Open Access
Assessing the causes of the low productivity of cider apple orchards in the Spanish region of Gipuzkoa
(ISHS, 2022) Miranda Jiménez, Carlos; Crespo Martínez, Sara; Oneka Mugica, Oihane; Laquidain Imirizaldu, María Jesús; Urrestarazu Vidart, Jorge; Santesteban García, Gonzaga; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura
Apple cider-making has a long tradition in many northern Spanish regions, such as Gipuzkoa in the Basque Country. The production in this region is largely based on traditional local cider cultivars for which very little information is available on their pollination requirements, resulting in a generalized low productivity of the orchards. In this work the self-(in)compatibility, S-alleles and pollen quality have been studied for the main cider varieties grown in Gipuzkoa, which represent a wide genetic diversity. The S-RNase genotype of 25 cultivars is firstly reported here, which allows allocating the cultivars in their corresponding incompatibility group. All the S-alleles have been previously described, being S26, S3 and S5 the most frequently found. Regarding pollen quality triploid cultivars, as expected, showed lower viability (<70%) and germination rates (<20%). Whereas most diploid cultivars showed good pollen viability (>80%) and germination (>30%) rates, it is noteworthy the low performance of ‘Urtebete’, very similar to that of triploids. Self-compatibility tests both in vitro and in situ showed low rates of fruit set and, together with an upper position of the stigmas related to stamens, reveal a low degree of self-compatibility for most cultivars. Surprisingly, two cultivars called ‘Moko’ and ‘Txalaka’, showed certain selfcompatibility with around 7% fruit set. All in all, the results will enable to improve traditional varieties orchard design as well as the profitability of apple cider farms in the region.
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
fruclimadapt: an R package for climate adaptation assessment of temperate fruit species
(Elsevier, 2021) Miranda Jiménez, Carlos; Urrestarazu Vidart, Jorge; Santesteban García, Gonzaga; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura
Climate strongly determines the growing range of fruit plant species that can be grown successfully in an area, and also the cultivars that will perform best. Therefore, the assessment of the adequacy of a climate is critical for decision-making in the design of fruit orchards and vineyards, and also for the evaluation of the potential consequences of future climate on fruit production. Bioclimatic indices and plant phenology models are commonly used to assess the suitability of climate for growing quality fruit and to provide temporal and spatial information about regarding ongoing and future changes. In this paper, we present fruclimadapt, a flexible and versatile package in the R language that streamlines the assessment of climate adaptation and the identification of potential risks for grapevines and fruit trees. A core set of functions allows to assess climate adaptation of fruit tree species by calculating specific bioclimatic index values and to evaluate potential threats to yield and fruit quality. Three additional sets of functions have been included as companions to: i) downscale daily meteorological values to hourly data, ii) estimate winter chill and forcing heat accumulation and iii) estimate the occurrence of phenological phases. fruclimadapt is currently available from the CRAN website (https://cran.r-project.org/package=fruclimadapt).
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
Applications of sensing for disease detection
(Springer, 2021) Castro, Ana Isabel de; Pérez Roncal, Claudia; Thomasson, J. Alex; Ehsani, Reza; López Maestresalas, Ainara; Yang, Chenghai; Jarén Ceballos, Carmen; Wang, Tianyi; Cribben, Curtis; Marín Ederra, Diana; Isakeit, Thomas; Urrestarazu Vidart, Jorge; López Molina, Carlos; Wang, Xiwei; Nichols, Robert L.; Santesteban García, Gonzaga; Arazuri Garín, Silvia; Peña, José Manuel; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Ingeniería; Ingeniaritza; Gobierno de Navarra / Nafarroako Gobernua; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
The potential loss of world crop production from the effect of pests, including weeds, animal pests, pathogens and viruses has been quantifed as around 40%. In addition to the economic threat, plant diseases could have disastrous consequences for the environment. Accurate and timely disease detection requires the use of rapid and reliable techniques capable of identifying infected plants and providing the tools required to implement precision agriculture strategies. The combination of suitable remote sensing (RS) data and advanced analysis algorithms makes it possible to develop prescription maps for precision disease control. This chapter shows some case studies on the use of remote sensing technology in some of the world’s major crops; namely cotton, avocado and grapevines. In these case studies, RS has been applied to detect disease caused by fungi using different acquisition platforms at different scales, such as leaf-level hyperspectral data and canopy-level remote imagery taken from satellites, manned airplanes or helicopter, and UAVs. The results proved that remote sensing is useful, effcient and effective for identifying cotton root rot zones in cotton felds, laurel wilt-infested avocado trees and escaaffected vines, which would allow farmers to optimize inputs and feld operations, resulting in reduced yield losses and increased profts.
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
Pollen viability, self-incompatibility, and a very singular S-allele structure between the reasons for the limited potential productivity of traditional Basque cider apple varieties
(Elsevier, 2023) Crespo Martínez, Sara; Oneka Mugica, Oihane; Laquidain Imirizaldu, María Jesús; Urrestarazu Vidart, Jorge; Santesteban García, Gonzaga; Miranda Jiménez, Carlos; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Cider regions conserve a broad diversity of traditional cultivars for which knowledge has hardly evolved. Key aspects of their reproductive biology are barely known, hindering improvement in orchard management and resulting in highly variable yields. In this study, we characterized key aspects of the reproductive biology of some traditional apple cultivars from the Basque-style cider-producing area in northern Spain (Basque Country and Navarre). We tested for pollen quality, self-compatibility, and cross-compatibility (S-genotyping). The pollen quality was good except for Urtebete, Errezila, Reineta Encarnada, and triploid varieties. Self-pollination results confirm the need for pollinators, as only Moko and Txalaka showed certain self-compatibility. Regarding Sgenotyping, the population proved very singular, with an atypically high frequency of S26, a frequent allele within crabapples, and the appearance of a novel unpublished allele (S60). The knowledge generated for this variety pool will contribute to a better choice of suitable pollinators, preventing the use of popular crabapple varieties that are demonstrated to be partly incompatible with them, and will lead to an increase in potential yields in the region.
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
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.