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| 1 | Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)显示文摘Low-temperature stresses limit the sustainability and productivity of grapevines when early spring frosts damage young grapevine leaves.Spring conditions often expose grapevines to low,but not damaging,chilling temperatures and these temperatures have been shown to increase freeze resistance in other model systems.In this study,we examined whole-transcriptome gene expression patterns of young leaf tissue from cuttings of five different grapevine cultivars,exposed to chill and freeze shock,in order to understand the underlying transcriptional landscape associated with cold stress response.No visible damage was observed when grapevine leaves were exposed to chilling temperatures while freeze temperatures resulted in variable damage in all cultivars.Significant differences in gene expression were observed between warm control conditions and all types of cold stress.Exposure to chill stress(4°C)versus freezing stress(−3°C)resulted in very different patterns of gene expression and enriched pathway responses.Genes from the ethylene signaling,ABA signaling,the AP2/ERF,WRKY,and NAC transcription factor families,and starch/sucrose/galactose pathways were among the most commonly observed to be differentially regulated.Preconditioning leaves to chill temperatures prior to freezing temperatures resulted in slight buffering of gene expression responses,suggesting that differences between chill and freeze shock perception complicates identification of candidate genes for cold resistance in grapevine.Overall,the transcriptional landscape contrasts observed between low temperature and freezing stresses demonstrate very different activation of candidate pathways impacting grapevine cold response. | Jason P.Londo Alisson P.Kovaleski Jacquelyn A.Lillis | 2018 | Horticulture Research2018，5，1： | 2 |
| 2 | Draft genome of the Native American cold hardy grapevine Vitis riparia Michx.‘Manitoba 37’显示文摘Vitis riparia,a critically important Native American grapevine species,is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic.This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species.Here we report an Illumina short-read 369X coverage,draft de novo heterozygous genome sequence of V.riparia Michx.‘Manitoba 37’with the size of~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp.Using RNAseq data,40,019 coding sequences were predicted and annotated.Benchmarking with Universal Single-Copy Orthologs(BUSCO)analysis of predicted gene models found 96%of the complete BUSCOs in this assembly.The assembly continuity and completeness were further validated using V.riparia ESTs,BACs,and three de novo transcriptome assemblies of three different V.riparia genotypes resulting in>98%of respective sequences/transcripts mapping with this assembly.Alignment of the V.riparia assembly and predicted CDS with the latest V.vinifera‘PN40024’CDS and genome assembly showed 99%CDS alignment and a high degree of synteny.An analysis of plant transcription factors indicates a high degree of homology with the V.vinifera transcription factors.QTL mapping to V.riparia‘Manitoba 37’and V.vinifera PN40024 has identified genetic relationships to phenotypic variation between species.This assembly provides reference sequences,gene models for marker development and understanding V.riparia’s genetic contributions in grape breeding and research. | Sagar Patel Michael Robben Anne Fennell Jason P.Londo Dilmini Alahakoon Roberto Villegas-Diaz Padmapriya Swaminathan | 2020 | Horticulture Research2020，7，1： | 1 |
| 3 | Rootstock effects on scion phenotypes in a‘Chambourcin’experimental vineyard显示文摘Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops.Grafting is a common horticultural practice that joins the roots(rootstock)of one plant to the shoot(scion)of another,providing an excellent method for investigating how these two organ systems affect each other.In this study,we used the French-American hybrid grapevine‘Chambourcin’(Vitis L.)as a model to explore the rootstock–scion relationship.We examined leaf shape,ion concentrations,and gene expression in‘Chambourcin’grown ungrafted as well as grafted to three different rootstocks(‘SO4’,‘1103P’and‘3309C’)across 2 years and three different irrigation treatments.We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation.For ion concentrations,the primary source of variation identified was the position of a leaf in a shoot,although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions.Lastly,we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines.Thus,our work reveals the subtle and complex effect of grafting on‘Chambourcin’leaf morphology,ionomics,and gene expression. | ZoëMigicovsky Zachary N.Harris Laura LKlein Mao Li Adam McDermaid Daniel H.Chitwood Anne Fennell Laszlo G.Kovacs Misha Kwasniewski Jason P.Londo Qin Ma Allison J.Miller | 2019 | Horticulture Research2019，6，1： | 1 |
| 4 | Transcriptomic analysis of grapevine in response to ABA application reveals its diverse regulations during cold acclimation and deacclimation显示文摘Abscisic acid(ABA)plays crucial regulatory roles in cold acclimation and deacclimation of grapevine,making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring.To understand the function of ABA,we conducted experiments during cold acclimation and deacclimation and evaluated the impact of exogenous ABA on the grapevine transcriptome.RNA-seq data were collected periodically hours or days after ABA treatment.Transcriptomic data were analyzed using principal component analysis(PCA),hierarchical clustering,unsupervised weighed gene co-expression network analysis(WGCNA),contrast-based differentially expressed genes(DEGs)identification and pre-ranked gene set enrichment analysis(GSEA).Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid(IAA)metabolism,galactose metabolism and ribosome biogenesis.We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes,suggesting the existence of a balancing system in response to excessive ABA.This balancing systems potentially eliminates the long-term negative effect on grapevine growing from using ABA in the field.These findings advance our understanding about the regulation of grapevine physiology during dormancy and supports the potential of applying ABA as a cultural practice to mitigate cold injury in winter and spring. | Hongrui Wang Imed E.Dami Hanna Martens Jason P.Londo | 2022 | Fruit Research2022，2，1： | 0 |
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