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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

ARF5/MONOPTEROS directly regulates miR390 expression in theArabidopsis thaliana primary root meristem

The root meristem is organized around a quiescent centre surrounded by stem cells that generate all cell types of the root. In the transit amplifying compartment progeny of stem cells further divide prior to differentiation. Auxin controls the size of this transit-amplifying compartment via Auxin Response Factors (ARF) that interact with Auxin Response Elements (AuxRE) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3 and ARF4 by triggering the production of trans-acting (ta)-siRNA from TAS3. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to auxin. A single AuxRE bound by ARF5/MONOPTEROS (MP) in miR390 promoter is necessary for miR390 expression in this compartment. We show that interfering with ARF5/MP dependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment. Our results show that ARF5/MP regulates directly the expression of miR390 in the basal root meristem. We propose that ARF5, miR390 and the ta-siRNAs-regulated ARFs are necessary to maintain the size of the transit-amplifying region of the meristem.\n\nOne sentence summaryThe expression of miR390 in the Arabidopsis basal root meristem is controlled by ARF5/MONOPTEROS.

plant biology↗

bioRxiv2018

Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of Radiation Use Efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programs in an attempt to alleviate this, however their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE we applied genome-wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31traits over two years under optimal growing conditions and genotyped using the 35K Wheat Breeders array. Marker-trait-association identified 94 SNPs significantly associated with yield, agronomic and phenology related traits along with RUE and biomass at various growth stages that explained 7-17 % of phenotypic variation. Common SNP markers were identified for grain yield, final biomass and RUE on chromosomes 5A and 7A. Additionally we show that landrace and synthetic derivative lines showed higher thousand grain weight (TGW), biomass and RUE but lower grain number (GNO) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker assisted breeding to systematically increase biomass, RUE and TGW and avoid the TGW/GNO and BM/HI trade-off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.

plant biology↗

bioRxiv2018

Subdivision of light signalling networks contributes to cellular partitioning of C4 photosynthesis in maize

Plants coordinate the expression of genes required to conduct photosynthesis in response to growth and environmental changes. In species that conduct two-cell C4 photosynthesis, the expression of photosynthesis genes is partitioned such that leaf mesophyll and vascular sheath cells accumulate different components of the photosynthetic pathway. The identity of the regulatory networks that facilitate this partitioning are unknown. Here we show that differences in light perception between mesophyll and bundle sheath cells facilitate differential regulation and accumulation of photosynthesis genes in the C4 crop Zea mays (maize). We show that transcripts encoding photoreceptors differentially accumulate in mesophyll and bundle sheath cells in a manner that is consistent with biophysical light filtration. We further show the blue light (but not red) is necessary and sufficient to activate photosystem II assembly in etiolated maize mesophyll cells, while both red and blue produce the same effect in C3 Hordeum vulgare (barley). Finally, we demonstrate that changes in abundance of >20% of genes that differentially accumulate between mesophyll and bundle sheath cells can be recapitulated by spectrum specific deetiolation of maize seedlings. These findings provide evidence that subdivision of light signalling networks is a key component of cellular partitioning of C4 photosynthesis in maize.

plant biology↗

bioRxiv2018

First Report of Recurrent Genomic Selection with Real Data in Popcorn and Genetic Gain Increases

Recurrent Selection increases the frequencies of favorable alleles for economically important traits, which in the case of popcorn are popping expansion and grain yield. However, is time-consuming, since each selection cycle consists of three stages: progeny development and evaluation, and recombination of the best families. With the Recurrent Genomic Selection use, the time required for each selection cycle can be shortened, as it allows the evaluation and recombination phases to be performed simultaneously, reducing the time needed to complete one selection cycle to only one growing season. In this respect, the objective of this study was to determine the selection accuracy and genetic gains for different selection strategies: PhEN = estimates based exclusively on the phenotypic data of 98 plants; PhEN + GEN = estimates based exclusively on the phenotypic and genotypic data of 98 plants; and GEN = estimates based exclusively on SNP marker genotyping. The following traits were evaluated: 100-grain weight, ear height, grain yield, popping expansion, plant height, and popcorn volume. Field trials were carried out with 98 S1 progenies, at two locations, in an incomplete block design with three replications. The parents of these progenies were genotyped with a panel of ~ 21K SNPs. From the results based on the predictions by strategy GEN, at different selection intensities, the average annual genetic gain for the different traits was 29.1% and 25.2% higher than that by the strategies PhEN and GEN + PhEN for 98 selection candidates; 148.3% and 140.9% higher for 500; and 187.9% and 179.4% higher for 1,000 selection candidates, respectively. Therefore, recurrent genomic selection may result in a high genetic gain, provided that: i) phenotyping is accurate; ii) selection intensity is explored by genotyping several plants, increasing the number of selection candidates, and iii) genomic selection is used for early selection in recurrent selection.

plant biology↗

bioRxiv2018

Cis-regulatory code for predicting plant cell-type specific high salinity response

Multicellular organisms have diverse cell types with distinct roles in development and responses to the environment. At the transcriptional level, the differences in environmental response between cell types are due to differences in regulatory programs. In plants, although cell-type environmental responses have been examined, details on how these responses are regulated remain spotty. Here, we identify a set of putative cis-regulatory elements (pCREs) enriched in the promoters of genes responsive to high salinity stress in six Arabidopsis thaliana root cell types. Using machine learning with pCREs as predictors, we establish cis-regulatory codes, i.e. models predicting whether a gene is responsive to high salinity for each cell type. These pCRE-based models outperform models utilizing in vitro binding data of 758 A. thaliana transcription factors. Surprisingly, organ pCREs identified based on whole root high salinity response can predict cell-type responses as well as pCREs derived from cell-type data -because organ and cell-type pCREs predict complementary subsets of high salinity response genes. Our findings not only advance our understanding of the regulatory mechanisms of plant spatial transcriptional response through cis-regulatory codes, but also suggest broad applicability of the approach to any species, particularly those with little or no trans regulatory data.

plant biology↗

bioRxiv2018

Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis.

Many eukaryotic proteins regulating phosphate (Pi) homeostasis contain SPX domains. We have previously shown that these domains act as cellular receptors for inositol pyrophosphate (PP-InsP) signaling molecules, suggesting that PP-InsPs may regulate Pi homeostasis. Here we report that simultaneous deletion of two diphosphoinositol pentakisphosphate kinases VIH1 and 2 in Arabidopsis impairs plant growth and leads to constitutive Pi starvation responses. We demonstrate that VIH1 and VIH2 are bifunctional cytosolic enzymes able to generate and break-down PP-InsPs. Point-mutants targeting the kinase and phosphatase active sites have opposing effects on plant Pi content and Pi starvation responses, while VIH1 and VIH2 protein levels remain constant in different Pi growth conditions. Enzymatic assays reveal that ATP-Mg2+ substrate levels can shift the relative kinase and phosphatase activities of full-length diphosphoinositol pentakisphosphate kinases. Deletion of phosphate starvation response transcription factors rescues vih1 vih2 mutant phenotypes, placing diphosphoinositol pentakisphosphate kinases and PP-InsPs in plant phosphate signal transduction cascades. We propose that VIH1 and VIH2 relay changes in cellular ATP concentration to changes in PPInsP levels, allowing plants to maintain cellular Pi concentrations constant and to trigger Pi starvation responses.

plant biology↗

bioRxiv2018

Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana

FRIGIDA (FRI) as the major regulator of flowering time in Arabidopsis accessions can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. Besides FLC, other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatiotemporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets MADS AFFECTING FLOWERING4 (MAF4) and MAF5 in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as pro-embryo stage is enough to upregulate FLC expression to delay flowering. Together, our findings confirm the spatiotemporal effect of FRI on delaying flowering, and propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI.\n\nHighlightRoot FRIDIGA activated the novel targets MAF4/5 to delay flowering; Temporal expressing FRIGIDA at as early as pro-embryo stage is efficient to delay flowering.

plant biology↗

bioRxiv2018

WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis

To maintain the balance between long-term stem cell self-renewal and differentiation, dynamic signals need to be translated into spatially precise and temporally stable gene expression states. In the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers differentiation while at the same time, pluripotent stem cells are maintained throughout the entire life-cycle. We find that stem cells are resistant to auxin mediated differentiation, but require low levels of signaling for their maintenance. We demonstrate that the WUSCHEL transcription factor confers this behavior by rheostatically controlling the auxin signaling and response pathway. Finally, we show that WUSCHEL acts via regulation of histone acetylation at target loci, including those with functions in the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly dynamic developmental signal into stable cell behavior with high spatial precision and temporal robustness.

plant biology↗

bioRxiv2018

From spatio-temporal morphogenetic gradients to rhythmic patterning at the shoot apex

Rhythmic patterning is central to the development of eukaryotes, particularly in plant shoot post-embryonic development. The plant hormone auxin drives rhythmic patterning at the shoot apical meristem, but the spatio-temporal dynamics of the auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin provides high-definition graded information not only in space but also in time. We provide evidence that developing organs are auxin-emitting centers that could self-organize spatio-temporal auxin gradients through a transport network converging on the meristem center. We further show that a memory of the exposition of cells to auxin allows to differentiate temporally sites of organ initiation, providing a remarkable example of how the dynamic redistribution of a morphogenetic regulator can be used to create rhythmicity.

plant biology↗

bioRxiv2018

A novel model plant to study the light control of seed germination

Timing of seed germination is crucial for seed plants and coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many receptors, signalling cascades, and hormonal control elements. In contrast, seed germination of several other plants is inhibited by light, but the molecular basis of this converse response is unknown. We describe Aethionema arabicum (Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as it comprises accessions with natural variation between light-sensitive and light-neutral responses. Inhibition is independent of light wavelength and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination as in Arabidopsis, but transcriptome comparisons of light- and dark-exposed Aethionema arabicum seeds revealed that expression of genes for key regulators upon light exposure undergo converse changes, resulting in antipodal hormone regulation. This illustrates that similar modular components of a pathway in light-inhibited, light-neutral and light requiring germination among the Brassicaceae have been assembled by evolution to produce divergent pathways, likely as adaptive traits.\n\nHighlightIn contrast to light requirement for Arabidopsis seed germination, germination of several Aethionema arabicum accessions is inhibited by light, due to antipodal transcriptional regulation of hormone balance.

plant biology↗

bioRxiv2018

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina

The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age pathway. The AP2 orthologue in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 2 (PEP2), was previously reported to regulate flowering through the vernalization pathway by enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the orthologue of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering independently of PEP1. To characterize the function of PEP2 we analyzed the transcriptomes of pep2 and pep1 mutants. The majority of differentially expressed genes were detected between pep2 and the wild type or between pep2 and pep1, highlighting the importance of the PEP2 role that is independent of PEP1. Here we demonstrate that PEP2 prevents the upregulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY) and APETALA1 (AaAP1) which ensure floral commitment during vernalization. Young pep2 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in the main shoot apex and in the axillary branches. These multiple roles of PEP2 in vernalization response contribute to the A. alpina life-cycle.\n\nHIGHLIGHTThe Arabis alpina APETALA2 orthologue, PERPETUAL FLOWERING2, regulates the age-dependent response to vernalization and it is required to facilitate the activation of the A. alpina FLOWERING LOCUS C after vernalization.

plant biology↗

bioRxiv2018

Effect of simulated microgravity on gene expression during embryogenesis of Arabidopsis thaliana

Gravitational force is one of environmental factors that influence growth and development of plants. Changes in this force, including microgravity, can be one of the stress factor which plants have to adapt to cope with. That kind of stress can lead to several abnormalities such as chromosomal breakage, morphological abnormalities or changes in gene expression. The aim of this study was to examine the influence of simulated microgravity on gene expression of Arabidopsis thaliana embryos by use Random Positioning Machine (RPM). RPM is laboratory facility that can generate conditions comparable to the true microgravity. This paper studies effect of simulated microgravity on expression of genes which are involved in plant embryogenesis (LEAFY COTYLEDON, LATE EMBRYOGENESIS ABUNDANT), antioxidative system (CATALASE), mechanical stimuli (TOUCH) and gravitropism (SCARECROW, SHOOT GRAVITROPISM2). Changes in gene expression were detected using quantitative real-time PCR (qRT-PCR). Several of tested genes had increased transcript levels after the influence of simulated microgravity. Specifically, catalase (CAT3), LECs (LEC1), touch (TCH2/CML24), and gravitropism (SGR2) genes achieved significantly increased relative expression (level [≥] 2). The changes in the levels of expression on embryos of Arabidopsis depend on the type of genes and principally on the timing of the influence of the simulated microgravity.

plant biology↗

bioRxiv2018

In vivo phosphatidylserine variations steer Rho GTPase signaling in a cell-context dependent manner

AbstractRho GTPases are master regulators of cell signaling, but how they are regulated depending on the cellular context is unclear. Here, we show that the phospholipid phosphatidylserine acts as a developmentally-controlled lipid rheostat that tunes Rho GTPase signaling in Arabidopsis. Live super-resolution single molecule imaging revealed that RHO-OF-PLANT6 (ROP6) is stabilized by phosphatidylserine into plasma membrane (PM) nanodomains, which is required for auxin signaling. Furthermore, we uncovered that the PM phosphatidylserine content varies during plant root development and that the level of phosphatidylserine modulates the quantity of ROP6 nanoclusters induced by auxin and hence downstream signaling, including regulation of endocytosis and gravitropism. Our work reveals that variations in phosphatidylserine levels are a physiological process that may be leveraged to regulate small GTPase signaling during development.\n\nOne Sentence SummaryPhosphatidylserine acts as a developmentally-controlled lipid rheostat that regulates cellular auxin sensitivity and plant development.

plant biology↗

bioRxiv2018

Common garden experiment reveals altered nutritional values and DNA methylation profiles in micropropagated three elite Ghanaian sweet potato genotypes

Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on the production of key nutrients by field-grown plants has not been previously studied. Here we assessed the extent of in vitro culture induced somaclonal variation, at a phenotypic, compositional and genetic/epigenetic level, by comparing field-maintained and micropropagated lines of three elite Ghanaian sweet potato genotypes grown in a common garden. Although micropropagated plants presented no observable morphological abnormalities compared to field maintained lines, they presented significantly lower levels of iron, total protein, zinc, and glucose. Methylation Sensitive Amplification Polymorphism analysis showed a high level of in vitro culture induced molecular variation in micropropagated plants. Epigenetic, rather than genetic variation, accounts for most of the observed molecular variability. Taken collectively, our results highlight the importance of ensuring the clonal fidelity of the micropropagated biofortified lines in order to reduce potential losses in the nutritional value prior to their commercial release.

plant biology↗

bioRxiv2018

Ecological occurrence and plant regeneration of embryoid of the endangered and endemic plant Dysosma versipellis in China

In this study, the effective callus culture, somatic embryogenesis, and plant regeneration system of Dysosma versipellis, which is an endangered and endemic plant in China, were established under specific culture conditions. Using the D. versipellis leaves, petioles, and roots as explants, DPS software orthogonal design method and SPSS Duncans multiple range test were used to investigate their effects of D. versipellis on callus formation, embryoid induction, and plant regeneration by adding different phytohormones. Results showed that leaves and petioles were the most suitable materials in inducing callus. The effect of phytohormone on callus formation followed the order of 2,4-dichlorophenoxyacetic acid (2,4-D)>thidiazuron (TDZ)> kinetin>naphthylacetic acid (NAA)>2-ip. The best medium for callus formation was MS+2,4-D 1 mg/L+NAA 0.05 mg/L+TDZ 0.5 mg/L+2-ip 1 mg/L. The optimal medium to induce the formation of granular callus embryoid was MS+0.5 mg/L 6-BA+0.1 mg/L NAA, and the induction rate was 71.33%. The embryoid rooting and plant regeneration medium was MS+0.5 mg/L IBA+0.5 mg/L GA3. The optimal medium formula obtained in this study was suitable for the rapid induction of callus, embryoid, and plant regeneration of D. versipellis under in vitro culture conditions. Further study on the action mechanism, signal regulation mechanism, and artificial seed production of fungal elicitors affecting the accumulation of podophyllotoxin is important.

plant biology↗

bioRxiv2018

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 324 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate promising avenues for increasing grain yield by exploiting variation in traits relating to the number of grains per unit area, as well as phenological traits influencing grain-filling duration of genotypes.

plant biology↗

bioRxiv2018

Effects of Biogas Slurry on Fruit Economic Traits and Soil Nutrient of Camellia oleifera Abel

Soil nutrients play a principal role in Camellia oleifera Abel (oil-seed camellia) production. Camellia oleifera absorbs nutrients from surrounding soils and its production is highly influenced by nutrients or fertilization. In this study, we investigated the effects of biogas slurry applications on soil nutrients and economic traits of C. oleifera fruits. Five different amounts of fertilizing biogas slurry (0, 10, 20, 30, or 40 kg/plant/year from three applications per year) were applied to C. oleifera plants in 2015 and 2016. Rhizosphere soil nutrients and C. oleifera fruit economic traits (yield, seed rate, and oil yield)were measured. Fertilization with biogas slurryincreasedsoil organic matter, available nitrogen (N), phosphorus (P), and potassium (K) in both 2015 and 2016. Increases in soil available N, P, and Kwere largest at the highest slurry application rate and second largest at the second highest application rate. Fruit economic traits were maximized at the two highest application rates. Oil yield was correlated withsoil available P in 2015 and 2016, and soil organic matter in 2015. Fertilization with biogas slurry decreased saturated fatty acid content in fruit but had no effect on unsaturated fatty acid content. In conclusion, fertilization with biogas slurry increases rhizosphere soil nutrients and fruit economic traits of C. oleifera with the rates of at least 30 kg/plant/year having the most positive effects.

plant biology↗

bioRxiv2018

Transcriptome dynamics in developing leaves from C3 and C4 Flaveria species reveal determinants of Kranz anatomy

C4 species have evolved more than 60 times independently from C3 ancestors. This multiple and parallel evolution of the complex C4 trait indicates common underlying evolutionary mechanisms that might be identified by comparative analysis of closely related C3 and C4 species. Efficient C4 function depends on a distinctive leaf anatomy that is characterized by enlarged, chloroplast rich bundle sheath cells and a narrow vein spacing. To elucidate molecular mechanisms generating this so called Kranz anatomy, we analyzed a developmental series of leaves from the C4 plant Flaveria bidentis and the closely related C3 species Flaveria robusta using leaf clearing and whole transcriptome sequencing. Applying non-negative matrix factorization on the data identified four different zones with distinct transcriptome patterns in growing leaves of both species. Comparing these transcriptome patterns revealed an important role of auxin metabolism and especially auxin homeostasis for establishing the high vein density typical for C4 leaves.

plant biology↗