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bioRxiv2018

Molecular bases for the constitutive photomorphogenic phenotypes in Arabidopsis

Summary statementStrikingly similar morphological and gene expression phenotypes among cop1, spaQ and pifQ mutants suggest that the cop phenotype of the cop1 and spaQ mutants might be due in part to a reduced level of PIFs\n\nAbstractThe transition from skotomorphogenesis to photomorphogenesis is regulated in part by COP1/SPA complex and PIFs in Arabidopsis. The constitutive photomorphogenic (cop) phenotypes of the cop1 and spaQ mutants were shown to be due to a high abundance of the positively acting transcription factors. Here we show that the four major PIF proteins are unstable in cop1 mutant, and an overexpression of P1F1, P1F3, P1F4 and P1F5 suppresses the cop1 phenotypes in the dark. A comparison of the transcriptome data among cop1, spaQ and pifQ reveals remarkably overlapping gene expression profiles with a preferential regulation of the PIF direct target genes. Additionally, HFR1 strongly inhibits the in vivo binding and transcriptional activation activity of PIF1 in the dark. Taken together, these data suggest that the cop phenotypes of the cop1 and spaQ mutants might be due to a combination of the reduced level of PIFs, increased level of the positive factors (e.g., HY5/HFR1 and others), and the HFR1-mediated inhibition of PIF targeted gene expression in the dark.

plant biology↗

bioRxiv2018

The genetics and genome-wide screening of perennialism loci in Zea diploperennis

Perennialism is common among the higher plants, yet we know little about its inheritance. To address this, six hybrids were made by reciprocally crossing perennial Zea diploperennis Iltis, Doebley & R. Guzman with three varieties/inbred lines of annual maize (Z. mays L. spp. mays). We specifically focused on the plants ability to regrow after flowering and senescence. All the F1 plants demonstrated senescence and regrowth for several cycles, indicating a dominant effect of the Z. diploperennis alleles. The regrowth ability was stably transmitted to progeny of the hybrids in segregation ratios that suggested the trait was controlled by two dominant, complementary loci. Genome-wide screening with genotyping-by-sequencing (GBS) identified two major regrowth loci reg1 and reg2 on chromosomes 2 and 7, respectively. GBS results were validated using a larger F2 population and PCR markers derived from the single nucleotide polymorphisms within the locus intervals. These markers will be employed to select near-isogenic lines for the two loci and to identify candidate genes in the loci in Z. diploperennis.\n\nSignificance StatementOur study contributes to our general understanding of inheritance of perennialism in the higher plants. Previous genetic studies of the perennialism in Zea have yielded contradictory results. We take a reductionist approach by specifically focusing on the plants ability to regenerate new shoots after senescence without regard to associated traits, such as rhizome formation, tillering or environmental impacts. Using this criterion, inheritance of perennialism in Zea appears to be dominantly and qualitatively inherited. Importantly, our data indicate that there is no major barrier to transferring this trait into maize or other grass crops for perennial crop development, which enhances sustainability of grain crop production in an environmentally friendly way.

plant biology↗

bioRxiv2018

Maize EHD1 is Required for Kernel Development and Vegetative Growth through Regulating Auxin Homeostasis

The roles of EHDs in clathrin-mediated endocytosis (CME) in plants are poorly understood. Here, we isolated a maize mutant, designated as ehd1, which showed defects in kernel development and vegetative growth. Positional cloning and transgenic analysis revealed that ehd1 encodes an EHD protein. Internalization of the endocytic tracer FM4-64 was significantly reduced in ehd1 mutant and ZmEHD1 knock-out mutants. We further demonstrated that ZmEHD1 and ZmAP2 {sigma} subunit physically interact in the plasma membranes. Cellular IAA levels were significantly lower in ehd1 mutant than in wild-type maize. Auxin distribution and ZmPIN1a-YFP localization were altered in ehd1 mutant. Exogenous application of 1-NAA but not GA3 rescued the seed germination and seedling emergency phenotypic defects of ehd1 mutants. Taken together, these results indicate that ZmEHD1 regulates auxin homeostasis by mediating CME through its interaction with the ZmAP2 {sigma} subunit, which is crucial for kernel development and vegetative growth of maize.

plant biology↗

bioRxiv2018

Transcriptomic response in symptomless roots of clubroot infected kohlrabi mirrors resistant plants

BackgroundClubroot disease caused by Plasmodiophora brassicae (Phytomyxea, Rhizaria) is one of the economically most important diseases of Brassica crops. The formation of hypertrophied roots accompanied by altered metabolism and hormone homeostasis is typical for infected plants. Not all roots of infected plants show the same phenotypic changes. While some roots remain uninfected, others develop galls of diverse size. The aim of this study was to analyse and compare the intra-plant heterogeneity of P. brassicae root galls and symptomless roots of the same host plants (Brassica oleracea var. gongylodes) collected from a commercial field in Austria using transcriptome analyses.\n\nResultsTranscriptomes were markedly different between symptomless roots and gall tissue. Symptomless roots showed transcriptomic traits previously described for resistant plants. Genes involved in host cell wall synthesis and reinforcement were up-regulated in symptomless roots indicating elevated tolerance against P. brassicae. By contrast, genes involved in cell wall degradation and modification processes like expansion were up-regulated in root galls. Hormone metabolism differed between symptomless roots and galls. Brassinosteroid-synthesis was down-regulated in root galls, whereas jasmonic acid synthesis was down-regulated in symptomless roots. Cytokinin metabolism and signalling were up-regulated in symptomless roots with the exception of one CKX6 homolog, which was strongly down-regulated. Salicylic acid (SA) mediated defence response was up-regulated in symptomless roots, compared with root gall tissue. This is probably caused by a secreted benzoic acid salicylic acid methyl transferase from the pathogen (PbBSMT), which was one of the highest expressed pathogen genes in gall tissue. The PbBSMT derived Methyl-SA potentially leads to increased pathogen tolerance in uninfected roots.\n\nConclusionsInfected and uninfected roots of clubroot infected plants showed transcriptomic differences similar to those previously described between clubroot resistant and susceptible hosts. The here described intra-plant heterogeneity suggests, that for a better understanding of clubroot disease targeted, spatial analyses of clubroot infected plants will be vital in understanding this economically important disease.

plant biology↗

bioRxiv2018

Key to identification of starch grains used as foods

The description of starch grains is important in different areas, such as bromatological, taxonomic, or archaeobotanic analyzes, among others. Although there are data on the microscopic description of starches used as foods, this work has proposed the development of a key to identify the starch grains in 13 raw materials obtained in specialized stores, markets and fairs to facilitate its identification. For optical microscopy, the material was deposited on a slide, being sealed with a coverslip in 50% glycerin. The samples were also mounted on double-sided tape and colloidal graphite on aluminum stubs and analyzed in scanning electron microscopy (SEM). Therefore, an unpublished starch identification key is proposed, together with the update of important data for its morphological description.

plant biology↗

bioRxiv2018

Functional dissection of the ARGONAUTE7 promoter

ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA-guided manner. Arabidopsis thaliana has ten ARGONAUTE (AGO) genes, with specialized roles in RNA-directed DNA methylation, post-transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO1, AGO10, and AGO7 using yeast 1-hybrid assays. A ranked list of candidate DNA-binding TFs revealed binding of the AGO7 promoter by a number of proteins in two families: the miR156-regulated SPL family and the miR319-regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO7, nor for the function of AGO7 in leaf shape. Normal AGO7 transcription levels and function appear to depend instead on an adjacent 124-bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO7-triggered TAS3 pathway functions in timing and polarity.

plant biology↗

bioRxiv2018

The SUMO conjugation complex self-assembles into nuclear bodies independent of SIZ1 and COP1

One sentence SummarySUMO conjugation activity causes formation of SUMO nuclear bodies, which strongly overlap with COP1 bodies thanks to a substrate-binding (VP) motif in the E3 ligase SIZ1 that acts as bridge protein.\n\nAbstractAttachment of the small ubiquitin-like modifier SUMO to substrate proteins modulates their turnover, activity or interaction partners. An unresolved question is how this SUMO conjugation activity concentrates the enzymes involved and the substrates into uncharacterized nuclear bodies (NBs). We here define the requirements for the formation of SUMO NBs and for their subsequent co-localisation with the master regulator of growth, the E3 ubiquitin ligase COP1. COP1 activity results in degradation of transcription factors, which primes the transcriptional response that underlies elongation growth induced by night-time and high ambient temperatures (skoto- and thermomorphogenesis, respectively). SUMO conjugation activity itself is sufficient to target the SUMO machinery into NBs. Co-localization of these bodies with COP1 requires besides SUMO conjugation activity, a SUMO acceptor site in COP1 and the SUMO E3 ligase SIZ1. We find that SIZ1 docks in the substrate-binding pocket of COP1 via two VP motifs - a known peptide motif of COP1 substrates. The data reveal that SIZ1 physically connects COP1 and SUMO conjugation activity in the same NBs that can also contain the blue-light receptors CRY1 and CRY2. Our findings thus suggest that sumoylation apparently coordinates COP1 activity inside these NBs; a mechanism that potentially explains how SIZ1 and SUMO both control the timing and amplitude of the high-temperature growth response. The strong co-localization of COP1 and SUMO in these NBs might also explain why many COP1 substrates are sumoylated.\n\nFunding informationThe Netherlands Scientific Organisation (ALW-VIDI grant 864.10.004 to HvdB) and the Topsector T&U program Better Plants for Demands (grant 1409-036 to HvdB), including the partnering breeding companies, supported this work; FM is financially supported by Keygene N.V. (The Netherlands).

plant biology↗

bioRxiv2018

Optimized Cas9 expression systems for highly efficient Arabidopsis genome editing facilitate isolation of complex alleles in a single generation

Genetic resources for the model plant Arabidopsis comprise mutant lines defective in almost any single gene in reference accession Columbia. However, gene redundancy and/or close linkage often render it extremely laborious or even impossible to isolate a desired line lacking a specific function or set of genes from segregating populations. Therefore, we here evaluated strategies and efficiencies for the inactivation of multiple genes by Cas9-based nucleases and multiplexing. In first attempts, we succeeded in isolating a mutant line carrying a 70 kb deletion, which occurred at a frequency of ~1.6% in the T2 generation, through PCR-based screening of numerous individuals. However, we failed to isolate a line lacking Lhcb1 genes, which are present in five copies organized at two loci in the Arabidopsis genome. To improve efficiency of our Cas9-based nuclease system, regulatory sequences controlling Cas9 expression levels and timing were systematically compared. Indeed, use of DD45 and RPS5a promoters improved efficiency of our genome editing system by approximately 25-30-fold in comparison to the previous ubiquitin promoter. Using an optimized genome editing system with RPS5a promoter-driven Cas9, putatively quintuple mutant lines lacking detectable amounts of Lhcb1 protein represented approximately 30% of T1 transformants. These results show how improved genome editing systems facilitate the isolation of complex mutant alleles, previously considered impossible to generate, at high frequency even in a single (T1) generation.

plant biology↗

bioRxiv2018

Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

plant biology↗

bioRxiv2018

Maize YABBY drooping leaf genes regulate floret development and floral meristem determinacy

Floret units in cereals produce grain, directly impacting yield. Here we report mutations in the maize CRABS CLAW (CRC) co-orthologs drooping leaf1 (drl1) and drl2 alter the development of ear and tassel florets. Pistillate florets of drl1 ears appear sterile and display ectopic unfused carpels that fail to enclose an expanded nucellus. Staminate florets of drl1 tassels have extra stamens and retain fertile anthers. Natural variation and transposon alleles of drl2 enhance drl1 floret phenotypes by reducing floral meristem (FM) determinacy. The drl paralogs are co-expressed in lateral floral organ primordia, but not within the FM. Together, the expression patterns and indeterminate mutant FMs suggest that the drl genes regulate FM activity and impose meristem determinacy by a non-cell autonomous signal. Genetic interaction analyses of drl mutants with maize floral mutants indicate that the drl genes are required throughout floret development, illustrating their importance for proper floret patterning in maize.

plant biology↗

bioRxiv2018

Transcriptome Analysis of Distinct Cold Tolerance Strategies in the Rubber Tree (Hevea brasiliensis)

Natural rubber is an indispensable commodity used in approximately 40,000 products and is fundamental to the tire industry. Among the species that produce latex, the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg.], a species native to the Amazon rainforest, is the major producer of latex used worldwide. The Amazon Basin presents optimal conditions for rubber tree growth, but the occurrence of South American leaf blight, which is caused by the fungus Microcyclus ulei (P. Henn) v. Arx, limits rubber tree production. Currently, rubber tree plantations are located in scape regions that exhibit suboptimal conditions such as high winds and cold temperatures. Rubber tree breeding programs aim to identify clones that are adapted to these stress conditions. However, rubber tree breeding is time-consuming, taking more than 20 years to develop a new variety. It is also expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Transcriptome sequencing using next-generation sequencing (RNA-seq) is a powerful tool to identify a full set of transcripts and for evaluating gene expression in model and non-model species. In this study, we constructed a comprehensive transcriptome to evaluate the cold response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Furthermore, we identified putative microsatellite (SSR) and single-nucleotide polymorphism (SNP) markers. Alternative splicing, which is an important mechanism for plant adaptation under abiotic stress, was further identified, providing an important database for further studies of cold tolerance.

plant biology↗

bioRxiv2018

The fungal root endophyte Serendipita indica modifies extracellular nucleotides to subvert plant immunity

One sentence abstractImmune modulation by metabolites in plant fungus interaction\n\nAbstractExtracellular adenosine 5'-triphosphate (eATP) is an essential signaling molecule that mediates different cellular processes through its interaction with membrane-associated receptor proteins in animals and plants. eATP regulates plant growth, development and responses to biotic and abiotic stresses. Its accumulation in the apoplast induces ROS production and cytoplasmic calcium increase mediating a defense response to invading microbes. We demonstrate that perception of eATP is important in plant-fungus interaction and that during colonization by the beneficial root endophyte Serendipita indica accumulation of eATP in the apoplast occurs at early symbiotic stages. We show by liquid chromatography-tandem mass spectrometry, cytological and functional analysis that S. indica subvert eATP host response by secreting SiE5NT, an enzymatically active ecto-5'nucleotidase capable of hydrolyzing eATP to adenosine. A. thaliana lines producing extracellular SiE5NT are signi?cantly better colonized and have reduced eATP levels and defense signaling, indicating that SiE5NT functions as a compatibility factor. Our data show that extracellular bioactive nucleotides play an important role in fungus-root interactions and that fungi can modify plant derived metabolites in the apoplast to modulate host immunity.

plant biology↗

bioRxiv2018

Label free quantitative proteomics of Qualea grandiflora Mart. (Vochysiaceae) roots indicates an aluminium requirement for growth and development.

Aluminium in acid soils is a hindrance to crop growth. Nonetheless, Brazilian Cerrado possesses many species such as Qualea grandiflora, which are adapted to acid soils with large amounts of Al and accumulate this metal in its tissues and organs. Nonetheless, the mechanisms involved in these processes are poorly understood, mainly at molecular level. Thus, a root proteomic analysis was accomplished to identify Al-responsive proteins in Q. grandiflora plants. Concomitantly, a root growth analysis of plants grown with and without Al supplementation was conducted to determine the effects of Al on the whole plant. Subsequently, proteins from both treatments were identified and quantified by LC-MS/MS in a label-free fashion. From the 2,520 identified proteins, 410 were differentially abundant between the two treatments, which were associated with carbohydrate metabolism, redox activity, stress response and catabolism of organic compounds. Furthermore, Al was crucial for the growth and development of Q. grandiflora. In fact, this species may have an Al-dependent metabolism. Moreover, it was possible to correlate plant growth to Al-upregulated proteins that were directly involved in cell wall synthesis, oxidative phosphorylation, genetic information processing, and amino acid metabolism. Additionally, this work provides an extensive dataset of Al-regulated protein in Q. grandiflora, which will be crucial to understanding the functions of Al in this species.

plant biology↗

bioRxiv2018

Epigallocatechin-3-gallate yield in different temperature gradients in green tea (Camellia sinensis) brewing

IntroductionEpigallocatechin-3-gallate (EGCG) is a chemical catechin, a natural organic compound found in green teas with strong antioxidative effects. EGCG degrades or epimerizes according to temperature, fluctuating its concentration in green tea (Camellia sinensis). This study is conducted to determine the specified correlation between EGCG and tea temperature, and to conclude with the optimal temperature for EGCG yield.\n\nMethodsEGCG concentrations in different solutions of green tea are analyzed using a high-performance liquid chromatography (HPLC), with a diode array detector (DAD). The solutions are created from green tea brewed in water from 20{degrees}C to 100{degrees}C at increments of 20{degrees}C and undergo an ultrasonic bath of 30 minutes before being analyzed.\n\nResultsThere is a discernible difference between EGCG concentrations in all temperatures. At 20, 40, 60, 80 and 100{degrees}C, the concentrations are 6.18 g/mL, 32.37 g/mL, 57.36 g/mL, 36.13 g/mL, and 44.85 g/mL, respectively. EGCG concentration maximizes at 60{degrees}C. The lowest EGCG concentration yield is at 20{degrees}C.\n\nConclusionThe results of our experiments lead us to recommend hot brewing over cold brewing for green tea if one wishes to maximize the potential of the effects of EGCG due to its higher concentration.

plant biology↗

bioRxiv2018

Function of the Pedicellate Spikelet and Awn in Sorghum and Related Grasses

Sorghum and its relatives in the grass tribe Andropogoneae bear their flowers in pairs of spikelets, in which one spikelet (seed-bearing, or SS) of the pair produces a seed and the other is sterile or male (staminate). This division of function does not occur in other major cereals such as wheat or rice. Additionally, one bract of the seed-bearing spikelet often produces a long extension, the awn, which is in the same position as but independently derived from that of wheat and rice. The function of the sterile spikelet is unknown and that of the awn has not been tested in Andropogoneae. We used radioactive and stable isotopes of carbon, as well as RNA-seq of metabolically important enzymes to show that the sterile spikelet assimilates carbon, which is translocated to the largely heterotrophic SS, thereby functioning as a nurse tissue. The awn shows no evidence of photosynthesis. These results apply to distantly related species of Andropogoneae. Thus, the sterile spikelet, but not the awn, could affect yield in the cultivated species and fitness in the wild ones.

plant biology↗

bioRxiv2018

Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato

Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family microRNAs (miRNAs) that are in a distinct 22nt class of miRNAs with a double mode of action. First they cleave the target RNA, as with the canonical 21nt miR-NAs, and second they trigger secondary siRNA production using the target RNA as a template. Here we address the extent to which the miR482/2118 family affects expression of NLR mR-NAs and disease resistance. First we show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is conserved motif in multiple NLR mRNAs whereas, for miR2118b, it is a novel non-coding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118 we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight but, nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars.

plant biology↗

bioRxiv2018

Molecular Mechanisms Governing Shade Responses in Maize

Light is one of the most important environmental factors affecting plant growth and development. Plants use shade avoidance and shade tolerance strategies to adjust their growth and development thus increase their success in the competition for incoming light. To investigate the mechanism of shade responses in maize (Zea mays), we examined the anatomical and transcriptional dynamics of the early shade response in seedlings of the B73 inbred line. Transcriptome analysis identified 912 differentially expressed genes, including genes involved in light signaling, auxin responses, and cell elongation pathways. Grouping transcription factor family genes and performing enrichment analysis identified multiple types of transcription factors that are differentially regulated by shade and predicted putative core genes responsible for regulating shade avoidance syndrome. For functional tests, we ectopically over-expressed ZmHB53, a type II HD-ZIP transcription factor gene significantly induced by shade, in Arabidopsis thaliana. Transgenic Arabidopsis plants overexpressing ZmHB53 exhibited narrower leaves, earlier flowering, and enhanced expression of shade-responsive genes, suggesting that ZmHB53 participates in the regulation of shade responses in maize. This study increases our understanding of the regulatory network of the shade response in maize and provides a useful resource for maize genetics and breeding.\n\nHighlightOur findings not only increase the understanding of the regulatory network of the shade avoidance in maize, and also provide a useful resource for maize genetics and breeding.

plant biology↗

bioRxiv2018

A draft reference genome sequence for Scutellaria baicalensis Georgi

Scutellaria baicalensis Georgi is an important medicinal plant used worldwide. Information about the genome of this species is important for scientists studying the metabolic pathways that synthesise the bioactive compounds in this plant. Here, we report a draft reference genome sequence for S. baicalensis obtained by a combination of Illumina and PacBio sequencing, which was assembled using 10 X Genomics and Hi-C technologies. We assembled 386.63 Mb of the 408.14 Mb genome, amounting to about 94.73% of the total genome size, and the sequences were anchored onto 9 pseudochromosomes with a super-N50 of 33.2 Mb. The reference genome sequence of S. baicalensis offers an important foundation for understanding the biosynthetic pathways for bioactive compounds in this medicinal plant and for its improvement through molecular breeding.

plant biology↗