The genetic basis of grape and wine aroma

The grape is one of the oldest and most important horticultural crops.Grape and wine aroma has long been of cultural and scientific interest.The diverse compound classes comprising aroma result from multiple biosynthetic pathways.Only fairly recently have researchers begun to elucidate the genetic mechanisms behind the biosynthesis and metabolism of grape volatile compounds.This review summarizes current findings regarding the genetic bases of grape and wine aroma with an aim towards highlighting areas in need of further study.From the literature,we compiled a list of functionally characterized genes involved in berry aroma biosynthesis and present them with their corresponding annotation in the grape reference genome.

Shifting dynamics of nature, society and agriculture in the Hindu Kush Himalayas: Perspectives for future mountain development

Current approaches for sustainable mountain development have several persisting warning signals. Economic globalization, profitoriented market development, and infrastructure development have significantly altered traditional nature-society interactions, increased environmental pressures, and challenged agricultural sustainability in the mountains. Some of the effects of globalization could also be beneficial. Social differentiation and disintegration of mountain communities' have weakened their collective stakes on natural resources resulting in decline in initiatives such as community forestry, collective water management, domestication of rapidly disappearing herbal species, and balancing of economic and ecological concerns. Population growth, food insecurity, unemployment, and increasing economic gaps between rich and poor have led to out-migration of youth. Sustained action promoting ownership of new initiatives for rehabilitating degraded mountain landscapes through macro-level global/national initiatives, mountain specific planning and development efforts is severely lacking in many areas on the Hindu Kush Himalayan region. Therefore, there is an urgent need for widening the scope of efforts directed to help mountain areas and communities, and a future thinking approach to enhance the sustainability of mountain areas as they are a valuable natural resource for humankind. This paper discusses the issues, opportunities, and provides suggestions for the future of mountain development.

Genetic mapping and survey of powdery mildew resistance in the wild Central Asian ancestor of cultivated grapevines in Central Asia

Cultivated grapevines(Vitis vinifera)lack resistance to powdery mildew(PM)with few exceptions.Resistance to this pathogen within V.vinifera has been reported in earlier studies and identified as the Ren1 locus in two Central Asian table grape accessions.Other PM-resistant cultivated varieties and accessions of the wild ancestor V.vinifera subsp.sylvestris were soon identified raising questions regarding the origin of the resistance.In this study,F1 breeding populations were developed with a PM susceptible V.vinifera subsp.vinifera breeding line and a PM-resistant subsp.sylvestris accession.Genotyping was carried out with five Ren1 locus linked SSR markers.A PM resistance locus explaining up to 96%of the phenotypic variation was identified in the same genomic position,where the Ren1 locus was previously reported.New SSR marker alleles linked with the resistance locus were identified.We report results of PM resistance in multiple accessions of subsp.sylvestris collected as seed lots or cuttings from five countries in the Caucasus and Central Asia.A total of 20 females from 11 seed lots and 19 males from nine seed lots collected from Georgia,Armenia,and Azerbaijan were resistant to PM.Three male and one female plant collected as cuttings from Afghanistan and Iran were also resistant to PM.Allelic analysis of markers linked with the Ren1 locus in conjunction with disease evaluation data found a high diversity of allelic haplotypes,which are only possible via recombination events occurring over a long time period.Sequence analysis of two alleles of the SSR marker that cosegregates with the resistance found SNPs that were present in the wild progenitor and in cultivated forms.Variable levels of PM resistance among the tested accessions were also observed.These lines of evidence suggest that the powdery mildew fungus may have been present in Asia for a longer time than currently thought,giving the wild progenitor V.vinifera subsp.sylvestris time to coevolve with and develop resistance to this pathogen.

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew

Grape powdery mildew(PM),caused by the biotrophic ascomycete Erysiphe necator,is a devastating fungal disease that affects most Vitis vinifera cultivars.We have previously identified a panel of V.vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype.In this study,we show that in addition to the typical Ren1-associated late post-penetration resistance,these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen.To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance,we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection.Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype.Responses to E.necator in all resistant accessions were characterized by an early up-regulation of 13 genes,most encoding putative defense functions,and a late down-regulation of 32 genes,enriched in transcriptional regulators and protein kinases.Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18.We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions‘Karadzhandahal’,DVIT3351.27,and O34-16 and the other genotypes.This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V.vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

Standardizing and Centralizing Datasets for Efficient Training of Agricultural Deep Learning Models

In recent years,deep learning models have become the standard for agricultural computer vision.Such models are typically fine-tuned to agricultural tasks using model weights that were originally fit to more general,non-agricultural datasets.This lack of agriculture-specific fine-tuning potentially increases training time and resource use,and decreases model performance,leading to an overall decrease in data efficiency.To overcome this limitation,we collect a wide range of existing public datasets for 3 distinct tasks,standardize them,and construct standard training and evaluation pipelines,providing us with a set of benchmarks and pretrained models.We then conduct a number of experiments using methods that are commonly used in deep learning tasks but unexplored in their domain-specific applications for agriculture.Our experiments guide us in developing a number of approaches to improve data efficiency when training agricultural deep learning models,without large-scale modifications to existing pipelines.Our results demonstrate that even slight training modifications,such as using agricultural pretrained model weights,or adopting specific spatial augmentations into data processing pipelines,can considerably boost model performance and result in shorter convergence time,saving training resources.Furthermore,we find that even models trained on low-quality annotations can produce comparable levels of performance to their high-quality equivalents,suggesting that datasets with poor annotations can still be used for training,expanding the pool of currently available datasets.Our methods are broadly applicable throughout agricultural deep learning and present high potential for substantial data efficiency improvements.

Cytokinin but not gibberellin application had major impact on the phenylpropanoid pathway in grape

Cytokinin and gibberellic acid(GA)are growth regulators used to increase berry size in seedless grapes and it is of interest to understand their effects on the phenylpropanoid pathway and on ripening processes.GA 3 and synthetic cytokinin forchlorfenuron(N-(2-chloro-4-pyridyl)-N′-phenylurea,CPPU)and their combination were applied to 6 mm diameter fruitlets of‘Sable Seedless’,and berries were sampled 51 and 70 days(d)following application.All treatments increased berry size and delayed sugar accumulation and acid degradation with a stronger effect of CPPU.CPPU,but not GA,reduced berry color and the levels of anthocyanins.While CPPU reduced the levels of anthocyanins by more than 50%,the combined treatment of GA+CPPU reduced the levels by about 25%at 51 d.CPPU treatment had minor effects on flavonols content but increased the levels of monomeric flavan-3-ols by more than two-fold.Phloroglucinol analysis using HPLC showed that proanthocyanidin content was significantly increased by CPPU,whereas mean degree of polymerization was reduced from 26 to 19.Volatile analysis by GC-MS showed changes in composition with CPPU or GA treatment with potential impact on flavor.RNA-seq analysis showed that GA had a minor overall effect on the transcriptome whereas CPPU had pronounced effects on gene expression at both 51 and 70 d.Comparing the control and CPPU at similar Brix of ca.19.7°,a reduced expression of stilbene synthases(STSs)including their regulators MYB14 and MYB15,and other phenylpropanoid-related genes was observed in CPPU-treated grapes.Overall,our study shows that CPPU had a major influence on the phenylpropanoid pathway and affected multiple ripening-related processes.

Towards an open grapevine information system

Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated research.Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature,in many domains of study,including grapevine research,there is a need to improve the findability,accessibility,interoperability and reusability(FAIR-ness)of these data.Considering the heterogeneous nature of the data produced,the transnational nature of the scientific community and the experience gained elsewhere,we have formed an open working group,in the framework of the International Grapevine Genome Program(www.vitaceae.org),to construct a coordinated federation of information systems holding grapevine data distributed around the world,providing an integrated set of interfaces supporting advanced data modeling,rich semantic integration and the next generation of data mining tools.To achieve this goal,it will be critical to develop,implement and adopt appropriate standards for data annotation and formatting.The development of this system,the GrapeIS,linking genotypes to phenotypes,and scientific research to agronomical and oeneological data,should provide new insights into grape biology,and allow the development of new varieties to meet the challenges of biotic and abiotic stress,environmental change,and consumer demand.

Comparative experiments and effectiveness evaluation on vertical blowing fans(VBF)for frost protection

Experiments were conducted to evaluate the performance of vertical blowing fans(VBF)for frost protection in a vineyard on a steep slope near Napa Valley in Northern California,USA,and a tea plantation located on undulating terrain in Zhenjiang,China.Minimum temperature comparisons from within the grape vineyard on nights with and without VBF operation with control station minimum temperatures exhibited no temperature benefit.Profile measurements from the test in China indicated that there was an increase in temperature when the VBF was first started,but that benefit was lost over time.No clear benefit from using the VBF was observed.Observation of frost deposition and thermal imagery also showed no benefit except for within about 5 m of the VBF.Based on this work,the effectiveness of the VBF for frost protection was not validated.