Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops

Hu, Jin; Zhu, Jun; Xu, Hongwei

doi:10.1007/s001220051478

Cited by 209 publications

(327 citation statements)

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“…Moreover, a small number of morphological characters (≈20-30) are generally described for annual crop species, where less than a half of them suffice and are required for assessing distinctness (UPOV, 1989(UPOV, , 1996(UPOV, , 1998. Those are some of the reasons why core collections for crop species have been traditionally obtained using a reduced set of passport, eco-geographical and morphological data (Balakrishnan et al, 2000;Hu et al, 2000;Li et al, 2004) and only at a later stage the genetic diversity of the constituted core collection has been assessed with molecular markers (Hokanson et al, 1998, Grenier et al, 2000, Liu et al, 2001. However, there are reasons to take a different approach to constitute core collections for many woody perennial species.…”

Section: Discussionmentioning

confidence: 99%

“…The cost and effort of conducting the morphological characterization of a woody perennial collection can be consequently much higher than for assessing with molecular markers (Karp et al, 1997). Additionally, genetic sorting based on phenotypic data could not correctly reflect the genetic diversity of the initial germplasm resources due to environmental errors in the field or genotype-ambient interaction (Hu et al, 2000). Therefore, in regional and national apple collections not yet characterized, molecular markers could constitute a rapid and economic tool for the estimation of genetic variability and the constitution of core subsets, so in a later stage it will be feasible to perform an exhaustive and efficient characterization through agro-morphological descriptors at the core collection.…”

Section: Discussionmentioning

confidence: 99%

“…The procedure of stepwise clustering with random sampling proposed by Hu et al (2000) was employed in developing three core subsets, one from each source of data: the subset named CS was obtained from microsatellite data, CI subset was obtained from isozyme data and CM from morpho-agronomic traits data. Dice distance and unweighted pair-group average method (UPGMA) of hierarchical cluster analysis (Sneath and Sokal, 1973) were used for grouping accessions.…”

Section: Construction Of Core Collectionsmentioning

confidence: 99%

“…Various types of data have been used to analyze the genetic diversity in the collections, including morphological, agronomic and eco-geographical traits or molecular and biochemical markers (van Hintum et al, 2000), and each of these has its advantages and disadvantages. In the case of crops, core collections have been habitually obtained from passport, eco-geographical and morphological data (Balakrishnan et al, 2000;Grenier et al, 2000;Hu et al, 2000;Li et al, 2004), because these collections are usually very large (thousands of accessions) and the use of molecular markers in the entire collection is not feasible because of the cost (Grenier et al, 2000;Hu et al, 2000). Woody perennial collections constitute a different case, because they usually hold fewer accessions, maintained as clones in field genebanks.…”

Section: Introductionmentioning

confidence: 99%

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Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data

Santesteban

Jiménez

Royo

2009

Span. j. agric. res.

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Various types of data have been used for sampling plant core collections, including morphological, agronomic and ecogeographical traits, and molecular and biochemical markers. However, little is known about the ability of woody perennial core collections to retain the diversity and structure of the whole collection for characters that were not considered in the selection, especially when molecular markers are used. In this study, three core subsets were established for the apple germplasm bank curated at the Public University of Navarre (UPNa, Spain): based upon the diversity found with 10 SSR markers, another based upon the diversity assessed with 12 isozyme loci; and a third based upon morpho-agronomic diversity evaluated by 23 morpho-agronomic traits. Comparisons between these three subsets and to the whole collection were assessed to determine the impact of the data used in the selection on phenotypic and genetic diversity and on their population structure. The three subsets had a similar diversity and they did not differ from the original collection, according to Nei and Shannon-Weaver indices. The allelic/class frequencies were also always maintained in the three subsets. Overall, the kind of data used to constitute a core collection had little influence on the phenotypic and genetic diversity retained, so in the case of apple collections the use of molecular markers is preferable for this task because they allow a rapid and reliable characterization.Additional key words: characterization, germplasm, isozyme, Malus × domestica, microsatellite, pomology, stepwise clustering. Resumen Evaluación de la diversidad genética y fenotípica retenida en colecciones nucleares de manzano formadas a partir de caracterizaciones agro-morfológicas o molecularesLas colecciones nucleares de plantas pueden formarse a partir de la información obtenida en caracterizaciones morfológicas, agronómicas o eco-geográficas, así como a partir de caracterizaciones bioquímicas o moleculares. Un aspecto poco estudiado de la formación y validación de colecciones nucleares es la capacidad de éstas para conservar la estructura y diversidad de la colección global en aquellos caracteres que no han sido empleados para formar la colección nuclear. En el presente estudio se determinaron tres colecciones nucleares para el Banco de Germoplasma de Manzano de la Universidad Pública de Navarra: para el primero se emplearon los datos de caracterización de 10 marcadores SSR, la segunda fue formada a partir de la caracterización hecha con 12 loci de isoenzimas, y la tercera se construyó a partir de la información proporcionada por 23 caracteres morfo-agronómicos. Se comparó la estructura y diversidad genotípica y fenotípica de las tres colecciones, entre sí y respecto de la colección original, para determinar el impacto que sobre dicha estructura y diversidad tenía el tipo de dato con que se formó la colección nuclear. Las tres colecciones conservaron una diversidad similar y no difirieron de la original en sus índices de Nei y Shannon-Weaver, y ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Construction Of Core Collectionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data

Santesteban

Jiménez

Royo

2009

Span. j. agric. res.

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“…De acordo com Hu et al (2000), o coeficiente de similaridade pode ser obtido por: Um outro critério utilizado para verificar a eficácia de representatividade das coleções nucleares foi o coeficiente de determinação (R 2 ), que foi determinado pela razão entre a soma de quadrados dos desvios, entre acessos selecionados para compor a coleção nuclear e a soma de quadrados total dos desvios da coleção de germoplasma (Cruz, 1997). Os acessos foram selecionados pelo método de Tocher com critério de aglomeração inverso.…”

Section: Methodsunclassified

Estratégias de amostragem e estabelecimento de coleções nucleares

Vasconcelos

Cruz

Bhering

et al. 2007

Pesq. agropec. bras.

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Resumo -O objetivo deste trabalho foi avaliar a influência da intensidade de amostragem, do tamanho da coleção de germoplasma inicial e da variância da amostragem sobre a qualidade das respectivas coleções nucleares, quanto à representatividade das coleções iniciais. Foram simulados sete tamanhos de coleções iniciais e utilizadas seis intensidades de amostragem para estabelecimento de coleções nucleares, utilizando caracteres morfoagronômicos. Determinaram-se o número de grupos formados, o coeficiente de coincidência entre a coleção nuclear e a coleção inicial e o coeficiente de determinação dos acessos amostrados para comporem a coleção nuclear. Também foi proposto o uso de uma estratégia alternativa para estabelecer coleções nucleares, de forma a maximizar a diversidade entre os acessos. O tamanho da coleção inicial influencia a intensidade de amostragem empregada na obtenção da coleção nuclear. A amostragem de acessos pelo método de Tocher, com critério de aglomeração inverso, mostrou-se eficiente na obtenção de coleções nucleares. As diferentes magnitudes de variância das coleções iniciais não influenciaram os coeficientes de determinação (R 2 ) nem os coeficientes de coincidência entre a coleção inicial e as respectivas coleções nucleares.Termos para indexação: coleção de germoplasma, coleção nuclear, intensidade de amostragem, coeficiente de coincidência, método de Tocher. Strategies for sampling and establishment of core collectionsAbstract -The objective of this work was to evaluate the effect of sampling intensity, initial collection's size and its variance over the quality of the respective core collections, in terms of representation of the initial collections. Therefore, simulations were performed for seven sizes of the initial collections and six sampling intensities for the establishment of core collections were used, comprising morpho-agronomic traits. Groups formed were determined, as well as the coincidence coefficient between the core and the initial collection, and the determination coefficient of the accessions sampling to compose the core collection. The use of an alternative strategy was proposed to establish core collections, this strategy maximizes the diversity among the accessions. The size of initial collections affects the sampling intensity to be used to obtain a core collection. The selection of accessions with the method of Tocher, comprising criteria of inverse grouping, was efficient for the formation of the core collections. The different magnitudes of variance of the initial collections did not affect either the coefficient of determination (R 2 ) or the coincidence rate between initial collections and respective core collection.

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Preservation of Genetic Resources in the National Plant Germplasm Clonal Collections

Volk

Walters

2003

Plant Breeding Reviews

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Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops

Cited by 209 publications

References 11 publications

Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data

Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data

Estratégias de amostragem e estabelecimento de coleções nucleares

Preservation of Genetic Resources in the National Plant Germplasm Clonal Collections

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