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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 77,600 bioRxiv papers from 336,315 authors.

Most downloaded bioRxiv papers, since beginning of last month

in category plant biology

2,288 results found. For more information, click each entry to expand.

1: Plants emit informative airborne sounds under stress
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Posted to bioRxiv 28 Dec 2018

Plants emit informative airborne sounds under stress
837 downloads plant biology

I. Khait, Ohad Lewin-Epstein, R. Sharon, K. Saban, R. Perelman, A. Boonman, Y. Yovel, L. Hadany

Stressed plants show altered phenotypes, including changes in color, smell, and shape. Yet, the possibility that plants emit airborne sounds when stressed – similarly to many animals – has not been investigated. Here we show, to our knowledge for the first time, that stressed plants emit airborne sounds that can be recorded remotely, both in acoustic chambers and in greenhouses. We recorded ∼65 dBSPL ultrasonic sounds 10 cm from tomato and tobacco plants, implying that these sounds could be detected by some organisms from up to several meters away. We developed machine learning models that were capable of distinguishing between plant sounds and general noises, and identifying the condition of the plants – dry, cut, or intact – based solely on the emitted sounds. Our results suggest that animals, humans, and possibly even other plants, could use sounds emitted by a plant to gain information about the plant’s condition. More investigation on plant bioacoustics in general and on sound emission in plants in particular may open new avenues for understanding plants and their interactions with the environment, and it may also have a significant impact on agriculture.

2: Viola unica (Violaceae L.), a very rare, high elevation, single site new species endemic to the northern semi-desert Altiplano of Chile
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Posted to bioRxiv 11 Dec 2019

Viola unica (Violaceae L.), a very rare, high elevation, single site new species endemic to the northern semi-desert Altiplano of Chile
435 downloads plant biology

John Michael Watson, Ana Rosa Flores

While examining the Viola collection at the herbarium (SGO) of the Museo Nacional de Historia Natural (MNHN), Santiago, we encountered a folder with a single unidentified specimen consisting of a solitary rosette. It had been found in northern Chile near the border with Bolivia, where considerable mining activity takes place. The plant appeared to differ from all others related to it as known to ourselves, and on investigation it did indeed prove to be undescribed. It is presented herein, together with a detailed analysis and preliminary partial revision of related taxa, including a key. Key words: Altiplano, Andes, copper mining, endangered, section Andinium, solitary specimen, Tarapaca Region, Triflabellatae, unknown collector.

3: A new role for histone demethylases in the maintenance of plant genome integrity
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Posted to bioRxiv 03 Mar 2020

A new role for histone demethylases in the maintenance of plant genome integrity
400 downloads plant biology

Javier Antunez-Sanchez, Matthew Naish, Juan Sebastian Ramirez-Prado, Sho Ohno, Ying Huang, Alexander Dawson, Deborah Manza-Mianza, Federico Ariel, Cecile Raynaud, Anjar Wilbowo, Josquin Daron, Minako Ueda, David Latrasse, R. Keith Slotkin, Detlef Weigel, Moussa Benhamed, Jose Gutierrez-Marcos

Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development and adaptation to environmental fluctuations in most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the inheritance of epigenetic imprints, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases in plants contribute towards maintaining distinct transcriptional states during development and help safeguard genome integrity following sexual reproduction.

4: Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis
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Posted to bioRxiv 11 Mar 2020

Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis
360 downloads plant biology

Guy Wachsman, Jingyuan Zhang, Miguel A. Moreno-Risueno, Charles T. Anderson, Philip N. Benfey

In Arabidopsis, lateral roots initiate along the primary root in a process preceded by periodic gene expression, a phenomenon known as the root clock. Many genes involved in lateral root initiation have been identified. However, very little is known about the structural changes underlying the initiation process nor about how root clock function is regulated. In genetic screens, we identified the vesicle trafficking regulators, GNOM and its suppressor, AGD3, as critical to root clock function. We show that GNOM is required for the proper distribution of pectin, a mediator of intercellular adhesion, and that pectin esterification state is essential for a functional root clock. We found that in sites of lateral root primordia emergence, both esterified and de-esterified pectin are differentially distributed. Using a reverse genetic approach, we identified significant enrichment of GO terms associated with pectin modifying enzymes in the oscillation zone were the root clock is established. In agreement with a recent study on the function of pectin in pavement cell morphogenesis, our results indicate that the balance between esterified and de-esterified pectin is essential for proper root clock function and the subsequent initiation of lateral root primordia.

5: Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity
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Posted to bioRxiv 09 Mar 2020

Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity
339 downloads plant biology

Mona Bassal, Petra Majovsky, Domenika Thieme, Tobias Herr, Mohammad Abukhalaf, Mohamed Ayash, MHD Rami Al Shweiki, Carsten Proksch, Ali Hmedat, Jörg Ziegler, Steffan Neumann, Wolfgang Hoehenwarter

Proteome remodeling is a fundamental adaptive response and proteins in complex and functionally related proteins are often co-expressed. Using a deep sampling strategy we define Arabidopsis thaliana tissue core proteomes at around 10,000 proteins per tissue and absolutely quantify (copy numbers per cell) nearly 16,000 proteins throughout the plant lifecycle. A proteome wide survey of global post translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue and age specific roles of entire signaling modules regulating transcription in photosynthesis, seed development and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of Cysteine-rich Receptor-like Kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were co-expressed tissue and age specifically indicating functional promiscuity in the assembly of these little described protein complexes in Arabidopsis. Treatment of seedlings with flg22 for 16 hours allowed us to characterize proteome architecture in basal immunity in detail. The results were complemented with parallel reaction monitoring (PRM) targeted proteomics, phytohormone, amino acid and transcript measurements. We obtained strong evidence of suppression of jasmonate (JA) and JA-Ile levels by deconjugation and hydroxylation via IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2) under the control of JASMONATE INSENSITIVE 1 (MYC2). This previously unknown regulatory switch is another part of the puzzle of the as yet understudied role of JA in pattern triggered immunity. The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community.

6: A simple method for spray-on gene editing in planta
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Posted to bioRxiv 25 Oct 2019

A simple method for spray-on gene editing in planta
334 downloads plant biology

Cara Doyle, Katie Higginbottom, Thomas A. Swift, Mark Winfield, Christopher Bellas, David Benito-Alifonso, Taryn Fletcher, M. Carmen Galan, Keith Edwards, Heather M. Whitney

Potential innovation in Plant research using gene-edited and genetically modified plants is currently being hindered by inefficient and costly plant transformation. We show that carbon dots formed from natural materials (quasi-spherical, <10nm nanoparticles) can act as a fast vehicle for carrying plasmids into mature plant cells, resulting in transient plant transformation in a number of important crop species with no negative impacts on photosynthesis or growth. We further show that GFP, Cas9, and gRNA introduced into wheat via foliar application (spraying on) of plasmid coated carbon dots are expressed and, in the case of Cas9, make genome edits in SPO11 genes. Therefore, we present a protocol for spray-on gene editing that is simple, inexpensive, fast, transforms in planta , and is applicable to multiple crop species. We believe this technique creates many opportunities for the future of plant transformation in research and shows great promise for plant protein production systems.

7: External mechanical cues reveal core molecular pathway behind tissue bending in plants
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Posted to bioRxiv 06 Mar 2020

External mechanical cues reveal core molecular pathway behind tissue bending in plants
317 downloads plant biology

Anirban Baral, Emily Morris, Bibek Aryal, Kristoffer Jonsson, Stéphane Verger, Tongda Xu, Malcolm Bennett, Olivier Hamant, Rishikesh P Bhalerao

Tissue folding is a central building block of plant and animal morphogenesis. In dicotyledonous plants, hypocotyl folds to form hook after seedling germination that protects their aerial stem cell niche during emergence from soil. Auxin response factors and auxin transport are classically thought to play a key role in this process. Here we show that the microtubule-severing enzyme katanin contributes to hook formation. However, by exposing hypocotyls to external mechanical cues mimicking the natural soil environment, we reveal that auxin response factors ARF7/ARF19, auxin influx carriers, and katanin are dispensable for apical hook formation, indicating that these factors primarily play the role of catalyzers of tissue bending in the absence of external mechanical cues. Instead, our results reveal the key roles of the non-canonical TMK-mediated auxin pathway, PIN efflux carriers and cellulose microfibrils as components of the core pathway behind hook formation in presence or absence of external mechanical cues.

8: The Irish potato famine pathogen subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface
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Posted to bioRxiv 21 Mar 2020

The Irish potato famine pathogen subverts host vesicle trafficking to channel starvation-induced autophagy to the pathogen interface
312 downloads plant biology

Pooja Pandey, Alexandre Y Leary, Yasin Tümtas, Zachary Savage, Bayantes Dagvadorj, Emily Tan, Virendrasinh Khandare, Cian Duggan, Temur Yusunov, Mathias Madalinski, Federico Gabriel Mirkin, Sebastian Schornack, Yasin F Dagdas, Sophien Kamoun, Tolga O Bozkurt

Eukaryotic cells deploy autophagy to eliminate invading microbes. In turn, pathogens have evolved effector proteins to counteract antimicrobial autophagy. How and why adapted pathogens co-opt autophagy for their own benefit is poorly understood. The Irish famine pathogen Phythophthora infestans secretes the effector protein PexRD54 that selectively activates an unknown plant autophagy pathway, while antagonizing antimicrobial autophagy. Here we show that PexRD54 induces autophagosome formation by bridging small GTPase Rab8a-decorated vesicles with autophagic compartments labelled by the core autophagy protein ATG8CL. Rab8a is required for pathogen-triggered and starvation-induced but not antimicrobial autophagy, revealing that specific trafficking pathways underpin selective autophagy. We discovered that Rab8a contributes to basal immunity against P. infestans, but PexRD54 diverts a sub-population of Rab8a vesicles to lipid droplets that associate with autophagosomes. These are then diverted towards pathogen feeding structures that are accommodated within the host cells. We propose that PexRD54 mimics starvation-induced autophagy by channeling host endomembrane trafficking towards the pathogen interface possibly to acquire nutrients. This work reveals that effectors can interconnect independent host compartments to stimulate complex cellular processes that benefit the pathogen.

9: Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL
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Posted to bioRxiv 29 Mar 2020

Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL
294 downloads plant biology

Jeremy Sloan, Jana Hankenjos, Michael Gebert, Olga Ermakova, Andrea Gumiero, Gunter Stier, Klemens Wild, Irmgard Sinning, Jan U. Lohmann

Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.

10: Adaptive evolution of DNA methylation reshaped gene regulation in maize
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Posted to bioRxiv 15 Mar 2020

Adaptive evolution of DNA methylation reshaped gene regulation in maize
285 downloads plant biology

Gen Xu, Jing Lyu, Qing Li, Han Liu, Dafang Wang, Mei Zhang, Nathan M. Springer, Jeffrey Ross-Ibarra, Jinliang Yang

DNA methylation is a ubiquitous chromatin feature \---| in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward methylation mutation rates and selection coefficients. We only found weak evidence for direct selections on methylations in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selections. Further investigation revealed that DMRs are enriched in 5' untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. And functional analyses suggested that these DMRs likely served as cis-acting elements that modulated gene regulation after domestication. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.

11: LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate
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Posted to bioRxiv 18 Mar 2020

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate
277 downloads plant biology

Run Jin, Samantha Klasfeld, Meilin Fernandez Garcia, Jun Xiao, Soon-Ki Han, Adam Konkol, Yang Zhu, Doris Wagner

Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet no bonafide pioneer transcription factor has - been identified in this kingdom. Here we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds in a sequence-specific manner and with high affinity to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1, where it co-occupies DNA with histones. Moreover, the LFY DNA contact helix shares defining properties with those of strong nucleosome binding pioneer factors. At the AP1 locus, LFY unlocks chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later and require activity of additional, non-pioneer transcription, factors. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between plant and animal pioneer transcription factors. Further analyses aimed at elucidating the defining characteristics of pioneer transcription factors will allow harnessing these for enhanced cell fate reprogramming.

12: Oil body formation in Marchantia polymorpha is controlled by MpC1HDZ and serves as a defense against arthropod herbivores
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Posted to bioRxiv 03 Mar 2020

Oil body formation in Marchantia polymorpha is controlled by MpC1HDZ and serves as a defense against arthropod herbivores
242 downloads plant biology

Facundo Romani, Elizabeta Banic, Stevie N. Florent, Takehiko Kanazawa, Jason Q.D. Goodger, Remco Mentink, Tom Dierschke, Sabine Zachgo, Takashi Ueda, John L. Bowman, Miltos Tsiantis, Javier E. Moreno

The origin of a terrestrial flora in the Ordovician required adaptation to novel biotic and abiotic stressors. Oil bodies, a synapomorphy of liverworts, accumulate secondary metabolites, but their function and development are poorly understood. Oil bodies of Marchantia polymorpha develop within specialized cells as one single large organelle. Here, we show that a CLASS I HOMEODOMAIN LEUCINE-ZIPPER (C1HDZ) transcription factor controls the differentiation of oil body cells in two different ecotypes of the liverwort M. polymorpha , a model genetic system for early divergent land plants. In flowering plants, these transcription factors primarily modulate responses to abiotic stresss including drought. However, loss-of-function alleles of the single ortholog gene, Mp C1HDZ , in M. polymorpha did not exhibit phenotypes associated with abiotic stress. Rather Mp c1hdz mutant plants were more susceptible to herbivory and total plant extracts of the mutant exhibited reduced antibacterial activity. Transcriptomic analysis of the mutant revealed a reduction in expression of genes related to secondary metabolism that was accompanied by a specific depletion of oil body terpenoid compounds. Through time lapse imaging we observed that MpC1HDZ expression maxima precede oil body formation indicating that MpC1HDZ mediates differentiation of oil body cells. Our results indicate that M. polymorpha oil bodies, and MpC1HDZ, are critical for defense against herbivory but not for abiotic stress-tolerance. Thus, C1HDZ genes were co-opted to regulate separate responses to biotic and abiotic stressors in two distinct land plant lineages.

13: Structure-function analysis of Arabidopsis TOPLESS reveals conservation of repression mechanisms across eukaryotes
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Posted to bioRxiv 05 Mar 2020

Structure-function analysis of Arabidopsis TOPLESS reveals conservation of repression mechanisms across eukaryotes
230 downloads plant biology

Alexander R. Leydon, Wei Wang, Samuel Juarez-Solis, Joseph E Zemke, Mollye L. Zahler, Ning Zheng, Jennifer L. Nemhauser

The corepressor TOPLESS (TPL) is recruited to many promoters, yet the mechanisms by which it inhibits expression of genes is poorly understood. Using a synthetic auxin response circuit in Saccharomyces cerevisiae , we identified two regions of Arabidopsis thaliana TPL that could independently function as repression domains: the LIS1 homology domain (LisH) and the CT11-RanBPM (CRA) domain. The CRA repressor domain required direct interaction with the Mediator subunit MED21 for full function. While corepressor multimerization is highly conserved, we found that multimer formation had minimal influence on TPL repression strength in yeast or in plants. Finally, we showed that the LisH domain may have a conserved role in repression in different proteins, as a LisH domain from the human TBL1 protein could replace TPL in synthetic assays. Our work provides insight into the molecular mechanisms of transcriptional repression, while also characterizing short, autonomous repression domains to augment synthetic biology toolkits.

14: MiRNA and phasiRNAs-mediated regulation of TIR-NBS-LRR defense genes in Arabidopsis thaliana
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Posted to bioRxiv 03 Mar 2020

MiRNA and phasiRNAs-mediated regulation of TIR-NBS-LRR defense genes in Arabidopsis thaliana
219 downloads plant biology

Diego López-Márquez, Ángel Del-Espino, Nieves López-Pagán, Edgar A. Rodríguez-Negrete, Ignacio Rubio-Somoza, Javier Ruiz-Albert, Eduardo R. Bejarano, Carmen R. Beuzón

Plants encode large numbers of intracellular immune receptors known as resistance (R) proteins or nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs), involved in perception of pathogen-derived effectors and activation of immunity. Here, we report a two-tiered regulatory network mediated by microRNA and secondary phased small RNAs (phasiRNA) that targets the silencing of dozens of NLR genes encoding yet uncharacterized members of the Toll/interleukin-1 (TIR)-NBS-LRR (TNLs) subfamily in Arabidopsis. We show that miR825-5p downregulates expression of Arabidopsis AT5G38850 gene (renamed as microRNA-silenced TNL 1 or MIST1) by targeting the sequence coding for a highly conserved functional amino acid motif (TIR2) within the TIR domain of the receptor. Further, we show that MIST1 functions as a regulatory hub, since miRNA825-5p triggers RDR6-mediated processing of MIST1 transcripts, to generate trans-acting phasiRNAs that in turn target, a wide network of TNL genes for gene silencing. Regulation through MIST1 affects disease resistance against the model bacterial pathogen Pseudomonas syringae, since altered levels of miRNA825-5p lead to changes in Arabidopsis ability to establish basal defenses against this pathogen. MiR825-5p is expressed in unchallenged adult leaves and its production is down regulated in response to PAMPs such as bacterial flagellin but also fungal chitin.

15: Plants with self-sustained luminescence
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Posted to bioRxiv 18 Oct 2019

Plants with self-sustained luminescence
213 downloads plant biology

Tatiana Mitiouchkina, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M Markina, Tatiana V Chepurnyh, Elena B Guglya, Tatiana A Karataeva, Kseniia A Palkina, Ekaterina S Shakhova, Liliia I Fakhranurova, Sofia V Chekova, Aleksandra S Tsarkova, Yaroslav V Golubev, Vadim V Negrebetsky, Sergey A Dolgushin, Pavel V Shalaev, Olesya A Melnik, Victoria O Shipunova, Sergey M Deyev, Andrey I Bubyrev, Alexander S Pushin, Vladimir V Choob, Sergey V Dolgov, Fyodor A. Kondrashov, Ilia V. Yampolsky, Karen S. Sarkisyan

In contrast to fluorescent proteins, light emission from luciferase reporters requires exogenous addition of a luciferin substrate. Bacterial bioluminescence has been the single exception, where an operon of five genes is sufficient to produce light autonomously. Although commonly used in prokaryotic hosts, toxicity of the aldehyde substrate has limited its use in eukaryotes. Here we demonstrate autonomous luminescence in a multicellular eukaryotic organism by incorporating a recently discovered fungal bioluminescent system into tobacco plants. We monitored these light-emitting plants from germination to flowering, observing temporal and spatial patterns of luminescence across time scales from seconds to months. The dynamic patterns of luminescence reflected progression through developmental stages, circadian oscillations, transport, and response to injuries. As with other fluorescent and luminescent reporters, we anticipate that this system will be further engineered for varied purposes, especially where exogenous addition of substrate is undesirable.

16: Disruption of CYCLOPHILIN 38 function reveals a photosynthesis-dependent systemic signal controlling lateral root emergence
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Posted to bioRxiv 12 Mar 2020

Disruption of CYCLOPHILIN 38 function reveals a photosynthesis-dependent systemic signal controlling lateral root emergence
211 downloads plant biology

Lina Duan, Juan Manuel Pérez-Ruiz, Francisco Javier Cejudo, José R. Dinneny

Photosynthesis in leaves generates the fixed-carbon resources and essential metabolites that support sink tissues, such as roots. One of these products, sucrose, is known to promote primary root growth, but it is not clear what other molecules may be involved and whether other stages of root system development are affected by photosynthate levels. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the CYCLOPHILIN 38 (CYP38) gene, which causes an accumulation of pre-emergent stage lateral roots, with a minor effect on primary root growth. CYP38 was previously reported to maintain the stability of Photosystem II (PSII) in chloroplasts. CYP38 expression is enriched in the shoot and grafting experiments show that the gene acts non-cell autonomously to promote lateral root emergence. Growth of wild-type plants under low light conditions phenocopied the cyp38 lateral root emergence phenotype as did the inhibition of PSII-dependent electron transport or NADPH production. Importantly, the cyp38 root phenotype is not rescued by exogenous sucrose, suggesting the involvement of another metabolite. Auxin (IAA) is an essential hormone promoting root growth and its biosynthesis from tryptophan is dependent on reductant generated during photosynthesis. Both WT seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. The cyp38 lateral root defect is rescued by IAA treatment, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. Metabolomic profiling shows that the accumulation of several defense-related metabolites are also photosynthesis-dependent, suggesting that the regulation of a number of energy-intensive pathways are down-regulated when light becomes limiting.

17: Speed breeding: a powerful tool to accelerate crop research and breeding
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Posted to bioRxiv 09 Jul 2017

Speed breeding: a powerful tool to accelerate crop research and breeding
209 downloads plant biology

Amy Watson, Sreya Ghosh, Matthew J Williams, William S. Cuddy, James Simmonds, María-Dolores Rey, M. Asyraf Md. Hatta, Alison Hinchliffe, Andrew Steed, Daniel Reynolds, Nikolai Adamski, Andy Breakspear, Andrey Korolev, Tracey Rayner, Laura E. Dixon, Adnan Riaz, William Martin, Merrill Ryan, David Edwards, Jacqueline Batley, Raman Harsh, Christian Rogers, Claire Domoney, Graham Moore, Wendy Harwood, Paul Nicholson, Mark J. Dieters, Ian H. DeLacy, Ji Zhou, Cristobal Uauy, Scott A. Boden, Robert F. Park, Brande B. H. Wulff, Lee T. Hickey

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand [1]. This slow improvement rate is attributed partly to the long generation times of crop plants. Here we present a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programs. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully-enclosed controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies, and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent and potential for adaptation to larger-scale crop improvement programs. Cost-saving through LED supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing, and genomic selection, accelerating the rate of crop improvement.

18: The SUMO E3 Ligase SIZ1 Positively Regulates Active DNA Demethylation by Stabilizing ROS1 in Arabidopsis thaliana
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Posted to bioRxiv 05 Mar 2020

The SUMO E3 Ligase SIZ1 Positively Regulates Active DNA Demethylation by Stabilizing ROS1 in Arabidopsis thaliana
203 downloads plant biology

Xiangfeng Kong, Yechun Hong, Yi-Feng Hsu, Huan Huang, Jian-Kang Zhu

The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hypermethylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately 1,400 genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared to that in wild type plants, the protein level of ROS1 is significantly decreased, even though there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1 positively regulates active DNA demethylation by promoting the stability of ROS1 protein through SUMOylation.

19: Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome
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Posted to bioRxiv 23 Feb 2020

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome
198 downloads plant biology

Siwen Deng, Daniel Caddell, Chunbo Li, Lindsay Dahlen, Lorenzo Washington, Devin Coleman-Derr

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to host genotype, and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.

20: Genome-wide quantitative trait loci mapping on Verticilliumw
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Posted to bioRxiv 01 Oct 2019

Genome-wide quantitative trait loci mapping on Verticilliumw
195 downloads plant biology

Md Harun or Rashid, Peng-tao Li, Tingting Chen, Koffi Kibalou Palanga, Wan-kui Gong, Qun Ge, Ju-wu Gong, Ai-ying Liu, Quan-wei Lu, Latyr Diouf, Zareen Sarfraz, Muhammad Jamshed, Yu-zhen Shi, You-lu Yuan

Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistant VW. However, multiple attempts to improve the VW resistance of the most widely cultivated Upland cotton have brought in little significant progress, and it seems necessary and urgent to develop Chromosome segment substitution lines (CSSLs) for merging the superior genes related with high yield and wide adaptation from G. hirsutum and VW resistance and excellent fiber quality from G. barbadense . In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed by G. hirsutum CCRI36 and G. barbadense Hai1 to conduct quantitative trait locus (QTL) mapping on VW resistance, and a total of 53 QTLs relevant to VW disease index (DI) were identified together with the phenotypic data of 2 years investigations in two fields with two replications per year. All the QTLs were distributed on 20 chromosomes with phenotypic variation of 3.74-11.89%, of which 29 stable ones were consistent in at least two environments. Based on Meta-analysis on the 53 QTLs, 43 novel ones were identified, while 10 ones consistent to previously identified QTLs. Meanwhile, 32 QTL hotspot regions were detected, including 15 ones were novel. This study concentrates on QTL identification and screening hotspot region related with VW in the 300 CSSLs, which lay a solid platform not only for revealing the genetic and molecular mechanisms of VW resistance, but also for further fine mapping, gene cloning and molecular designing in breeding program for resistant cotton varieties.

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