Z. and Tsado, E. K. (2013). Principal component analysis of morphological traits in thirty-nine accessions of rice (Oryza sativa L.) grown in a rainfed lowland ecology of Nigeria. Journal of Plant Breeding and Crop Science, 4(6), 120-126. https://doi.org/10.5897/JPBCS12.065
- Golparvar, A. R., Ghasemi-Pirbalouti, A. and Madani, H. (2006). Genetic control of some physiological attributes in wheat under drought stress conditions. Pakistan Journal of Biological Sciences, 9(8), 1442-1446. https://doi.org/10.3923/pjbs.2006.1442.1446
- Guei, R. G., Sanni, K. A. and Fawole, A. F. J. (2005). Genetic diversity of rice (Oryzasativa). Agron Africaine, 5, 17–28.
- Hailu, A. F. (2016). Principal component analysis of morphological traits in thirty-six accessions of amaranths (Amaranthus Spp.) grown in a rainfed under Mizanand Tepe Condtions, South West Ethiopia. Journal of Biology, Agriculture and Healthcare, 6(1), 113-121.
- Hoque, M. N. and Rahman, L. (2007). Estimation of euclidean distance for different morpho-physiological characters in some wild and cultivated rice genotypes (Oryza sativa L.). Journal of Biological Sciences, 7(1), 86-88. https://doi.org/10.3923/jbs.2007.86.88
- Hylander, N. (1960). The genus Hosta. Journal of the Royal Horticultural Society, 85, 356–369.
- Jolliffe, I. T. (2002). Principal component analysis, 2nd edn. Springer Series in Statistics, Springer – Verlag New York Inc, New York.
- Kumar, S. R., Arumugam, T. and Anandakumar, C. R. (2013). Genetic diversity in egg plant (Solanum melongena L.). Plant Gene Trait, 4(2), 4-8.
- Maekawa, F. (1940). The genus Hosta. Journal of the Faculty of Science, the University of Tokyo. Sect. 1, Bot. 5, 317–425.
- Maekawa, F. and Kaneko, K. (1968). Evolution of karyotype in Hosta (Liliaceae). Journal of Japanese Botany, 43, 132–140.
- Mahendran, R., Veerabadhiran, P., Robin, S. and Raveendran, M. (2015). Principal component analysis of rice germplasm accessions under high temperature stress. International Journal of Agricultural Science and Research, 5(3), 355-360.
- Maji, A. T. and Shaibu, A. A. (2012). Application of principal component analysis for rice germplasm characterization and evaluation. Journal of Plant Breeding and Crop Science, 4(6), 87-93. https://doi.org/10.5897/jpbcs11.093
- Novembre, J. and Stephens, M. (2008). Interpreting principal component analyses of spatial population genetic variation. Nature Genetics, 40, 646–649. https://doi.org/10.1038/ng.139 PMid:18425127 PMCid:PMC3989108
- Prabakaran, S. (2010). Evaluation of local types of brinjal (Solanum melongena L.). M. Sc., (Hort.) Thesis, Agricultural College and Research Institute, TNAU, Madurai.
- Prabhu, M., Natarajan, S. and Pugalendhi, L. (2009). Variability and heritability studies in F5 and F6 progenies of brinjal. American-Eurasian Journal of Sustainable Agriculture, 3(3), 306-309.
- Schmid, W.G. 1991. The genus Hosta: Gibōshi Zoku (ギボウシ属). London and Portland: Timber Press. pp. 27-110.
- Shahidullah, S. M., Hanafi, M. M., Ashrafuzzaman, M., Ismail, M. R. and Salam, M. A. (2009). Phenological characters and genetic divergence in aromatic rices. African Journal Biotechnology, 8, 3199–3207.
- Shekar, C. K., Ashok, P. and Sasikala, K. (2012). Studies on heritability and multivariate analyses in brinjal (Solanum melongena L.). Vegetable Crops Research Bulletin, 76, 79-88. https://doi.org/10.2478/v10032-012-0005-2
- Sikder, R. K., Rahman, M. A., Asif, M. I., Jamal Uddin, A. F. M. and Mehraj, H. (2015). Genetic variability, distance and traits interrelationship analysis of Nerica and Inpari rice varieties. Scientia Agriculturae, 10(1), 44-48.
- Touhiduzzaman, Sikder, R. K., Asif, M. I., Mehraj, H. and Jamal Uddin, A. F. M. (2016). Correlation and genetic distance on sixteen rice varieties grown under SRI. Advances in Plants & Agriculture Research, 3(3), 00100.
- Varthini, V. N., Robin, S., Sudhakar, D., Raveendran, M., Rajeswari, S. and Manonmani, S. (2014). Evaluation of rice genetic diversity and variability in a population panel by principal component analysis. Indian Journal of Science and Technology, 7(10), 1555-1562.
Open Access | Read Article
© 2017 The Authors. This article published by Journal BiNET is freely available for anyone to read, share, download, print, permitted for unrestricted use and build upon, provided that the original author(s) and publisher are given due credit. All Published articles are distributed under the Creative Commons Attribution 4.0 International License.
Require any edit or correction or changes in article? Please contact HERE.