Combinations of distance measures and clustering algorithms in pepper germplasm characterization

Gisely Paula Gomes,Cláudia P Sudré,Leandro Sa Gonçalves,Viviane Yumi Baba,Cintia Dos S Bento,Rosana Rodrigues,Odair P Dos Santos

doi:10.1590/s0102-053620190207

Abstract

ABSTRACT Characterization and evaluation of genotypes conserved in the germplasm banks have become of great importance due to gradual loss of genetic variability and search for more adapted and productive genotypes. This can be obtained through several ways, generating quantitative and qualitative data. Joint analysis of those variables may be considered a strategy for an accurate germplasm characterization. In this study we aimed to evaluate different clustering techniques for characterization and evaluation of Capsicum spp. accessions using combinations of specific measures for quantitative and qualitative variables. A collection of 56 Capsicum spp. accessions was characterized based on 25 morphoagronomic descriptors. Six quantitative distances were used [A1) average of the range-standardized absolute difference (Gower), A2) Pearson correlation, A3) Kulczynski, A4) Canberra, A5) Bray-Curtis, and A6) Morisita] combined with distance for qualitative data [Simple Coincidence (B1)]. Clustering analyses were performed using agglomerative hierarchical methods (Ward, the nearest neighbor, the farthest neighbor, UPGMA and WPGMA). All combined distances were highly correlated. UPGMA clustering was the most efficient through cophenetic correlation and 2-norm analyses, showing a concordance between the two methods. Six clusters were considered an ideal number by UPGMA clustering, in which Gower distance showed a better adjustment for clustering. Most combined distances using UPGMA clustering allowed the separation of the accessions in relation to species, using both quantitative and qualitative data, which could be an alternative for simultaneous joint analysis, aiming to compare different clusters.

Highlights

Com o aumento da perda da variabilidade genética e a procura por genótipos mais adaptados e produtivos, a caracterização e a avaliação dos genótipos conservados em um banco de germoplasma são de elevada importância
With increasing extinction risks and loss of genetic variability, centers for plant genetic resource conservation (CPGRC) have been established worldwide. These CPGRC can be conserved as seed and pollen collections, in the field and in vitro, constituting what is called germplasm bank (Engels & Visser, 2003)
CPGRV conserved in germplasm banks include newly breeding and obsolete cultivars, local varieties, breeding lines obtained as intermediate products and genetic stocks, such as gene, chromosomal, and genomic mutants and wild relative (Ríos, 2015)

Summary

Introduction

Com o aumento da perda da variabilidade genética e a procura por genótipos mais adaptados e produtivos, a caracterização e a avaliação dos genótipos conservados em um banco de germoplasma são de elevada importância. A maioria das distâncias combinadas utilizando o agrupamento UPGMA permitiu a separação dos acessos em relação às espécies, utilizando simultaneamente dados quantitativos e qualitativos podendo ser uma alternativa para análise simultânea de dados conjuntos, visando uma comparação entre diferentes agrupamentos. CPGRV conserved in germplasm banks include newly breeding and obsolete cultivars, local varieties, breeding lines obtained as intermediate products and genetic stocks, such as gene, chromosomal, and genomic mutants and wild relative (Ríos, 2015). Many useful traits such as nutritional quality, resistance and/or tolerance to biotic and abiotic stresses are found among the accessions conserved in the germplasm bank. Few studies have used this strategy mainly due to the lack of knowledge of which statistics techniques allow this approach, in addition to the tendency of researchers to give more importance to those variables which are directly related to traits to be improved in a breeding program (Gonçalves et al, 2008; Moura et al, 2010)

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