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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. 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)

   Abstract BackgroundBud 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. ResultsThe 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. ConclusionsThe 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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3. 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)

   SUMMARY 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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4. Coordination of spring vascular and organ phenology in deciduous angiosperms growing in seasonally cold climates

   https://doi.org/10.1111/nph.17289  

   Savage, Jessica A.; Chuine, Isabelle (March 2021, New Phytologist)

   Summary In seasonally cold climates, many woody plants tolerate chilling and freezing temperatures by ceasing growth, shedding leaves and entering dormancy. At the same time, transport within these plants often decreases as the vascular system exhibits reduced functionality. As spring growth requires water and nutrients, we ask the question: how much does bud, leaf and flower development depend on the vasculature in spring? In this review, we present what is known about leaf, flower and vascular phenology to sort out this question. In early stages of bud development, buds rely on internal resources and do not appear to require vascular support. The situation changes during organ expansion, after leaves and flowers reconnect to the stem vascular system. However, there are major gaps in our understanding of the timing of vascular development, especially regarding the phloem, as well as the synchronization among leaves, flowers, stem and root vasculature. We believe these gaps are mainly the outcome of research completed in silo and urge future work to take a more integrative approach. We highlight current challenges and propose future directions to make rapid progress on this important topic in upcoming years. 

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5. The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts

   https://doi.org/10.7554/eLife.56076  

   Bakker, Rachael; Mani, Madhav; Carthew, Richard W (June 2020, eLife)

   Morphogen signaling contributes to the patterned spatiotemporal expression of genes during development. One mode of regulation of signaling-responsive genes is at the level of transcription. Single-cell quantitative studies of transcription have revealed that transcription occurs intermittently, in bursts. Although the effects of many gene regulatory mechanisms on transcriptional bursting have been studied, it remains unclear how morphogen gradients affect this dynamic property of downstream genes. Here we have adapted single molecule fluorescence in situ hybridization (smFISH) for use in the Drosophila wing imaginal disc in order to measure nascent and mature mRNA of genes downstream of the Wg and Dpp morphogen gradients. We compared our experimental results with predictions from stochastic models of transcription, which indicated that the transcription levels of these genes appear to share a common method of control via burst frequency modulation. Our data helps further elucidate the link between developmental gene regulatory mechanisms and transcriptional bursting. 

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