Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

UMR-AGAP Equipe DAVV (Diversité, adaptation et amélioration de la vigne) ; équipe ID (Intégration de Données)International audienceAbstractBackgroundAs for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies.ResultsStarting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance).ConclusionsOur association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment

Whole-genome genotyping of grape using a panel of microsatellite

The use of microsatellite markers in large-scale genetic studies is limited by its low throughput and high cost and labor requirements. Here, we provide a panel of 45 multiplex PCRs for fast and cost-efficient genome-wide fluorescence-based microsatellite analysis in grapevine. The developed multiplex PCRs panel (with up to 15-plex) enables the scoring of 270 loci covering all the grapevine genome (9 to 20 loci/chromosome) using only 45 PCRs and sequencer runs. The 45 multiplex PCRs were validated using a diverse grapevine collection of 207 accessions, selected to represent most of the cultivated Vitis vinifera genetic diversity. Particular attention was paid to quality control throughout the whole process (assay replication, null allele detection, ease of scoring). Genetic diversity summary statistics and features of electrophoretic profiles for each studied marker are provided, as are the genotypes of 25 common cultivars that could be used as references in other studies

Análisis de correlación canónica para relacionar caracteres de la planta con componentes del rendimiento en genotipos de pimiento rojo (Capsicum annuum L. var. conoides (Mill.) Irish)

In this study, a canonical correlation analysis (CCA) was used to estimate relationships between plant characters (X set-fruit length (FL), fruit width (FW), fruit wall thickness (FWT), placenta length, stem thickness, plant height (PH), leaf length, leaf width, flowering time (50%), and time to maturity), and yield components (Y set-total fruit weight per plant (FW/P), average fruit weight and number of fruits per plant (FN/P)) of 56 red peppers (Capsicum annuum L. var. conoides (Mill.) Irish) in populations collected from the Samsun province in the Black Sea Region of Turkey. All canonical correlation coefficients (0.708, 0.635, 0.413) between the pairs of canonical variables were found to be significant (P < 0.01). The findings obtained from the CCA indicate that FN/P had the largest contribution for the explanatory capacity of canonical variables estimated from yield components of 56 red pepper populations when compared with other yield components. FL and PH had largest contribution for the explanatory capacity of canonical variables estimated from plant characters when compared with other characters. The results of this study show that PH, FWT and FW should be used with the aim of increasing yield per plant in red pepper genotypes.En este estudio se utilizó un análisis de correlación canónica (CCA) para estimar las relaciones existentes entre caracteres de la planta (X set -longitud del fruto (FL), anchura del fruto (FW), espesor de la pared del fruto (FWT), longitud de la placenta, espesor del tallo, altura de la planta (PH), longitud y anchura de la hoja, tiempo a 50% de floración y tiempo de madurez), y componentes del rendimiento (Y set-peso de frutos total por planta (FW/P), peso y número medio de frutos por planta (FN/P)) de 56 pimientos rojos (Capsicum annuum L. var. conoides (Mill.) Irish) en poblaciones recolectadas en la provincia Samsun de la región del Mar Negro de Turquía. Se encontró que todos los coeficientes de correlación canónica (0,708; 0,635; 0,413) entre las parejas de variables canónicas fueron significativos (P < 0,01). El CCA indicó que, entre los componentes del rendimiento, la relación FN/P fue la que más contribuyó en la capacidad explicatoria de las variables canónicas estimadas de las 56 poblaciones de pimiento. En el caso de los caracteres de la planta, FL y PH fueron los que más contribuyeron en la capacidad explicatoria de las variables canónicas estimadas. Este estudio muestra que se deben usar los caracteres PH, FWT y FW para incrementar el rendimiento de los genotipos de pimiento rojo

Canonical correlation analysis for the determination of relationships between plant characters and yield components in red pepper [Capsicum annuum L. var. conoides (Mill.) Irish] genotypes

In this study, a canonical correlation analysis (CCA) was used to estimate relationships between plant characters [X set-fruit length (FL), fruit width (FW), fruit wall thickness (FWT), placenta length, stem thickness, plant height (PH), leaf length, leaf width, flowering time (50%), and time to maturity], and yield components [Y set-total fruit weight per plant (FW/P), average fruit weight and number of fruits per plant (FN/P)] of 56 red peppers [Capsicum annuum L. var. conoides (Mill.) Irish] in populations collected from the Samsun province in the Black Sea Region of Turkey. All canonical correlation coefficients (0.708, 0.635, 0.413) between the pairs of canonical variables were found to be significant (P < 0.01). The findings obtained from the CCA indicate that FN/P had the largest contribution for the explanatory capacity of canonical variables estimated from yield components of 56 red pepper populations when compared with other yield components. FL and PH had largest contribution for the explanatory capacity of canonical variables estimated from plant characters when compared with other characters. The results of this study show that PH, FWT and FW should be used with the aim of increasing yield per plant in red pepper genotypes.En este estudio se utilizó un análisis de correlación canónica (CCA) para estimar las relaciones existentes entre caracteres de la planta [X set -longitud del fruto (FL), anchura del fruto (FW), espesor de la pared del fruto (FWT), longitud de la placenta, espesor del tallo, altura de la planta (PH), longitud y anchura de la hoja, tiempo a 50% de floración y tiempo de madurez], y componentes del rendimiento [Y set-peso de frutos total por planta (FW/P), peso y número medio de frutos por planta (FN/P)] de 56 pimientos rojos [Capsicum annuum L. var. conoides (Mill.) Irish] en poblaciones recolectadas en la provincia Samsun de la región del Mar Negro de Turquía. Se encontró que todos los coeficientes de correlación canónica (0,708; 0,635; 0,413) entre las parejas de variables canónicas fueron significativos (P < 0,01). El CCA indicó que, entre los componentes del rendimiento, la relación FN/P fue la que más contribuyó en la capacidad explicatoria de las variables canónicas estimadas de las 56 poblaciones de pimiento. En el caso de los caracteres de la planta, FL y PH fueron los que más contribuyeron en la capacidad explicatoria de las variables canónicas estimadas. Este estudio muestra que se deben usar los caracteres PH, FWT y FW para incrementar el rendimiento de los genotipos de pimiento rojo

Electrodeposition and Characterization of Co/Cu Multilayers

Co/Cu multilayers having different bilayer number (total thickness) were electrodeposited on polycrystalline Cu substrates with a strong [100] texture from an electrolyte including Co and Cu ions under potentiostatic control. The structural data from X-ray diffraction (XRD) revealed that all films have face-centered cubic (fcc) structure, but their crystal textures change from [100] to [111] as the bilayer number increases. The magnetic analysis by vibrating sample magnetometer (VSM) showed that the magnetic moment per volume decreases as the bilayer number increases. Magnetoresistance (MR) measurements were made at room temperature in the magnetic fields of ±12 kOe using the Van der Pauw (VDP) method with four probes. The samples with the bilayer number less than 111 exhibited giant magnetoresistance (GMR) with a negligible amount of anisotropic magnetoresistance (AMR), while the ones with the bilayer number larger than 111 have pure GMR effect