Comparison of multivariate statistical algorithms to cluster tomato heirloom accessions

Gonçalves, Leandro Simões Azeredo; Rodrigues, Rosana; Amaral, Antônio Teixeira do; Karasawa, Mina; Sudré, Cláudia Pombo

doi:10.4238/vol7-4gmr526

Cited by 94 publications

(81 citation statements)

References 19 publications

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“…In contrast, the Ward method showed the most unsatisfactory results (0.27 < r c < 0.62; -20379 < D < 32370; 1333 < S < 1703). Similar results were found by Gonçalves et al (2008) in studies with tomato accessions and by Sesli and Yegenoglu (2010) in studies with wild olives. In general, our results support the findings reported by Mohammadi and Prasanna (2003) in that the UPGMA is among agglomerative hierarchical methods most commonly used.…”

Section: Resultssupporting

confidence: 86%

“…Among the statistical methods used for diversity studies are i) similarity (and dissimilarity) coefficients, ii) hierarchical grouping methods and grouping methods by optimization, and iii) data projection in two-dimensional space (Duarte et al, 1999;Mohammadi and Prasanna, 2003). In view of the large number of statistical methods available in the literature and the fact that existing comparative studies reveal that the choice of statistical methods can affect the results (Meyer et al, 2004;Gonçalves et al, 2008;Cerqueira-Silva et al, 2009;Sesli and Yegenoglu, 2010;Alves et al, 2012), it is important to establish criteria for choosing statistical methods that are appropriate for the reality of each study to be conducted. M.M.…”

Section: Introductionmentioning

confidence: 99%

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Short Communication Comparison of methods for estimates of molecular genetic diversity in genus Croton: influence of coefficients, clustering strategies and data projection

Scaldaferri¹,

Freitas²,

Vieira³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. We investigated 10 similarity (and disimilarity) coefficients in a set of 40 wild genotypes of Croton linearifolius subjected to analyses using hierarchical grouping methods, grouping methods by optimization and data projection in two-dimensional space. Genotypes were characterized by analyzing DNA polymorphism with the use of 15 ISSR and 12 RAPD markers. The distance measurements were compared by the Spearman correlation test, projection in twodimensional space and grouping efficiency evaluation. The Spearman correlation coefficients between the 10 coefficients evaluated were 5567 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (3): 5566-5573 (2014) Comparison of coefficients in Croton with molecular markers significant (P < 0.001) and indicated significant changes in genotype ranking due to type of coefficient used (0.76 ≤ r s ≤ 1). Wide variation was also observed in the efficiency of clustering methods, where the unweighted pair group method with arithmetic mean was the most suitable (0.3 ≤ D ≤ 1.5 ; 0.41 ≤ r c ≤ 0.77; 5.99 ≤ S ≤ 12.61). Projection efficiencies in two-dimensional space showed high-stress values (65 < S < 89%). Similar to the results observed for hierarchical clustering methods and for projection in two-dimensional space, the formation of groups with grouping methods by optimization showed variations when using different coefficients. We believe that the results confirm the influence of coefficients in studies of genetic diversity, showing the need to use criteria and standards for selecting appropriate methods for genetic studies of the genus Croton.

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Section: Resultssupporting

confidence: 86%

Section: Introductionmentioning

confidence: 99%

Short Communication Comparison of methods for estimates of molecular genetic diversity in genus Croton: influence of coefficients, clustering strategies and data projection

Scaldaferri¹,

Freitas²,

Vieira³

et al. 2014

Genet. Mol. Res.

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“…As espécies silvestres, as variedades locais e as cultivares obsoletas podem fornecer genes que conferem maior adaptação a estresses ambientais, bem como resistência a inúmeras pragas e doenças (GEPTS, 2006;GONÇALVES et al, 2008). Entretanto, esses acessos mantidos em bancos de germoplasma devem ser caracterizados e avaliados com o objetivo de conhecer os materiais genéticos antes de introduzilos em programa de melhoramento, evitando o uso de genomas reduntantes, comumente denonimados duplicatas (FRANCO et al, 2005;GEPTS, 2006;SUDRÉ et al, 2010).…”

Section: Introductionunclassified

“…Na caracterização e avaliação dos acessos, informações sobre variáveis quantitativas e qualitativas proporcionam maior acurácia na identificação de genomas contrastantes (MOHAMMADI; PRASANNA, 2003;FRANCO, 2004;GONÇALVES et al, 2008;GONÇALVES et al, 2009;SUDRÉ et al, 2010). Logicamente que tal situação decorre de uma maior capitalização da expressão gênica em uma única matriz de dados reunindo os diferentes tipos de variáveis (GONÇALVES et al, 2009).…”

Section: Introductionunclassified

Divergência genética entre acessos de mamoeiro por meio de variáveis morfoagronômicas

et al. 2012

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ResumoO presente trabalho teve como objetivo quantificar a variabilidade genética entre 46 acessos de mamoeiro dos grupos Solo e Formosa utilizando 19 variáveis morfoagronômicas separadamente e em conjunto, e verificar a eficiência da análise conjunta no estudo da diversidade genética. O experimento foi conduzido em três épocas distintas (maio e agosto de 2007, e novembro de 2008), no município de Linhares-ES, utilizando-se delineamento em blocos casualizados, com duas repetições e 20 plantas por parcela em fileira dupla. As características quantitativas foram submetidas à análise de variância e posteriormente, utilizadas para estimar a distância de Mahalanobis, enquanto para os descritores qualitativos utilizouse o coeficiente de coincidência simples. A análise conjunta das variáveis quantitativas e qualitativas foi estimada com base no algoritmo de Gower. As matrizes de distâncias foram comparadas usando a correlação de Mantel com 1000 permutações. Posteriormente, foi realizado o agrupamento dos acessos pelo método UPGMA. Embora tenha sido constituído número igual de grupos (sete), os dois tipos de variáveis separadamente ou em conjunto não possibilitaram a formação de agrupamentos consideravelmente semelhantes para o grupo Formosa. Ao contrário, os acessos do grupo heterótico Solo ficaram alocados praticamente no grupo I em relação a todos os métodos de distância. O agrupamento formado pelos dados em conjunto proporcionou maior disjunção dos genótipos, decorrente de maior homogeneidade dentro dos grupos e heterogeneidade entre os grupos. Palavras-chave: Carica papaya L., análise combinada, banco de germoplasma, algoritmo de Gower AbstractThis study aimed to quantify genetic variability among 46 accessions of papaya from 'Solo' and 'Formosa' groups using 19 morphoagronomic traits separately and simultaneously, and to evaluate the efficiency of simultaneous analysis. The experiment was conducted for three growing seasons (May and August 2007, and November 2008), in Linhares-ES, using a randomized block design with two replications and 20 plants in two rows per plot. Quantitative traits were analyzed by analysis of variance and then used to estimate the Mahalanobis distance, while for the qualitative traits it was used the coefficient of simple coincidence. The genetic distance for the joint analysis was estimated based on the algorithm of Gower. The matrices of distance were compared using the Mantel correlation with 1000 permutations. The clusters of accessions were performed by UPGMA. Although they have made the same number of groups (seven), both types of variables separately and jointly did not allow the 1 Engº Agrº, Doutorando em Produção Vegetal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, UENF, Campos dos Goytacazes, RJ.

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“…These analyses help to identify parents to be used in crop improvement programs (Cruz et al, 2011). They also allow for identifying groups with higher similarity on one side, emphasizing the need for new samples and the existence of duplicates on the other, which might be eliminated, reducing costs and workforce required for the conservation of accessions (Gonçalves et al, 2008). Genetic diversity is obtained through dissimilarity measures.…”

Section: Introductionmentioning

confidence: 99%

Integration of quantitative and qualitative descriptors for genetic diversity studies of watermelon accessions

Lima¹,

Queiróz²,

Oliveira³

et al. 2017

Aust J Crop Sci

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Most of genetic diversity studies are based only on quantitative descriptors. The aim of this study was to apply different analysis strategies with quantitative and qualitative descriptors to identify which is the most suitable to integrate descriptors for genetic diversity studies of watermelon (Citrullus lanatus) germplasm using different assays. A total of 20 watermelon accessions were evaluated in the State of Rio Grande do Norte and two commercial cultivars were used as witness (control) (Crimson Sweet and Charleston Gray) in two cultivation seasons (2014/2015), using 49 descriptors, in which 26 were quantitative and 23 were qualitative. The genetic diversity of the accessions was obtained using eight analysis strategies that combined the Mahalanobis Distance, Average Standardized Euclidean Distance (SED), and Weighted Average Euclidean Distance, followed by groupings using the Tocher optimization method. A wide morphological variability was observed between and within accessions. The eight different strategies of genetic dissimilarity analyses resulted in 36 different groups. The clustering strategy, by which dissimilarity between accessions calculated using SED (quantitative descriptors) and WED (qualitative descriptors) is the most suitable for integrating quantitative and qualitative descriptors in genetic diversity studies of watermelon germplasm.

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Comparison of multivariate statistical algorithms to cluster tomato heirloom accessions

Cited by 94 publications

References 19 publications

Short Communication Comparison of methods for estimates of molecular genetic diversity in genus Croton: influence of coefficients, clustering strategies and data projection

Short Communication Comparison of methods for estimates of molecular genetic diversity in genus Croton: influence of coefficients, clustering strategies and data projection

Divergência genética entre acessos de mamoeiro por meio de variáveis morfoagronômicas

Integration of quantitative and qualitative descriptors for genetic diversity studies of watermelon accessions

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