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1. Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine

   https://doi.org/10.3390/plants10040669  

   Smita, Shuchi ; Robben, Michael ; Deuja, Anup ; Accerbi, Monica ; Green, Pamela J. ; Subramanian, Senthil ; Fennell, Anne ( April 2021 , Plants)

   null (Ed.)

   Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD buds. Gene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1. 

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2. Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca)

   https://doi.org/10.1093/treephys/tpz053  

   Conrad, Anna O. ; Yu, Jiali ; Staton, Margaret E. ; Audergon, Jean-Marc ; Roch, Guillaume ; Decroocq, Veronique ; Knagge, Kevin ; Chen, Huadong ; Zhebentyayeva, Tetyana ; Liu, Zongrang ; et al ( July 2019 , Tree Physiology)

   Trees use many mechanisms to adapt and respond to stressful conditions. The phenylpropanoid pathway in particular is known to be associated with a diverse suite of plant stress responses. In this study, we explored the relationship between the phenylpropanoid pathway metabolite production, gene expression and adaptive trait variation associated with floral bud reactivation during and following dormancy in Prunus armeniaca L. (apricot). Concentrations of eight phenylpropanoid metabolites were measured during chill accumulation and at developmental stages corresponding to the emergence of sepals and petals in floral buds of varieties that differ phenotypically in bloom date (BD). A significant interaction effect of chill hours and BD phenotype on the concentration of each of the compounds was observed (mixed analysis of variance, P < 0.05), with the concentration of most phenylpropanoid metabolites dropping precipitously when sepals and petals emerged. While phenylpropanoid biosynthetic gene expression patterns were more variable in general, expression changed over time and was impacted, although to a lesser degree, by BD phenotype. Furthermore, separation of BD phenotypic groups was most pronounced when early and late BD varieties were at different developmental stages, i.e., 800 chill hours. Taken together, these results suggest that the phenylpropanoid pathway is associated with floral bud reactivation in apricot. Furthermore, we show that the phenylpropanoid pathway is also impacted by phenological trait variation associated with dormancy. A better understanding of how apricot and other perennial tree species respond and adapt to environmental perturbations will be critical for improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.

    

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3. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’

   https://doi.org/10.1038/s41438-020-0316-2  

   Patel, Sagar ; Robben, Michael ; Fennell, Anne ; Londo, Jason P. ; Alahakoon, Dilmini ; Villegas-Diaz, Roberto ; Swaminathan, Padmapriya ( June 2020 , Horticulture Research)

   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 ofV. ripariaMichx. ‘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 usingV. ripariaESTs, BACs, and three de novo transcriptome assemblies of three differentV. ripariagenotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of theV. ripariaassembly and predicted CDS with the latestV. 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 theV. viniferatranscription factors. QTL mapping toV. riparia‘Manitoba 37’ andV. viniferaPN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understandingV. riparia’s genetic contributions in grape breeding and research.

    

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4. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3‐MYBs in grapevine

   https://doi.org/10.1111/tpj.15686  

   Orduña, Luis ; Li, Miaomiao ; Navarro‐Payá, David ; Zhang, Chen ; Santiago, Antonio ; Romero, Pablo ; Ramšak, Živa ; Magon, Gabriele ; Höll, Janine ; Merz, Patrick ; et al ( March 2022 , The Plant Journal)

   The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis viniferaL.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP‐Seq) allows for the genome‐wide TF‐binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP‐Seq of MYB14/MYB15 was combined with aggregate gene co‐expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47STSfamily genes. Moreover, all three MYBs bind to severalPAL,C4H, and4CLgenes, in addition to shikimate pathway genes, theWRKY03stilbenoid co‐regulator and resveratrol‐modifying gene candidates among which ROMT2‐3 were validated enzymatically. A high proportion of DAP‐Seq bound genes were induced in the activated transcriptomes of transientMYB15‐overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3‐MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP‐Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome‐wide approaches in the context of non‐model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.

    

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5. From buds to shoots: insights into grapevine development from the Witch’s Broom bud sport

   https://doi.org/10.1186/s12870-024-04992-y  

   Ritter, Eleanore J. ; Cousins, Peter ; Quigley, Michelle ; Kile, Aidan ; Kenchanmane Raju, Sunil K. ; Chitwood, Daniel H. ; Niederhuth, Chad ( April 2024 , BMC Plant Biology)

   Bud sports occur spontaneously in plants when new growth exhibits a distinct phenotype from the rest of the parent plant. The Witch’s Broom bud sport occurs occasionally in various grapevine (Vitis vinifera) varieties and displays a suite of developmental defects, including dwarf features and reduced fertility. While it is highly detrimental for grapevine growers, it also serves as a useful tool for studying grapevine development. We used the Witch’s Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis. We analyzed the phenotypes of two independent cases of the Witch’s Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild type counterparts. To do so, we quantified various shoot traits, performed 3D X-ray Computed Tomography on dormant buds, and landmarked leaves from the samples. We also performed Illumina and Oxford Nanopore sequencing on the samples and called genetic variants using these sequencing datasets.

   The Dakapo and Merlot cases of Witch’s Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witch’s Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We identified 968–974 unique genetic mutations in our two Witch’s Broom cases that are potential causal variants of the bud sports. Examining gene function and validating these genetic candidates through PCR and Sanger-sequencing revealed one strong candidate mutation in Merlot Witch’s Broom impacting the gene GSVIVG01008260001.

   The Witch’s Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another and likely have distinct genetic bases. Future work on Witch’s Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

    

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