Comparison of similarity coefficients used for cluster analysis with dominant markers in maize (Zea mays L)

Abstract

The objective of this study was to evaluate whether different similarity coefficients used with dominant markers can influence the results of cluster analysis, using eighteen inbred lines of maize from two different populations, BR-105 and BR-106. These were analyzed by AFLP and RAPD markers and eight similarity coefficients were calculated: Jaccard, Sorensen-Dice, Anderberg, Ochiai, Simple-matching, Rogers and Tanimoto, Ochiai II and Russel and Rao. The similarity matrices obtained were compared by the Spearman correlation, cluster analysis with dendrograms (UPGMA, WPGMA, Single Linkage, Complete Linkage and Neighbour-Joining methods), the consensus fork index between all pairs of dendrograms, groups obtained through the Tocher optimization procedure and projection efficiency in a two-dimensional space. The results showed that for almost all methodologies and marker systems, the Jaccard, Sorensen-Dice, Anderberg and Ochiai coefficient showed close results, due to the fact that all of them exclude negative co-occurrences. Significant alterations in the results for the Simple Matching, Rogers and Tanimoto, and Ochiai II coefficients were not observed either, probably due to the fact that they all include negative co-occurrences. The Russel and Rao coefficient presented very different results from the others in almost all the cases studied and should not be used, because it excludes the negative co-occurrences in the numerator and includes them in the denominator of their expression. Due to the fact that the negative co-occurrences do not necessarily mean that the regions of the DNA are identical, the use of coefficients that do not include negative co-occurrences was suggested.

Diversidade genética entre híbridos de laranja-doce e tangor 'Murcott' avaliada por fAFLP e RAPD

“…Em milho, a comparação de diferentes coeficientes de similaridade demonstrou que o tipo de marcador molecular utilizado em análises de similaridade pode causar alterações nas análises e interpretações dos resultados (Meyer et al, 2004). Em estudos de diversidade com dados gerados por marcadores dominantes, como RAPD e AFLP, coeficientes que não consideram as ausências de fragmentos como evidências de homologia, tais como Jaccard, Sorensen-Dice, Anderberg e Ochiai's, são os mais indicados (Meyer et al, 2004 Marcadores moleculares são considerados excelentes ferramentas para avaliação da diversidade genética em muitas espécies de plantas (Garcia et al, 1998). No melhoramento de espécies perenes de longo ciclo vegetativo como os citros, essa ferramenta pode direcionar a seleção precoce de híbridos mais próximo ao parental de interesse.…”

“…Marcadores monomórficos para a progênie não foram considerados na análise, conforme Oliveira et al (2002a). Cada banda foi considerada um único locus genético, não levando em consideração possível alelismo entre diferentes tipos de AFLP, conforme utilizado por Meyer et al (2004). A heterozigosidade dos parentais foi comparada pelo somatório do número de bandas presentes nos parentais que se segregavam dentro da população de híbridos (Barbosa Neto et al, 1996).…”

Agrobiodiversity in Cucurbita spp. landraces collected in Rio de Janeiro assessed by molecular markers

“…The dissimilarity matrix was built through the software Genes (Cruz 2006) and the dendrograms generated with the support of the R program (http:// www.r-project.org). In order to accomplish the dissimilarity matrix, the arithmetic complement of Jaccard was used, as suggested by Meyer et al (2004). Cluster analysis carried out from the data of this matrix were performed through the hierarchical method Unweighted Paired Group Method using Arithmetic averages (UPGMA).…”

Chemical similarity among domesticated and wild genotypes of peanut based on n-alkanes profiles

“…However, in some instances, the use of different similarity coefficients does not significantly alter the final result (Meyer et al, 2004). For example, the use of the Jaccard coefficient did not alter the layout of the phenogram shown in Figure 1.…”

“…According to Nogueira & Santos (2000), peanut genotypes analyzed showed different physiological responses to water deficit. These authors evaluated the performance of the BR1, BRS 151 L-7 and BRS Havana genotypes under water stress, and concluded that the first shows the lowest values of diffusive resistance and negative values of water potential, and for this reason is considered the most appropriate genotype for the northeastern region of Brazil.…”