Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection

Hokanson, Stan C.; Szewc-McFadden, Amy K.; Lamboy, Warren F.; McFerson, James R.

doi:10.1007/s001220050943

Cited by 309 publications

(234 citation statements)

References 54 publications

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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%

“…In the case of molecular markers, it is noteworthy that a reduced set of isozyme loci (12) resulted as valid as a similar magnitude (10 loci) but much more polymorphic SSR set to obtain a representative core subset. Such number of markers is generally accepted as sufficient to establish genetic identities (Hokanson et al, 1998;Laurens et al, 2004;Galli et al, 2005;Kitahara et al, 2005;Guarino et al, 2006). However, a different allelic distribution and lower diversity indices would have been expected for the CI subset at any of the SSR loci or morpho-agronomic traits evaluated, due to the kind of information provided by each type of marker.…”

Section: Discussionmentioning

confidence: 99%

“…Woody perennial collections constitute a different case, because they usually hold fewer accessions, maintained as clones in field genebanks. For instance, the world's largest Malus germplasm collections maintain over no more than 2500 accessions, and most of national or regional collections hold less than 500 accessions (Hokanson et al, 1998;Maggioni et al, 2004). Additionally, management costs in field banks are usually higher than those to maintain seed banks, they are highly vulnerable to environmental conditions, and field analyses are usually a lengthy and costly process, as it may be necessary waiting for several years from planting the trees to obtain their first crop.…”

Section: Introductionmentioning

confidence: 99%

“…In the last years, microsatellite markers (SSR) have become favored for establishing unique genetic identities or fingerprints and assessing genetic diversity within a collection, because of their high polymorphism level, reproducibility and relative ease of analysis (Schlötterer, 2004). Several studies have found that a reduced set of SSR markers (around 6-12) can unambiguously differentiate accessions (Hokanson et al, 1998;Laurens et al, 2004;Galli et al, 2005;Kitahara et al, 2005;Guarino et al, 2006).…”

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: Introductionmentioning

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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“…By contrast, PCR-amplified sequencetagged microsatellite sites (STMS) are codominantly inherited, and often detect numerous alleles at each individual locus. Lately, several microsatellite DNA studies have demonstrated high levels of marker heterozygosity in the family Rosaceae (Guilford et al, 1997;Hokanson et al, 1998;Sosinski et al, 2000;Esselink et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC.

Nybom

Esselink²,

Werlemark

et al. 2003

Heredity

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According to previous cytological evidence, the hemisexual dog-rose species, Rosa sect. Caninae, transmit only seven chromosomes (derived from seven bivalents) through their pollen grains, whereas egg cells contain 21, 28 or 35 chromosomes (derived from seven bivalents and 14, 21 or 28 univalents) depending on ploidy level. Two sets of reciprocal pairwise interspecific crosses involving the pentaploid species pair R. dumalis and R. rubiginosa, and the pentaploid/tetraploid species pair R. sherardii and R. villosa, were analysed for 13 and 12 microsatellite DNA loci, respectively. Single loci were represented by a maximum of three simultaneously occurring alleles in R. villosa, and four alleles in the other three parental plants. In the experimentally derived offspring, the theoretical maximum of five alleles was found for only one locus in the pentaploid progenies. Microsatellite DNA allele composition was identical with that of the maternal parent in 10 offspring plants, which were probably derived through apomixis. Almost all microsatellite DNA alleles were shared with the maternal parent also in the remaining offspring, but 1-4 alleles shared only with the paternal parent, indicating sexual seed formation. Analysis of quantitative peak differences allowed a tentative estimation of allelic configuration in the individual plants, and suggested that bivalent formation preferentially takes place between chromosomes that consistently share the same microsatellite alleles and therefore appear to be highly homologous. Moreover, alleles that were shared between the species in each cross combination comparatively often appear to reside on the bivalent-forming chromosomes, whereas species-specific alleles instead occur comparatively often on the univalent-forming chromosomes and are therefore inherited through the maternal parent only. Recombination then takes place between very similar genomes also in interspecific crosses, resulting in a reproduction system that is essentially a mixture between apomixis and selfing.

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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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Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection

Cited by 309 publications

References 54 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

Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC.

Preservation of Genetic Resources in the National Plant Germplasm Clonal Collections

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