C. Miranda

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.

BackgroundThe 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.ResultsA 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.ConclusionsThe 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.

Vegetative Growth, Reproductive Development and Vineyard Balance

In the last decades, viticultural research has made important progress due to the implementation of many technical advances to this field. In addition to “classical” viticultural research, it is now possible to analyze vine behaviour with many different approaches, such as plant physiology, genomics, proteomics, precision viticulture and so on. These changes extend our understanding of viticulture, but they may also lead to a certain heterogeneity in the methodology used to estimate the basic characteristics of the vineyards (e.g.: vegetative and reproductive growth). Even worse, measurements of those parameters are sometimes neglected. In order to optimize the relevance and inter-disciplinarity of our work, and its applicability to the vineyard, we should tend toward protocol standardization, the most suitable measurements and ways of expressing results should be determined for each circumstance. This chapter attempts to shed some light on some methodological aspects related to the measurement of vine vegetative and reproductive growth and vineyard balance. We have tried to be comprehensive, but not exhaustive, since some topics are also the subject of other chapters in this book whereas others are beyond its scope.

Evaluating the Influence of the Microsatellite Marker Set on the Genetic Structure Inferred in Pyrus communis L.

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 (F ST>0.05) differentiation of the germplasm are detected.

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)1744-7348

Terahertz time domain spectroscopy allows contactless monitoring of grapevine water status

Agriculture is the sector with the greatest water consumption, since food production is frequently based on crop irrigation. Proper irrigation management requires reliable information on plant water status, but all the plant-based methods to determine it suffer from several inconveniences, mainly caused by the necessity of destructive sampling or of alteration of the plant organ due to contact installation. The aim of this work is to test if terahertz (THz) time domain reflectance measurements made on the grapevine trunk allows contactless monitoring of plant status. The experiments were performed on a potted 14-years-old plant, using a general purpose THz emitter receiver head. Trunk THz time-domain reflection signal proved to be very sensitive to changes in plant water availability, as its pattern follows the trend of soil water content and trunk growth variations. Therefore, it could be used to contactless monitor plant water status. Apart from that, THz reflection signal was observed to respond to light conditions which, according to a specifically designed girdling experiment, was caused by changes in the phloem. This latter results opens a promising field of research for contactless monitoring of phloem activity.

Evaluation of spectral-based and canopy-based vegetation indices from UAV and Sentinel 2 images to assess spatial variability and ground vine parameters

New remote sensing technologies have provided unprecedented results in vineyard monitoring. The aim of this work was to evaluate different sources of images and processing methodologies to describe spatial variability of spectral-based and canopy-based vegetation indices within a vineyard, and their relationship with productive and qualitative vine parameters. Comparison between image-derived indices from Sentinel 2 NDVI, unfiltered and filtered UAV NDVI and with agronomic features have been performed. UAV images allow calculating new non-spectral indices based on canopy architecture that provide additional and useful information to the growers with regards to within-vineyard management zone delineation.

Agronomic significance of the zones defined within vineyards early in the season using NDVI and fruit load information

Wine quality is known to be highly dependent on grape quality and, therefore, wineries aiming to produce premium wines are concerned with obtaining top quality grapes. However, since grape quality is not uniform within a vineyard sometimes it is necessary to evaluate which zones within a single vineyard are producing the best grapes in order to segregate them at harvest. The aim of this work was to compare the performance of two methods to delineate zones within vineyards: (1) expert knowledge (ExpZ); and (2) fuzzy k-means analysis (FuzZ) using NDVI and fruit load as information sources, procedures that were applied to 4 adjacent vineyards located in Villamanta, (Madrid, Spain). Both methodologies were suitable to delineate parts of a vineyard with differences in grape composition, although FuzZ provided a more significant zoning than ExpZ from an oenological point of view.

Influence of the freezing method on the changes that occur in grape samples after frozen storage

BACKGROUND Sample freezing is frequently used in oenological laboratories as a compromise solution to increase the number of samples that can be analysed, despite the fact that some grape characteristics are known to change after frozen storage. However, freezing is usually performed using standard freezers, which provide a slow freezing. The aim of this work was to evaluate whether blast freezing would decrease the impact of standard freezing on grape composition. RESULTS Grape quality parameters were assessed in fresh and in frozen stored samples that had been frozen using three different procedures: standard freezing and blast freezing using either a blast freezer or an ultra-freezer. The implications of frozen storage in grape samples reported in earlier research were observed for the three freezing methods evaluated. Although blast freezing improved repeatability for the most problematic parameters (tartaric acidity, TarA; total phenolics, TP), the improvement was not important from a practical point of view. However, TarA and TP were relatively repeatable among the three freezing procedures, which suggests that freezing had an effect on these parameters independently of the method used . According to our results, the salification potential of the must is probably implied in the changes observed for TarA, whereas for TP the precipitation of protoanthocyanins after association with cell wall material is hypothesized to cause the lack of repeatability between fresh and frozen grapes. CONCLUSIONS Blast freezing would not imply a great improvement if implemented in oenological laboratories, at least for the parameters included in this study.

Allometric relationships for estimating vegetative and reproductive biomass in grapevine (Vitis vinifera L.)

Background and Aims Vineyards, one of the most widespread agricultural systems, have significant but scarcely evaluated carbon sequestration potential. Allometry is a cost-effective approach to estimate plant biomass, but few studies – focused mainly on permanent structure carbon fixation – have dealt with it in grapevine. This study develops allometric models that accurately estimate grapevine standing biomass (total vine biomass at harvest), using extensive field-collected data sets. Methods and Results Data were obtained in vineyards located in Spanish regions representative of the variability found in warm semi-arid Mediterranean regions. We developed and validated functions to estimate vine biomass for all vine organs. The models obtained estimated accurately the biomass fixed by each organ separately and even more accurately at the whole plant scale. To illustrate the potential of the models, they satisfactorily assessed the influence of seasonal vine water status on vine biomass production and partitioning using an independent data set. Conclusions and Significance of the Study The models constitute a powerful tool to determine in a non-destructive and cost-effective manner standing biomass from simple vine measurements, which makes them suitable for quantifying carbon stocks and allocation patterns, and for evaluating the influence of climate or cultural practices at large scale to estimate better – at a regional or international level – the contribution of grapevine culture to CO2 balances.

Prediction of spatial variability of water status in a rain fed vineyard in Spain

Monitoring water status at different points within a single field is time-consuming and expensive. Nevertheless, it is necessary to consider within-field variability since water status is usually highly variable and has a large effect on grape quality. To overcome this situation, models that allow estimation of the relative difference in vine water status between a reference point and other points in the field have been developed. The aim of this work is to evaluate the performance of a model developed in South Eastern France for the spatial prediction of vine water status to the conditions of a traditional rain-fed vineyard in Rioja Alavesa, Spain. The model proved to be suitable to estimate grapevine water status variability within a medium size vineyard (4.2 ha) under the traditional growing conditions in Rioja Alavesa (gobelet trained cv. Tempranillo vines with no irrigation), although it was necessary to include some water status related information (in this case carbon isotope ratio (δ13C) from the previous season) to improve the performance and applicability of the model.