Combinations of distance measures and clustering algorithms in pepper germplasm characterization

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.

Selection in segregating populations of ornamental pepper plants (Capsicum annuum L.) using multidimensional scaling

“…Therefore, this technique is a strategy that must be considered for the study of diversity in segregating populations of Capsicum, especially when combined with the joint analysis of qualitative and quantitative characters. Therefore, a joint analysis of variables can provide a more complete indicator of the diversity in improvement programs (Gomes et al, 2019).…”

Caracterización morfoagronómica de la colección de germoplasma de ají dulce (Capsicum spp.) del caribe colombiano

“…Así mismo, al considerar la moda de los 19 descriptores cualitativos polimórficos de los grupos determinados, se encuentra que el GV difiere en 11 (57,9%), 12 (63,2%), 13 (68,4%) y 14 (73,7%) descriptores con los grupos GIII, GIV, GII y GI respectivamente (Tabla 4). (Gomes et al, 2019). Estos resultados concuerdan con los obtenidos por Sudré et al (2010), donde la caracterización morfo-agronómica usando simultáneamente variables morfológicas (cualitativas) y agronómicas (cuantitativas) permitió la separación de especies del género Capsicum en la colección de estudio.…”

Selection of ideal genotypes in peppers with ornamental potential

“…Peppers are widely grown in tropical and subtropical regions and are marketed worldwide in several forms, including as ornamental plants (Cardoso et al, 2018;Gomes et al, 2019). The genetic diversity of peppers of the genus Capsicum results in a wide and versatile marketing of these plants.…”