Genetic diversity of the Spanish apple genetic resources using SSRs

The Spanish Program of Plant Genetic Resources integrates, among others, the collections located at Public University of Navarre, Centro de Investigaciones Agrarias de Mabegondo, Cabildos (Tenerife, La Palma and Gran Canaria), University of Lleida, Estación Experimental de Aula Dei-CSIC and CITA of Aragon. Those collections include mainly local cultivars from their respective regions, covering most of the Spanish apple-growing areas. Though some previous studies about the genetic variability of apple genetics resources from Spain were already performed, a complete analysis is needed in order to evaluate the complete diversity of Malus spp. in Spain. For doing that, the Spanish Government funded the project ¿Harmonization of the methodology of characterization, assessment of genetic diversity and definition of the core collection of the apple germplasm conserved in Spanish genebanks¿. In total, we have evaluated 1206 accessions using standardized methodologies, with SSR markers and morphological descriptors. SSR fingerprinting was performed with 13 SSR markers. SSR profiles were obtained independently and allele sizes were compared using a common set of cultivars selected as references. Results showed 601 genotypes for 1206 accessions. Most of the genotypes (438) were identified only in one accession. The other 163 genotypes were repeated in two to 81 accessions (involving 767 accessions in total). The harmonization of morphological descriptors will allow us to determine if the accessions with the same genotype are synonymies or closely related individuals. Results of this study highlight the interest of coordinated actions in order to optimize the management of germplasm collections and to evaluate the complete genetic diversity of Malus spp. in Spain.Peer Reviewe

Genetic diversity of the Spanish apple genetic resources using SSRs: abstract

PublishedPoster number 6

Definición del núcleo optimizado de la colección de conservación del manzano español

5 Pags.- 1 Tabl.Este trabajo tiene como objetivo determinar la estrategia más adecuada para la selección del conjunto mínimo de accesiones (núcleo optimizado) que represente eficientemente la variación genética del manzano conservado en las colecciones españolas. Este núcleo optimizado mediante criterios genéticos constituirá la base de la colección nuclear de conservación, que podrá ser complementado con accesiones seleccionadas por otros criterios (morfo-fisiológicos, agronómicos, valor histórico, etc.). Se ha evaluado la eficiencia de estrategias de selección por búsqueda local estocástica avanzada (ASLS) que diferían tanto por el tamaño final del núcleo como por la combinación (y peso relativo) de las medidas de distancia genética y riqueza alélica a optimizar. Las estrategias empleadas han proporcionado núcleos optimizados con grandes diferencias en la diversidad conservada, así como en el nivel de representación de la estructura genética general. Teniendo en cuenta el uso principal de la colección nuclear, la estrategia que ofrece un mejor equilibrio entre representatividad y adecuación al uso es la que combina la optimización de la distancia media entre cada accesión de la colección y la entrada en el núcleo más cercana con el índice de Shannon y la recuperación de alelos.Este trabajo ha sido financiado por los proyectos INIA RF2011-00017-C05-00 y RTA2015-00052-C02-00Peer reviewe

Development of a standardized methodology for phenotypical characterizations in apple

4 Pags.- 2 Tabls. Articles derived from XIV EUCARPIA Symposium on Fruit Breeding and Genetics (Bologna,Italy. June 14-18 2015) . The definitive version is available at: http://www.actahort.org/index.htmThe description of phenotypic traits in apple cultivars is generally performed using internationally agreed descriptors such as UPOV guidelines, which defines for each trait several states of expression. However, it is not always possible to classify a cultivar unambiguously using those guidelines, because in practice the states are not clearly enough defined or the example cultivars are not always available in the collections. This work presents the results of a harmonization project performed by the teams responsible of the main apple germplasm collections in Spain. The objective was to develop a standardized method for the 57 traits included in the TG/14/9 UPOV guidelines for apple characterization, defining their states of expression in a clear and unambiguous way for Spanish germplasm. Phenotypic data collected for more than 1,600 accessions from Spanish collections were used and the method to define each state depended on the type of expression. For quantitative traits the number of states and their limits were defined according to the variability that exists within and between accessions. For qualitative traits, high-resolution images clearly depicting each state were selected. A standardized characterization protocol for the 57 traits of apple germplasm has been provided, enabling to comparing properly the phenotypes of Spanish genetic resources.This Project has been funded by the Spanish Ministry of Science and Innovation/National Institute for Agricultural and Food Research and Technology (RF2011- 00017-C05-00).Peer reviewe

Development of a standardized methodology for phenotypical characterizations in apple

1 pag.This work presents the results of a harmonization project performed by the teams responsible of the main apple germplasm collections in Spain. The objective was to develop a standardized method for the 57 traits included in the TG/14/9 UPOV guidelines for apple characterization, defining their states of expression in a clear and unambiguous way for Spanish germplasm.Peer reviewe

Definición del núcleo optimizado de la colección de conservación del manzano español

Este trabajo tiene como objetivo determinar la estrategia más adecuada para la selección del conjunto mínimo de accesiones (núcleo optimizado) que represente eficientemente la variación genética del manzano conservado en las colecciones españolas. Este núcleo optimizado mediante criterios genéticos constituirá la base de la colección nuclear de conservación, que podrá ser complementado con accesiones seleccionadas por otros criterios (morfo-fisiológicos, agronómicos, valor histórico, etc.). Se ha evaluado la eficiencia de estrategias de selección por búsqueda local estocástica avanzada (ASLS) que diferían tanto por el tamaño final del núcleo como por la combinación (y peso relativo) de las medidas de distancia genética y riqueza alélica a optimizar. Las estrategias empleadas han proporcionado núcleos optimizados con grandes diferencias en la diversidad conservada, así como en el nivel de representación de la estructura genética general. Teniendo en cuenta el uso principal de la colección nuclear, la estrategia que ofrece un mejor equilibrio entre representatividad y adecuación al uso es la que combina la optimización de la distancia media entre cada accesión de la colección y la entrada en el núcleo más cercana con el índice de Shannon y la recuperación de alelos.Publishe

Genetic diversity and structure of the Spanish apple genetic resources inferred using SSRs:: abstract

Publishe

Genetic diversity and structure of the Spanish apple genetic resources inferred using SSRs

1 Pag.A total of 1543 accessions from Spanish collections of Malus x domestica Borkh were evaluated with a set of 13 SSRs, including 11 recommended by ECP/GR Malus/Pyrus WG, in order to estimate their genetic diversity and to identify the genetic structure and relationships among their accessions, as part of the objectives of the project funded by INIA “Harmonization of the methodology of characterization, assessment of genetic diversity and definition of the core collection of the apple germplasm conserved in Spanish genebanks”.Peer reviewe

Analysis of the genetic diversity and structure of the Spanish apple genetic resources suggests the existence of an Iberian genepool

87 Pags.- 3 Tabls.- 5 Figs.- 1 Suppl. Fig.- 5 Suppl. Tabls. The definitive version is available at: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1744-7348The nature and structure of genetic diversity in the Spanish apple germplasm preserved at the national level was widely unknown, since studies performed to date on this topic have been exclusively carried out at the regional scale. Here, 1453 accessions from Spanish collections of Malus × domestica were evaluated with a common set of 13 SSR (Simple Sequence Repeats) markers in order to estimate genetic diversity, to identify the underlying genetic structure and to unravel the relationships among them and among a wide set of international cultivars for reference. In total, 737 unique genotypes were identified, 581 diploids and 156 triploids. Using a model-based Bayesian clustering procedure, two reconstructed populations were obtained for diploid genotypes; one retaining only Spanish cultivars (42% of genotypes), and a second containing all foreign cultivars the latter exhibiting evidence supporting the existence of a secondary sub-structure. Similarly, analysis performed on the 156 triploid genotypes also revealed two reconstructed populations; one exclusively associated with local Spanish genotypes (44%). The Jaccard coefficient allowed clustering by UPGMA (Unweighted Pair Group Method) diploid and triploid genotypes, and remarkable differences in allelic composition among the different partitioning levels were found. AMOVA analyses showed moderate but significant differentiation among the main groups (0.08 ≤ FST ≤ 0.12). Our results highlight an important fraction of the Spanish apple germplasm that constitutes a differentiated genepool with respect to the international and commercial apple cultivars. Moreover, the extent of the Spanish genetic diversity was spatially distributed along the northern Iberian Peninsula, suggesting an extensive migration of genotypes along the country. This study is the first valuable action for genetic conservation of apple at the national scale, and constitutes a decisive step towards the definition of a Spanish core collection that will be useful for further studies in dissecting the genetic control of important horticultural traits through genome-wide association analysis in apple.This work was supported by INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), under the Project: 'Harmonization of the methodology of characterization, assessment of genetic diversity and definition of the core collection of the apple germplasm conserved in Spanish genebanks (ref. RF2011-00017-C05)'.Peer reviewe

Diversidad genética de las colecciones españolas de manzano evaluada con SSR

2 Pags.La Red de Colecciones de manzano del Programa Nacional de Recursos Fitogenéticos integra, entre otras, a las colecciones situadas en la Universidad Pública de Navarra (UPNA), el Centro de Investigaciones Agrarias de Mabegondo (CIAM), Cabildos (Tenerife, La Palma y Gran Canaria), la Universidad de Lleida (UdL), el Servicio Regional de Investigación y Desarrollo de Asturias (SERIDA), la Estación Experimental de Aula Dei-CSIC (EEAD) y el Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA). Estas colecciones comprenden mayoritariamente cultivares locales prospectados en sus respectivas regiones y, en conjunto, representan la práctica totalidad de áreas productoras de manzano del país. Las colecciones habían sido caracterizadas, total o parcialmente, con caracteres morfológicos, agronómicos y moleculares, pero los métodos, caracteres y marcadores que se emplearon no estaban estandarizados, por lo que para evaluar de forma global la diversidad conservada por la Red era preciso realizar un trabajo previo de armonización. En este contexto, en 2012 se inició el Proyecto Coordinado "Armonización de la metodología de caracterización, evaluación de la diversidad genética y definición de la colección nuclear de los recursos genéticos de manzano conservados en los Bancos de Germoplasma españoles" (RF2011-00017-COS-OO), financiado por el INIA, e integrado por las colecciones citadas anteriormente. Su objetivo principal es el de optimizar el manejo de los recursos genéticos del manzano conservado en España, desarrollando e implantando metodologías y criterios comunes para la caracterización morfológica, agronómica, tecnológica y molecular de las colecciones. En esta comunicación presentamos los primeros resultados obtenidos de la armonización de las caracterizaciones moleculares.Este trabajo ha sido financiado por el proyecto INIA RF2011-00017-C05-00.Peer reviewe