Open Access
Genome-wide association mapping of flowering and ripening periods in apple
(Frontiers Media, 2017) Urrestarazu Vidart, Jorge; Muranty, Hélène; Denancé, Caroline; Leforestier, Diane; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Aubourg, Sébastien; Celton, Jean Marc; Daccord, Nicolas; Dondini, Luca; Gregori, Roberto; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava Gustavsson, Larisa; Troggio, Michela; Bianco, Luca; Velasco, Riccardo; Poncet, Charles; Théron, Anthony; Moriya, Shigeki; Bink, Marco C. A. M.; Laurens, François; Tartarini, Stefano; Durel, Charles Eric; Producción Agraria; Nekazaritza Ekoizpena
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
Open Access
Sampling stratification using aerial imagery to estimate fruit load in peach tree orchards
(MDPI, 2018) Miranda Jiménez, Carlos; Santesteban García, Gonzaga; Urrestarazu Vidart, Jorge; Loidi Erviti, Maite; Royo Díaz, José Bernardo; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura
A quick and accurate sampling method for determining yield in peach orchards could lead to better crop management decisions, more accurate insurance claim adjustment, and reduced expenses for the insurance industry. Given that sample size depends exclusively on the variability of the trees on the orchard, it is necessary to have a quick and objective way of assessing this variability. The aim of this study was to use remote sensing to detect the spatial variability within peach orchards and classify trees into homogeneous zones that constitute sampling strata to decrease sample size. Five mature peach orchards with different degrees of spatial variability were used. A regular grid of trees was established on each orchard, their trunk cross-sectional area (TCSA) was measured, and yield was measured as number of fruits/tree on the central tree of each one of them. Red Vegetation Index (RVI) was calculated from aerial images with 0.25 m pixel -1 resolution, and used, either alone or in combination with TCSA, to delineate sampling strata using cluster fuzzy k-means. Completely randomized (CRS) and stratified samplings were compared through 10,000 iterations, and the Minimum Sample Size required to obtain estimates of actual production for three quality levels of sampling was calculated in each case. The images allowed accurate determination of the number of trees, allowing a proper application of completely randomized sampling designs. Tree size and the canopy density estimated by means of multispectral indices are complementary parameters suitable for orchard stratification, decreasing the sample size required to determine fruit count up to 20–35% compared to completely randomized samples.
Open Access
Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level
(BioMed Central, 2016) Urrestarazu Vidart, Jorge; Denancé, Caroline; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Poncet, Charles; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Fernández Fernández, Felicidad; Evans, Kate M.; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava Gustavsson, Larisa; Miranda Jiménez, Carlos; Gassmann, Jennifer; Kellerhals, Markus; Suprun, Ivan; Pikunova, Anna V.; Krasova, Nina G.; Torutaeva, Elnura; Dondini, Luca; Tartarini, Stefano; Laurens, François; Durel, Charles Eric; Producción Agraria; Nekazaritza Ekoizpena
Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
Open Access
Evaluating the influence of the microsatellite marker set on the genetic structure inferred in Pyrus communis L.
(Public Library of Science, 2015) Urrestarazu Vidart, Jorge; Royo Díaz, José Bernardo; Santesteban García, Gonzaga; Miranda Jiménez, Carlos; Producción Agraria; Nekazaritza Ekoizpena
Fingerprinting information can be used to elucidate in a robust manner the genetic structure of germplasm collections, allowing a more rational and fine assessment of genetic resources. Bayesian model-based approaches are nowadays majorly preferred to infer genetic structure, but it is still largely unresolved how marker sets should be built in order to obtain a robust inference. The objective was to evaluate, in Pyrus germplasm collections, the influence of the SSR marker set size on the genetic structure inferred, also evaluating the influence of the criterion used to select those markers. Inferences were performed considering an increasing number of SSR markers that ranged from just two up to 25, incorporated one at a time into the analysis. The influence of the number of SSR markers used was evaluated comparing the number of populations and the strength of the signal detected, and also the similarity of the genotype assignments to populations between analyses. In order to test if those results were influenced by the criterion used to select the SSRs, several choosing scenarios based on the discrimination power or the fixation index values of the SSRs were tested. Our results indicate that population structure could be inferred accurately once a certain SSR number threshold was reached, which depended on the underlying structure within the genotypes, but the method used to select the markers included on each set appeared not to be very relevant. The minimum number of SSRs required to provide robust structure inferences and adequate measurements of the differentiation, even when low differentiation levels exist within populations, was proved similar to that of the complete list of recommended markers for fingerprinting. When a SSR set size similar to the minimum marker sets recommended for fingerprinting it is used, only major divisions or moderate (FST>0.05) differentiation of the germplasm are detected.
Open Access
Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying
(Public Library of Science, 2018) Urrestarazu Vidart, Jorge; Errea, Pilar; Miranda Jiménez, Carlos; Santesteban García, Gonzaga; Pina, Ana; Producción Agraria; Nekazaritza Ekoizpena
European plum (Prunus domestica L.) is an ancient domesticated species cultivated in temperate areas worldwide whose genetic structure has been scarcely analyzed to date. In this study, a broad representation of Spanish European plum germplasm collected in Northeastern Spain and a representative set of reference cultivars were compared using nuclear and chloroplast markers. The number of alleles per locus detected with the SSR markers ranged from 8 to 39, with an average of 23.4 alleles, and 8 haplotypes were identified. Bayesian model-based clustering, minimum spanning networks, and the analysis of molecular variance showed the existence of a hierarchical structure. At the first level, two genetic groups were found, one containing 'Reine Claude' type reference cultivars altogether with ca. 25% of local genotypes, and a second one much more diverse. This latter group split in two groups, one containing most (ca. 70%) local genotypes and some old Spanish and French reference cultivars, whereas the other included 24 reference cultivars and only six local genotypes. A third partition level allowed a significant finer delineation into five groups. As a whole, the genetic structure of European plum from Northeastern Spain was shown to be complex and conditioned by a geographical proximity factor. This study not only contributes to genetic conservation and breeding for this species at the national level, but also supports the relevance of undertaking similar tasks of collection and characterization in other unexplored areas. Moreover, this kind of research could lead to future coordinated actions for the examination of the whole European plum diversity, to define conservation strategies, and could be used to better understand the genetic control of traits of horticultural interest through association mapping.
Open Access
Evaluation of the incidence of severe trimming on grapevine (Vitis vinifera L.) water consumption
(Elsevier, 2019-03-01) Abad Zamora, Francisco Javier; Marín Ederra, Diana; Loidi Erviti, Maite; Miranda Jiménez, Carlos; Royo Díaz, José Bernardo; Urrestarazu Vidart, Jorge; Santesteban García, Gonzaga; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa, FPI-UPNA-2016; Gobierno de Navarra / Nafarroako Gobernua
Viticulture in Southern Europe heads towards a scenario of drier and warmer the growing seasons due to climate change. This decrease in the amount of water available for the vines and increase in evapotranspiration make necessary finding strategies to reduce vineyard water needs. In this context, the effect of severe trimming (40¿60% of shoot length), performed at pea-size stage, on plant water status was evaluated in four different vineyards located in North of Spain. Severe trimming improved plant water status clearly only when climate conditions were more demanding, whereas only a slight improvement or no change was observed elsewhere. Lower leaf areas resulted in less water deficit following a logarithmical trend revealing that the effect was more pronounced at low leaf area levels. Severe trimming had non-significant effects on cluster number, yield and cluster weight, but presents a tendency to reduce total soluble solids content and to increase total acidity, consequently delaying ripening.
Open Access
Severe trimming and enhanced competition of laterals as a tool to delay ripening in Tempranillo vineyards under semiarid conditions
(Université de Bordeaux, 2017) Santesteban García, Gonzaga; Miranda Jiménez, Carlos; Urrestarazu Vidart, Jorge; Loidi Erviti, Maite; Royo Díaz, José Bernardo; Producción Agraria; Nekazaritza Ekoizpena; Gobierno de Navarra / Nafarroako Gobernua
Aim: An advance in grapevine phenological stages (including ripening) is occurring worldwide due to global warming and, in the hottest seasons, already results in a lack of synchrony between sugar and phenolic ripeness, leading to unbalanced wines. In order to cope with this fact, a general effort is being made by researchers and growers aiming at delaying ripening through cultural practices, particularly under warm growing conditions, where these effects are more deleterious. The aim of this work is to evaluate to which extent severe trimming and enhanced competition of laterals can delay ripening in Tempranillo vineyards under semiarid conditions. Methods and results: The experiment took place during two consecutive seasons in Traibuenas (Navarra, Spain) in a cv. ‘Tempranillo’ vineyard trained to a vertical shoot positioned (VSP) spur-pruned bilateral cordon. Severe mechanical pruning was performed ca. 3 weeks after fruit-set in order to reduce leaf-to-fruit ratio, and in the trimmed plants, three irrigation doses were applied until harvest aiming at enhancing lateral growth, hypothesized to compete with ripening. All measurements were performed in six 10-vine replicates per treatment. Trimming significantly reduced leaf area and yield, resulting in higher water availability in trimmed plants. The whole ripening process was delayed by trimming: mid-veraison was delayed by about 5 days, and the delay in sugar accumulation and acid degradation was longer, differences being more marked in malic than in tartaric acid concentration. The use of increased irrigation levels compensated the losses in yield caused by trimming, enhanced laterals’ growth and implied an additional delay in ripening. Conclusion: trimming and increased irrigation had an additive effect in terms of delaying ripening, and they can be used jointly when that delay is needed. Significance and impact of the study: this study proves the potentiality of the joint use of trimming and increased irrigation to delay ripening, although it is necessary to analyze the implications the obtained delay has on other quality aspects. The lower anthocyanin and phenolic values observed in trimmed vines were not solely due to delayed ripening, as lower values were observed even when data were compared for a given total soluble solid content.
Open Access
Evaluation of the agronomic performance of 'Syrah' and 'Tempranillo' when grafted on 12 rootstocks
(Julius Kühn Institute (JKI), 2019) Marín Ederra, Diana; García, R.; Eraso Zabalegui, Javier; Urrestarazu Vidart, Jorge; Miranda Jiménez, Carlos; Royo Díaz, José Bernardo; Abad Zamora, Francisco Javier; Santesteban García, Gonzaga; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Gobierno de Navarra / Nafarroako Gobernua; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Beyond pest resistance, rootstocks significantly influence the performance of grapevine varieties. However, the effect of the rootstock is strongly affected by its interaction with the environment, and it is therefore necessary to evaluate their influence in a particular terroir. With the aim of evaluating the influence of 12 rootstocks on the agronomic performance of 'Syrah' and 'Tempranillo', a trial was established in 2011 and 2012 in Miranda de Arga (Navarra, Spain), under the typical environmental conditions of the Ebro Valley. Growth and yield, as well as industrial and phenolic maturity parameters were analysed during four consecutive seasons (2015-2018). Most rootstocks showed a similar performance with both varieties, not always following the trends reported in bibliography, which highlights the relevance of studying rootstocks in different conditions. 3309 C was the rootstock conferring the highest vigour, whereas the lowest were provided by 420 A MGt and 'Fercal'. The implications on grape composition were much more diverse, and were partially conditioned by yield. Results were obtained during the four first harvests of the vineyard, and could therefore change to some extent as the vineyard reaches stability.
Open Access
Integration of expert knowledge in the definition of Swiss pear core collection
(Nature Research, 2019) Urrestarazu Vidart, Jorge; Kägi, C.; Bühlmann, A.; Gassmann, Jennifer; Santesteban García, Gonzaga; Frey, Juerg E.; Kellerhals, Markus; Miranda Jiménez, Carlos; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura
Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of approaches that combine formal analytical procedures and expert knowledge on the efficiency of CC definition through a case study to establish a pear CC from the Swiss National Pear Inventory. The CC had to represent a maximum of the genetic diversity, not to exceed 150 accessions, and required to include a priority set (SPPS) with 86 genotypes selected based on expert knowledge. In total, nine strategies were evaluated, resulting of combining compositions of the dataset sampled, sampling sizes and methods. The CCs sampled by mixed approaches provided similar scores, irrespective of the approach considered, and obtained similar efficiency in optimizing the genetic diversity retained. Therefore, mixed approaches can be an appropriate choice for applications involving genetic conservation in tree germplasm collections.