Morphological phenotypic dispersion of garlic cultivars by cluster analysis and multidimensional scaling

Anderson Rodrigo Da Silva,Mário Puiatti,Fernando Luiz Finger,Antônio Policarpo Souza Carneiro,Paulo Roberto Cecon,Carlos Tadeu Dos Santos Dias

doi:10.1590/s0103-90162014000100005

Anderson Rodrigo Da Silva, Mário Puiatti + Show 4 more

Open Access

https://doi.org/10.1590/s0103-90162014000100005

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Abstract

Multivariate techniques have become a useful tool for studying the phenotypic diversity of Germplasm Bank accessions, since they make it possible to combine a variety of different information from these accessions. This study aimed to characterize the phenotypic dispersion of garlic (Allium sativum L.) using two multivariate techniques with different objective functions. Twenty accessions were morphologically characterized for bulb diameter, length, and weight; number of cloves per bulb; number of leaves per plant; and leaf area. Techniques based on generalized quadratic distance of Mahalanobis, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and nMDS (nonmetrric MultiDimensional Scaling) were applied and the relative importance of variables quantified. The two multivariate techniques were capable of identifying cultivars with different characteristics, mainly regarding their classification in subgroups of common garlic or noble garlic, according to the number of cloves per bulb. The representation of the phenotypic distance of cultivars by multidimensional scaling was slightly more effective than that with UPGMA clustering.

Highlights

Several countries, including the United States, the United Kingdom, Japan, Germany, Italy, Australia, Chile, the Czech Republic, and Brazil, have created Germplasm Banks for the conservation of garlic accessions (Allium sativum L.) due to limited species recombination (Matus et al, 1999, Stavelíková, 2008)
Multivariate techniques have become a useful tool for studying the phenotypic diversity of Germplasm Bank accessions, since they make it possible to combine a variety of different information from these accessions
Techniques based on generalized quadratic distance of Mahalanobis, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and nonmetric multidimensional scaling (nMDS) were applied and the relative importance of variables quantified

Summary

Introduction

Several countries, including the United States, the United Kingdom, Japan, Germany, Italy, Australia, Chile, the Czech Republic, and Brazil, have created Germplasm Banks for the conservation of garlic accessions (Allium sativum L.) due to limited species recombination (Matus et al, 1999, Stavelíková, 2008). The phenotypic variability in these banks should be quantified in order to allow an effective use of accession collections, and this warrants the need for studies on the morphological characterization of cultivars. In studies of the genetic divergence of garlic cultivars, UPGMA (Unweighted Pair Group Method with Arithmetic mean) clustering has been used by Mota et al (2004), Vieira and Nodari (2007), and Buso et al (2008). Multi-Dimensional Scaling (MDS) is an ordering technique for dimensional reduction that allows one to map individuals as points in low-dimensional space (generally 2D or 3D) (Manly, 2004; Borg and Groenen, 2005). MDS is especially useful when the relation between individuals is unknown (not an unusual case in germplasm banks), but it is possible to estimate a detachment matrix between them

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