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
Agronomic evaluation of eight 41 B × 110 richter grapevine genotypes as rootstock candidates for mediterranean viticulture
(KeAi Communications, 2023) Marín Ederra, Diana; Miranda Jiménez, Carlos; Abad Zamora, Francisco Javier; Urrestarazu Vidart, Jorge; Mayor Azcona, Blanca; Villa Llop, Ana; 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
Choosing the most appropriate rootstock(s) is a key decision for the profitability of vineyards; therefore, there must be a sufficient range of rootstocks in the market adapted to different environmental conditions and production objectives. However, rootstock-breeding programs have been scarce in recent decades, and most of the rootstocks used today were bred a century ago, when the needs of the sector were very different from today. In this work, we aimed to evaluate new rootstock candidates before their introduction in the market. An agronomic evaluation was conducted on eight novel rootstock genotypes obtained from the first generation of the cross-pollination of 41 B Millardet et de Grasset (41 B) and 110 Richter (110 R) grafted with ‘Syrah’ and ‘Tempranillo’ and planted in a typical vineyard of the Ebro Valley in Spain. During the four consecutive growing seasons (2016e2019), growth, yield and berry composition parameters at harvest were collected. A linear mixedeffects model was constructed, considering year and block as random effects. Multiple factor analysis and hierarchical clustering on principal components were performed to establish clusters of genotypes with similar behaviour. The rootstock candidates showed a very wide performance range compared to their parents. The trial allowed us to identify two very promising candidates (RG8 and RG10), whose registration as commercial rootstocks is already in progress.
Open Access
Recovery of ancient grapevine plant material in peri‑urban areas. A case of success in Pamplona (Spain) leading to the recovery of cv. Berués
(Elsevier, 2022) Crespo Martínez, Sara; Mayor Azcona, Blanca; Oneka Mugica, Oihane; Loidi Erviti, Maite; Villa Llop, Ana; Marín Ederra, Diana; Miranda Jiménez, Carlos; Santesteban García, Gonzaga; Urrestarazu Vidart, Jorge; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB; Agronomía, Biotecnología y Alimentación; Gobierno de Navarra / Nafarroako Gobernua
Viticulture was relatively important in the peri‑urban area of Pamplona till the end of the 19th century, but suffered a continued regression that has led to a nearly complete disappearance of vineyards. In this context, this work aims to evaluate the feasibility of recovering old grapevine germplasm in the peri‑urban area of Pamplona. The lack of a conventional source for recovering plant material (i.e. absence of old vineyards in the area) implied the need of designing an alternative prospecting procedure. This method included the analysis of the available historical information as open-access resources (orthophotos, land use maps and GIS applications) aiming to identify the areas with the highest probability of finding vines surviving from the general abandonment and uprooting of vineyards that had occurred in the 20th century. Based on the oldest on scale orthophoto available for Navarra, a vineyard land map of the peri‑urban area of Pamplona in year 1956 was built, allowing prospecting efforts to be focused on specific areas of primarily interest. Following this strategy, a total of 120 plants were collected, which corresponded to 44 genotypes. The most prominent achievement of this prospecting mission was the recovery of 15 accessions of Berués, a very old variety with a remarkable importance in the region according to old historical records, and considered to be disappeared. The methodology proposed was effective in searching for the oldest standing-alone plants surviving in the peri‑urban area of Pamplona, and may be adapted to assist the recovery of old grapevine germplasm in other currently non wine-growing regions/areas where viticulture was relevant some decades ago. © 2021
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
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
Dynamics of GFLV, GFkV, GLRaV-1, and GLRaV -3 grapevine viruses transport toward developing tissues
(Springer, 2023) Crespo Martínez, Sara; Ramírez Lacunza, Asier; Miranda Jiménez, Carlos; 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
Viral diseases in grapevine cause large economic losses due to decreased irregular yield and unbalanced ripening, and can even lead to plant mortality. There is a large number of grapevine viral agents, and a few of them have a prominent impact due to their worldwide distribution, virulence, and incidence. Although previous research has evaluated variations in viral load between organs and time since infection, there is still a lack of knowledge on how the viruses are transported toward developing tissues. In this work, we present the results of two experiments that contribute to understanding the spread dynamics of four major grapevine viruses (GFLV, GFkV, GLRaV-1, and GLRaV -3). Bud and leaf tissues were sampled from shoots obtained from cv. ‘Garnacha’ cuttings known to be infected with one of these viruses. Bud samples taken at early development stages were used to understand short-distance transport, while leaves taken from young shoots represented long-distance transport, driven mainly through the phloem. Our results show that all viruses were able to invade tissues from the beginning of development. The dissemination ability of GFLV was considerable, as the viral load detected in young organs was as high as in the dormant shoot. Furthermore, for GFLV and GFkV, it was shown that the viral load in young shoots does not follow the general assumption of older tissues accumulating a higher viral load but, conversely, a higher viral load closer to the shoot tip might be driven by the sink strength.
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
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
Assessment of flesh browning diversity in apple germplasm collections phenotyped by image analysis
(ISHS, 2023) Miranda Jiménez, Carlos; Irisarri, Patricia; Arellano Zapatero, Julia; Bielsa González, Francisco Javier; Valencia Leoz, Ana; Urrestarazu Vidart, Jorge; Pina, Ana; Santesteban García, Gonzaga; Castel, L.; Errea, Pilar; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Enzymatic flesh browning (EB) is one of the major problems affecting the quality and limiting the shelf life of minimally processed fruit. Traditionally, EB has been measured objectively using colourimeters. However, colourimeters are not suitable for phenotyping large quantities of fruit samples as they measure just one small area of a sample at a time, which hampers the acquisition of representative measurements and renders them time-consuming and costly. Previous research has shown that image analysis of digital photographs could be a viable alternative to obtain colour information of the entire surface of samples for large scale phenotyping, but to date there are no references for its practical application. The aim of this work was to assess the diversity in EB in a large set of cultivars phenotyped using digital photographs and a high-throughput analytical system based on image analysis developed by our team. A set of 143 cultivars from 104 genotypes, including modern references (16 cultivars) and traditional Spanish cultivars from UPNA (67 cultivars) and CITA (60 cultivars) germplasm collections was analysed in 2020 and 2021. The traditional cultivars were part of the core collection, which optimizes the representativeness of the genetic variation of apples preserved in Spanish collections. EB was evaluated in 10 fruits per cultivar and photographed at regular intervals from just after cutting to one hour later. A wide range of EB intensities was observed, with up to 20-fold differences between cultivars, which could be classified into five levels using two indices. The time at which EB was evaluated (30 or 60 min after slicing) had little influence on the classification. Traditional cultivars with low or very low EB were found to be comparable to those of references with less EB. The results show the potential of traditional germplasm to diversify the varietal offer and introduce new traits in apple breeding.
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.