Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106

Genome-wide identification of R2R3-MYB transcription factors in Betula platyphylla and functional analysis of BpMYB95 in salt tolerance

The Myeloblastosis (MYB) transcription factor (TF) family is one of the largest transcription factor families in plants and plays an important role in various physiological processes. At present, there are few reports on birch (Betula platyphylla Suk.) of R2R3-MYB-TFs, and most BpMYBs still need to be characterized. In this study, 111 R2R3-MYB-TFs with conserved R2 and R3 MYB domains were identified. Phylogenetic tree analysis showed that the MYB family members of Arabidopsis thaliana and birch were divided into 23 and 21 subgroups, respectively. The latter exhibited an uneven distribution across 14 chromosomes. There were five tandem duplication events and 17 segmental duplication events between BpMYBs, and repeat events play an important role in the expansion of the family. In addition, the promoter region of MYBs was rich in various cis-acting elements, and MYB-TFs were involved in plant growth and development, light responses, biotic stress, and abiotic stress. RNA-sequencing (RNA-seq) and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) results revealed that most R2R3-MYB-TFs in birch responded to salt stress. In particular, the expression of BpMYBs in the S20 subfamily was significantly induced by salt, drought, abscisic acid, and methyl jasmonate stresses. Based on the weighted co-expression network analysis of physiological and RNA-seq data of birch under salt stress, a key MYB-TF BpMYB95 (BPChr12G24087), was identified in response to salt stress, and its expression level was induced by salt stress. BpMYB95 is a nuclear localization protein with transcriptional activation activity in yeast and overexpression of this gene significantly enhanced salt tolerance in Saccharomyces cerevisiae. The qRT-PCR and histochemical staining results showed that BpMYB95 exhibited the highest expression in the roots, young leaves, and petioles of birch plants. Overexpression of BpMYB95 significantly improved salt-induced browning and wilting symptoms in birch leaves and alleviated the degree of PSII photoinhibition caused by salt stress in birch seedlings. In conclusion, most R2R3-MYB-TFs found in birch were involved in the salt stress response mechanisms. Among these, BpMYB95 was a key regulatory factor that significantly enhanced salt tolerance in birch. The findings of this study provide valuable genetic resources for the development of salt-tolerant birch varieties.

Insights into the genetic architecture of the reciprocal interspecific hybrids derived from Chrysanthemum dichrum and C. nankingense

Chrysanthemums are versatile ornamental plants, and improving leaf and flower traits is an important breeding objective. Distant hybridization is a powerful method for plant breeding and genetic improvement, whereas the genetic basis in interspecific F1 progeny of chrysanthemums needs to be better understood for breeding purposes. In this study, the leaf and floral traits of the 273 reciprocal interspecific F1 hybrids of diploid C. dichrum (YSJ) and C. nankingense (JHN) were analyzed along with their SNP-derived genetic structure to elucidate the influence of differences in genetic background between the parents on the hybrid performance. We then performed a genome-wide association analysis (GWAS) to reveal the investigated traits' genomic loci and candidate genes. Considerable phenotypic variation (8.81% ~ 55.78%) and heterosis with transgressive segregation in both directions were observed in the reciprocal progenies. We observed a higher level of phenotypic variation in JHN × YSJ rather than in YSJ × JHN. Also, a significant reciprocal effect was observed for most examined traits. Based on the SNP data, we separated the hybrid progenies into three groups (I, II, and III), albeit imperfectly dependent on the cross directions, except for some reciprocal hybrids clustering into group II. Group I from YSJ × JHN and Group III from YSJ × JHN differed with contrasting F ST and π ratios, indicating the genetic changes in the reciprocal populations. The outcome of GWAS via the IIIVmrMLM method detected 339 significant quantitative trait nucleotides (QTNs) and 40 suggestive QTNs, and the phenotypic variation explained by a single QTN ranged from 0.26% to 7.42%. Within 100 kb upstream and downstream of the important QTNs, we discovered 49 known genes and 39 new candidate genes for the investigated leaf and floral traits. Our study provides profound insights into the genetic architecture of reciprocal hybrid progenies of chrysanthemum species, facilitating future breeding activities.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01518-0.

Light has a principal role in the Arabidopsis transcriptomic response to the spaceflight environment

The Characterizing Arabidopsis Root Attractions (CARA) spaceflight experiment provides comparative transcriptome analyses of plants grown in both light and dark conditions within the same spaceflight. CARA compared three genotypes of Arabidopsis grown in ambient light and in the dark on board the International Space Station (ISS); Col-0, Ws, and phyD, a phytochrome D mutant in the Col-0 background. In all genotypes, leaves responded to spaceflight with a higher number of differentially expressed genes (DEGs) than root tips, and each genotype displayed distinct light / dark transcriptomic patterns that were unique to the spaceflight environment. The Col-0 leaves exhibited a substantial dichotomy, with ten-times as many spaceflight DEGs exhibited in light-grown plants versus dark-grown plants. Although the total number of DEGs in phyD leaves is not very different from Col-0, phyD altered the manner in which light-grown leaves respond to spaceflight, and many genes associated with the physiological adaptation of Col-0 to spaceflight were not represented. This result is in contrast to root tips, where a previous CARA study showed that phyD substantially reduced the number of DEGs. There were few DEGs, but a series of space-altered gene categories, common to genotypes and lighting conditions. This commonality indicates that key spaceflight genes are associated with signal transduction for light, defense, and oxidative stress responses. However, these key signaling pathways enriched from DEGs showed opposite regulatory direction in response to spaceflight under light and dark conditions, suggesting a complex interaction between light as a signal, and light-signaling genes in acclimation to spaceflight.

Wheat MIXTA-like Transcriptional Activators Positively Regulate Cuticular Wax Accumulation

MIXTA-like transcription factors AtMYB16 and AtMYB106 play important roles in the regulation of cuticular wax accumulation in dicot model plant Arabidopsis thaliana, but there are very few studies on the MIXTA-like transcription factors in monocot plants. Herein, wheat MIXTA-like transcription factors TaMIXTA1 and TaMIXTA2 were characterized as positive regulators of cuticular wax accumulation. The virus-induced gene silencing experiments showed that knock-down of wheat TaMIXTA1 and TaMIXTA2 expressions resulted in the decreased accumulation of leaf cuticular wax, increased leaf water loss rate, and potentiated chlorophyll leaching. Furthermore, three wheat orthologous genes of ECERIFERUM 5 (TaCER5-1A, 1B, and 1D) and their function in cuticular wax deposition were reported. The silencing of TaCER5 by BSMV-VIGS led to reduced loads of leaf cuticular wax and enhanced rates of leaf water loss and chlorophyll leaching, indicating the essential role of the TaCER5 gene in the deposition of wheat cuticular wax. In addition, we demonstrated that TaMIXTA1 and TaMIXTA2 function as transcriptional activators and could directly stimulate the transcription of wax biosynthesis gene TaKCS1 and wax deposition gene TaCER5. The above results strongly support that wheat MIXTA-Like transcriptional activators TaMIXTA1 and TaMIXTA2 positively regulate cuticular wax accumulation via activating TaKCS1 and TaCER5 gene transcription.

Comparative transcriptome analysis reveals genes involved in trichome development and metabolism in tobacco

BACKGROUND

The glandular trichomes of tobacco (Nicotiana tabacum) can efficiently produce secondary metabolites. They act as natural bioreactors, and their natural products function to protect plants against insect-pests and pathogens and are also components of industrial chemicals. To clarify the molecular mechanisms of tobacco glandular trichome development and secondary metabolic regulation, glandular trichomes and glandless trichomes, as well as other different developmental tissues, were used for RNA sequencing and analysis.

RESULTS

By comparing glandless and glandular trichomes with other tissues, we obtained differentially expressed genes. They were obviously enriched in KEGG pathways, such as cutin, suberine, and wax biosynthesis, flavonoid and isoflavonoid biosynthesis, terpenoid biosynthesis, and plant-pathogen interaction. In particular, the expression levels of genes related to the terpenoid, flavonoid, and wax biosynthesis pathway mainly showed down-regulation in glandless trichomes, implying that they lack the capability to synthesize certain exudate compounds. Among the differentially expressed genes, 234 transcription factors were found, including AP2-ERFs, MYBs, bHLHs, WRKYs, Homeoboxes (HD-ZIP), and C2H2-ZFs. These transcription factor and genes that highly expressed in trichomes or specially expressed in GT or GLT. Following the overexpression of R2R3-MYB transcription factor Nitab4.5_0011760g0030.1 in tobacco, an increase in the number of branched glandular trichomes was observed.

CONCLUSIONS

Our data provide comprehensive gene expression information at the transcriptional level and an understanding of the regulatory pathways involved in glandular trichome development and secondary metabolism.

Genetic interaction between TTG2 and AtPLC1 reveals a role for phosphoinositide signaling in a co-regulated suite of Arabidopsis epidermal pathways

The TTG2 transcription factor of Arabidopsis regulates a set of epidermal traits, including the differentiation of leaf trichomes, flavonoid pigment production in cells of the inner testa (or seed coat) layer and mucilage production in specialized cells of the outer testa layer. Despite the fact that TTG2 has been known for over twenty years as an important regulator of multiple developmental pathways, little has been discovered about the downstream mechanisms by which TTG2 co-regulates these epidermal features. In this study, we present evidence of phosphoinositide lipid signaling as a mechanism for the regulation of TTG2-dependent epidermal pathways. Overexpression of the AtPLC1 gene rescues the trichome and seed coat phenotypes of the ttg2-1 mutant plant. Moreover, in the case of seed coat color rescue, AtPLC1 overexpression restored expression of the TTG2 flavonoid pathway target genes, TT12 and TT13/AHA10. Consistent with these observations, a dominant AtPLC1 T-DNA insertion allele (plc1-1D) promotes trichome development in both wild-type and ttg2-3 plants. Also, AtPLC1 promoter:GUS analysis shows expression in trichomes and this expression appears dependent on TTG2. Taken together, the discovery of a genetic interaction between TTG2 and AtPLC1 suggests a role for phosphoinositide signaling in the regulation of trichome development, flavonoid pigment biosynthesis and the differentiation of mucilage-producing cells of the seed coat. This finding provides new avenues for future research at the intersection of the TTG2-dependent developmental pathways and the numerous molecular and cellular phenomena influenced by phospholipid signaling.

Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew

Exocyst component of 70-kDa (EXO70) proteins are constituents of the exocyst complex implicated in vesicle tethering during exocytosis. MILDEW RESISTANCE LOCUS O (MLO) proteins are plant-specific calcium channels and some MLO isoforms enable fungal powdery mildew pathogenesis. We here detected an unexpected phenotypic overlap of Arabidopsis thaliana exo70H4 and mlo2 mlo6 mlo12 triple mutant plants regarding the biogenesis of leaf trichome secondary cell walls. Biochemical and Fourier transform infrared spectroscopic analyses corroborated deficiencies in the composition of trichome cell walls in these mutants. Transgenic lines expressing fluorophore-tagged EXO70H4 and MLO exhibited extensive colocalization of these proteins. Furthermore, mCherry-EXO70H4 mislocalized in trichomes of the mlo triple mutant and, vice versa, MLO6-GFP mislocalized in trichomes of the exo70H4 mutant. Expression of GFP-marked PMR4 callose synthase, a known cargo of EXO70H4-dependent exocytosis, revealed reduced cell wall delivery of GFP-PMR4 in trichomes of mlo triple mutant plants. In vivo protein-protein interaction assays in plant and yeast cells uncovered isoform-preferential interactions between EXO70.2 subfamily members and MLO proteins. Finally, exo70H4 and mlo6 mutants, when combined, showed synergistically enhanced resistance to powdery mildew attack. Taken together, our data point to an isoform-specific interplay of EXO70 and MLO proteins in the modulation of trichome cell wall biogenesis and powdery mildew susceptibility.

A eudicot MIXTA family ancestor likely functioned in both conical cells and trichomes

The MIXTA family of MYB transcription factors modulate the development of diverse epidermal features in land plants. This study investigates the evolutionary history and function of the MIXTA gene family in the early-diverging eudicot model lineage Thalictrum (Ranunculaceae), with R2R3 SBG9-A MYB transcription factors representative of the pre-core eudicot duplication and thus hereby referred to as "paleoMIXTA" (PMX). Cloning and phylogenetic analysis of Thalictrum paleoMIXTA (ThPMX) orthologs across 23 species reveal a genus-wide duplication coincident with a whole-genome duplication. Expression analysis by qPCR confirmed that the highest expression is found in carpels, while newly revealing high expression in leaves and nuanced differences between paralogs in representative polyploid species. The single-copy ortholog from the diploid species T. thalictroides (TthPMX, previously TtMYBML2), which has petaloid sepals with conical-papillate cells and trichomes on leaves, was functionally characterized by virus-induced gene silencing (VIGS), and its role in leaves was also assessed from heterologous overexpression in tobacco. Another ortholog from a species with conical-papillate cells on stamen filaments, TclPMX, was also targeted for silencing. Overexpression assays in tobacco provide further evidence that the paleoMIXTA lineage has the potential for leaf trichome function in a core eudicot. Transcriptome analysis by RNA-Seq on leaves of VIGS-treated plants suggests that TthPMX modulates leaf trichome development and morphogenesis through microtubule-associated mechanisms and that this may be a conserved pathway for eudicots. These experiments provide evidence for a combined role for paleoMIXTA orthologs in (leaf) trichomes and (floral) conical-papillate cells that, together with data from other systems, makes the functional reconstruction of a eudicot ancestor most likely as also having a combined function.

Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color

Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.

LcMYB106 suppresses monoterpene biosynthesis by negatively regulating LcTPS32 expression in Litsea cubeba

Litsea cubeba, the core species of the Lauraceae family, is valuable for the production of essential oils due to its high concentration of monoterpenes (90%). The key monoterpene synthase and metabolic regulatory network of monoterpene biosynthesis have provided new insights for improving essential oil content. However, there are few studies on the regulation mechanism of monoterpenes in L. cubeba. In this study, we investigated LcTPS32, a member of the TPS-b subfamily, and identified its function as an enzyme for the synthesis of monoterpenes, including geraniol, α-pinene, β-pinene, β-myrcene, linalool and eucalyptol. The quantitative real-time PCR analysis showed that LcTPS32 was highly expressed in the fruits of L. cubeba and contributed to the characteristic flavor of its essential oil. Overexpression of LcTPS32 resulted in a significant increase in the production of monoterpenes in L. cubeba by activating both the MVA and MEP pathways. Additionally, the study revealed that LcMYB106 played a negative regulatory role in monoterpenes biosynthesis by directly binding to the promoter of LcTPS32. Our study indicates that LcMYB106 could serve as a crucial target for metabolic engineering endeavors, aiming at enhancing the monoterpene biosynthesis in L. cubeba.

Comparative morphoanatomy and transcriptomic analyses reveal key factors controlling floral trichome development in Aristolochia (Aristolochiaceae)

Trichomes are specialized epidermal cells in aerial plant parts. Trichome development proceeds in three stages, determination of cell fate, specification, and morphogenesis. Most genes responsible for these processes have been identified in the unicellular branched leaf trichomes from the model Arabidopsis thaliana. Less is known about the molecular basis of multicellular trichome formation across flowering plants, especially those formed in floral organs of early diverging angiosperms. Here, we aim to identify the genetic regulatory network (GRN) underlying multicellular trichome development in the kettle-shaped trap flowers of Aristolochia (Aristolochiaceae). We selected two taxa for comparison, A. fimbriata, with trichomes inside the perianth, which play critical roles in pollination, and A. macrophylla, lacking specialized trichomes in the perianth. A detailed morphoanatomical characterization of floral epidermis is presented for the two species. We compared transcriptomic profiling at two different developmental stages in the different perianth portions (limb, tube, and utricle) of the two species. Moreover, we present a comprehensive expression map for positive regulators and repressors of trichome development, as well as cell cycle regulators. Our data point to extensive modifications in gene composition, expression, and putative roles in all functional categories when compared with model species. We also record novel differentially expressed genes (DEGs) linked to epidermis patterning and trichome development. We thus propose the first hypothetical genetic regulatory network (GRN) underlying floral multicellular trichome development in Aristolochia, and pinpoint key factors responsible for the presence and specialization of floral trichomes in phylogenetically distant species of the genus.

HECT-type ubiquitin ligase KAKTUS mediates the proteasome-dependent degradation of cyclin-dependent kinase inhibitor KRP2 during trichome morphogenesis in Arabidopsis

Trichome development is a fascinating model to elaborate the plant cell differentiation and growth processes. A wealth of information has pointed to the contributions of the components associated with cell cycle control and ubiquitin/26S proteasome system (UPS) to trichome morphogenesis, but how these two pathways are connected remains obscure. Here, we report that HECT‐type ubiquitin ligase KAKTUS (KAK) targets the cyclin‐dependent kinase (CDK) inhibitor KRP2 (for kip‐related protein 2) for proteasome‐dependent degradation during trichome branching in Arabidopsis. We show that over‐expression of KRP2 promotes trichome branching and endoreduplication which is similar to kak loss of function mutants. KAK directly interacts with KRP2 and mediates KRP2 degradation. Mutation of KAK results in the accumulation of steady‐state KRP2. Consistently, in kak pKRP2:KRP2‐GFP plants, the trichome branching is further induced compared with the single mutant. Taken together, our studies bridge the cell cycle control and UPS pathways during trichome development and underscore the importance of post‐translational control in epidermal differentiation.

Time course of changes in the transcriptome during russet induction in apple fruit

BACKGROUND

Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear. Here, we present high-resolution transcriptomic data by controlled russet induction at very early stages of fruit development. During Phase I, a patch of the fruit surface is exposed to surface moisture. For Phase II, moisture exposure is terminated, and the formerly exposed surface remains dry. We targeted differentially expressed transcripts as soon as 24 h after russet induction.

RESULTS

During moisture exposure (Phase I) of 'Pinova' apple, transcripts associated with the cell cycle, cell wall, and cuticle synthesis (SHN3) decrease, while those related to abiotic stress increase. NAC35 and MYB17 were the earliest induced genes during Phase I. They are therefore linked to the initial processes of cuticle microcracking. After moisture removal (Phase II), the expression of genes related to meristematic activity increased (WOX4 within 24 h, MYB84 within 48 h). Genes related to lignin synthesis (MYB52) and suberin synthesis (MYB93, WRKY56) were upregulated within 3 d after moisture removal. WOX4 and AP2B3 are the earliest differentially expressed genes induced in Phase II. They are therefore linked to early events in periderm formation. The expression profiles were consistent between two different seasons and mirrored differences in russet susceptibility in a comparison of cultivars. Furthermore, expression profiles during Phase II of moisture induction were largely identical to those following wounding.

CONCLUSIONS

The combination of a unique controlled russet induction technique with high-resolution transcriptomic data allowed for the very first time to analyse the formation of cuticular microcracks and periderm in apple fruit immediately after the onset of triggering factors. This data provides valuable insights into the spatial-temporal dynamics of russeting, including the synthesis of cuticles, dedifferentiation of cells, and impregnation of cell walls with suberin and lignin.

Single-cell RNA landscape of the special fiber initiation process in Bombax ceiba

As a new source of natural fibers, the Bombax ceiba tree can provide thin, light, extremely soft and warm fiber material for the textile industry. Natural fibers are an ideal model system for studying cell growth and differentiation, but the molecular mechanisms that regulate fiber initiation are not fully understood. In B. ceiba, we found that fiber cells differentiate from the epidermis of the inner ovary wall. Each initiated cell then divides into a cluster of fiber cells that eventually develop into mature fibers, a process very different from the classical fiber initiation process of cotton. We used high-throughput single-cell RNA sequencing (scRNA-seq) to examine the special characteristics of fiber initiation in B. ceiba. A total of 15 567 high-quality cells were identified from the inner wall of the B. ceiba ovary, and 347 potential marker genes for fiber initiation cell types were identified. Two major cell types, initiated fiber cells and epidermal cells, were identified and verified by RNA in situ hybridization. A developmental trajectory analysis was used to reconstruct the process of fiber cell differentiation in B. ceiba. Comparative analysis of scRNA-seq data from B. ceiba and cotton (Gossypium hirsutum) confirmed that the additional cell division process in B. ceiba is a novel species-specific mechanism for fiber cell development. Candidate genes and key regulators that may contribute to fiber cell differentiation and division in B. ceiba were identified. This work reveals gene expression signatures during B. ceiba fiber initiation at a single-cell resolution, providing a new strategy and viewpoint for investigation of natural fiber cell differentiation and development.

Heavy Metal-Associated Isoprenylated Plant Proteins (HIPPs) at Plasmodesmata: Exploring the Link between Localization and Function

Heavy metal-associated isoprenylated plant proteins (HIPPs) are a metallochaperone-like protein family comprising a combination of structural features unique to vascular plants. HIPPs possess both one or two heavy metal-binding domains and an isoprenylation site, facilitating a posttranslational protein lipid modification. Recent work has characterized individual HIPPs across numerous different species and provided evidence for varied functionalities. Interestingly, a significant number of HIPPs have been identified in proteomes of plasmodesmata (PD)-nanochannels mediating symplastic connectivity within plant tissues that play pivotal roles in intercellular communication during plant development as well as responses to biotic and abiotic stress. As characterized functions of many HIPPs are linked to stress responses, plasmodesmal HIPP proteins are potentially interesting candidate components of signaling events at or for the regulation of PD. Here, we review what is known about PD-localized HIPP proteins specifically, and how the structure and function of HIPPs more generally could link to known properties and regulation of PD.

Function and molecular mechanism of a poplar placenta limited MIXTA gene in regulating differentiation of plant epidermal cells

The placenta in fruits of most plants either desiccate and shrink as the fruits mature or develop further to form the fleshy tissues. In poplars, placental epidermal cells protrude collectively to produce catkin fibers. In this study, three carpel limited MIXTA genes, PdeMIXTA02, PdeMIXTA03, PdeMIXTA04, were find to specifically expressed in carpel immediately after pollination. Heterologous expression of the three genes in Arabidopsis demonstrated that PdeMIXTA04 significantly promoted trichomes density and could restore trichomes in the trichomeless mutant. By contrast, such functions were not observed with PdeMIXTA02, PdeMIXTA03. In situ hybridization revealed that PdeMIXTA04 was explicitly expressed in poplar placental epidermal cells. We also confirmed trichome-specific expression of the PdeMIXTA04 promoter. Multiple experimental proofs have confirmed the interaction between PdeMIXTA04, PdeMYC and PdeWD40, indicating PdeMIXTA04 functioned through the MYB-bHLH-WD40 ternary complex. Our work provided distinctive understanding of the molecular mechanism triggering differentiation of poplar catkins.

Regulation of capsule spine formation in castor

Castor (Ricinus communis L.) is a dicotyledonous oilseed crop that can have either spineless or spiny capsules. Spines are protuberant structures that differ from thorns or prickles. The developmental regulatory mechanisms governing spine formation in castor or other plants have remained largely unknown. Herein, using map-based cloning in 2 independent F2 populations, F2-LYY5/DL01 and F2-LYY9/DL01, we identified the RcMYB106 (myb domain protein 106) transcription factor as a key regulator of capsule spine development in castor. Haplotype analyses demonstrated that either a 4,353-bp deletion in the promoter or a single nucleotide polymorphism leading to a premature stop codon in the RcMYB106 gene could cause the spineless capsule phenotype in castor. Results of our experiments indicated that RcMYB106 might target the downstream gene RcWIN1 (WAX INDUCER1), which encodes an ethylene response factor known to be involved in trichome formation in Arabidopsis (Arabidopsis thaliana) to control capsule spine development in castor. This hypothesis, however, remains to be further tested. Nevertheless, our study reveals a potential molecular regulatory mechanism underlying the spine capsule trait in a nonmodel plant species.

Identification of the passion fruit (Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses

Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.

Poplar coma morphogenesis and miRNA regulatory networks by combining ovary tissue sectioning and deep sequencing

Poplar coma, commonly referred to as "seed hairs", is a tuft of trichomes attached to the seed coat that helps seed dispersal. However, they can also trigger health impacts for humans, including sneezing, shortness of breath, and skin irritation. Despite efforts to study the regulatory mechanism of herbaceous trichome formation, poplar coma remains poorly understood. In this study, we showed that the epidermal cells of the funiculus and placenta are the origin of poplar coma based on observations of paraffin sections. Small RNA (sRNA) and degradome libraries were also constructed at three stages of poplar coma development, including initiation and elongation stages. Based on 7,904 miRNA-target pairs identified by small RNA and degradome sequencing, we constructed a miRNA-transcript factor and a stage-specific miRNA regulatory network. By combining paraffin section observation and deep sequencing, our research will provide greater insight into the molecular mechanisms of poplar coma development.

Plant deubiquitinases: from structure and activity to biological functions

This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.

Genomic divergence between two sister Ostrya species through linked selection and recombination

Studying the evolution of genomic divergence between lineages is a topical issue in evolutionary biology. However, the evolutionary forces that shape the heterogeneous divergence of the genomic landscape are still poorly understood. Here, two wind-pollinated sister-species (Ostrya japonica and O. chinensis) are used to explore what these potential forces might be. A total of 40 individuals from 16 populations across their main distribution areas in China were sampled for genome-wide resequencing. Population demography analyses revealed that these two sister-species diverged at 3.06-4.43 Mya. Both population contraction and increased gene flow were detected during glacial periods, suggesting secondary contact at those times. All three parameters (D XY, π, and ρ) decreased in those regions showing high levels of differentiation (F ST). These findings indicate that linked selection and recombination played a key role in the genomic heterogeneous differentiation between the two Ostrya species. Genotype-environment association analyses showed that precipitation was the most important ecological factor for speciation. Such environmentally related genes and positive selection genes may have contributed to local adaptation and the maintenance of species boundaries.

Perspectives for integrated insect pest protection in oilseed rape breeding

In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again. At the same time, new camera-based tracking technologies, new knowledge-based genomic technologies and new scientific insights into the ecology of insect-Brassica interactions are becoming available. Here we discuss and prioritise promising breeding strategies and direct and indirect breeding targets, and their time-perspective for future realisation in integrated insect pest protection of oilseed rape. In conclusion, researchers and oilseed rape breeders can nowadays benefit from an array of new technologies which in combination will accelerate the development of improved oilseed rape cultivars with multiple insect pest resistances/tolerances in the near future.

Genome-wide analysis of R2R3-MYB transcription factors in Japanese morning glory

The R2R3-MYB transcription factor is one of the largest transcription factor families in plants. R2R3-MYBs play a variety of functions in plants, such as cell fate determination, organ and tissue differentiations, primary and secondary metabolisms, stress and defense responses and other physiological processes. The Japanese morning glory (Ipomoea nil) has been widely used as a model plant for flowering and morphological studies. In the present study, 127 R2R3-MYB genes were identified in the Japanese morning glory genome. Information, including gene structure, protein motif, chromosomal location and gene expression, were assigned to the InR2R3-MYBs. Phylogenetic tree analysis revealed that the 127 InR2R3-MYBs were classified into 29 subfamilies (C1-C29). Herein, physiological functions of the InR2R3-MYBs are discussed based on the functions of their Arabidopsis orthologues. InR2R3-MYBs in C9, C15, C16 or C28 may regulate cell division, flavonol biosynthesis, anthocyanin biosynthesis or response to abiotic stress, respectively. C16 harbors the known anthocyanin biosynthesis regulator, InMYB1 (INIL00g10723), and putative anthocyanin biosynthesis regulators, InMYB2 (INIL05g09650) and InMYB3 (INIL05g09651). In addition, INIL05g09649, INIL11g40874 and INIL11g40875 in C16 were suggested as novel anthocyanin biosynthesis regulators. We organized the R2R3-MYB transcription factors in the morning glory genome and assigned information to gene and protein structures and presuming their functions. Our study is expected to facilitate future research on R2R3-MYB transcription factors in Japanese morning glory.

Prioritized candidate causal haplotype blocks in plant genome-wide association studies

Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects in many GWAS. In plant, the relatively small population size in GWAS and the high genetic diversity found in many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to prioritize the candidate causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, GMMAT, and BLINK in both simulated and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in high polygenicity simulation setting. Moreover, it resulted in smaller mapping intervals, especially in regions of high LD, achieved by prioritizing small candidate causal blocks in the larger haplotype blocks. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA’s results, and the average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved on mapping resolution to facilitate crop improvement.

Genome-wide association studies (GWAS) are commonly used in human and plant studies to identify genetic variants responsible for the phenotype of interest and provide foundations for studying disease mechanisms and crop improvement. Most GWAS models are developed and optimized using human datasets. However, the difference between human and plant datasets essentially limits their applications in plant studies, especially when mapping complex traits such as drought resistance and yield. In this study, we present a novel GWAS method, HapFM, tailored for plant datasets to overcome the difficulties of many conventional GWAS methods. HapFM resulted in higher statistical power than conventional GWAS methods for mapping complex traits in our simulation and real dataset analyses. In addition, HapFM reduced the mapping interval by prioritizing candidate causal regions in the genome, which benefits the downstream experimental studies. Last but not least, HapFM can incorporate biological annotations to increase statistical power further. Overall, HapFM balances statistical power, result interpretability, and downstream experimental verifiability.

Mutation of OsMYB60 reduces rice resilience to drought stress by attenuating cuticular wax biosynthesis

The cuticular wax layer on leaf surfaces limits non-stomatal water loss to the atmosphere and protects against pathogen invasion. Although many genes associated with wax biosynthesis and wax transport in plants have been identified, their regulatory mechanisms remain largely unknown. Here, we show that the MYB transcription factor OsMYB60 positively regulates cuticular wax biosynthesis and this helps rice (Oryza sativa) plants tolerate drought stress. Compared with the wild type (japonica cultivar 'Dongjin'), osmyb60 null mutants (osmyb60-1 and osmyb60-2) exhibited increased drought sensitivity, with more chlorophyll leaching and higher rates of water loss. Quantitative reverse-transcription PCR showed that the loss of function of OsMYB60 led to downregulation of wax biosynthesis genes, leading to reduced amounts of total wax components on leaf surfaces under normal conditions. Yeast one-hybrid, luciferase transient transcriptional activity, and chromatin immunoprecipitation assays revealed that OsMYB60 directly binds to the promoter of OsCER1 (a key gene involved in very-long-chain alkane biosynthesis) and upregulates its expression. Taken together, these results demonstrate that OsMYB60 enhances rice resilience to drought stress by promoting cuticular wax biosynthesis on leaf surfaces.

Comparative transcriptome analysis reveals key pathways and genes involved in trichome development in tea plant (Camellia sinensis)

Trichomes, which develop from epidermal cells, are considered one of the important characteristics of the tea plant [Camellia sinensis (L.) O. Kuntze]. Many nutritional and metabolomic studies have indicated the important contributions of trichomes to tea products quality. However, understanding the regulation of trichome formation at the molecular level remains elusive in tea plants. Herein, we present a genome-wide comparative transcriptome analysis between the hairless Chuyeqi (CYQ) with fewer trichomes and the hairy Budiaomao (BDM) with more trichomes tea plant genotypes, toward the identification of biological processes and functional gene activities that occur during trichome development. In the present study, trichomes in both cultivars CYQ and BDM were unicellular, unbranched, straight, and soft-structured. The density of trichomes was the highest in the bud and tender leaf periods. Further, using the high-throughput sequencing method, we identified 48,856 unigenes, of which 31,574 were differentially expressed. In an analysis of 208 differentially expressed genes (DEGs) encoding transcription factors (TFs), five may involve in trichome development. In addition, on the basis of the Gene Ontology (GO) annotation and the weighted gene co-expression network analysis (WGCNA) results, we screened several DEGs that may contribute to trichome growth, including 66 DEGs related to plant resistance genes (PRGs), 172 DEGs related to cell wall biosynthesis pathway, 29 DEGs related to cell cycle pathway, and 45 DEGs related to cytoskeleton biosynthesis. Collectively, this study provided high-quality RNA-seq information to improve our understanding of the molecular regulatory mechanism of trichome development and lay a foundation for additional trichome studies in tea plants.

Stalk cell polar ion transport provide for bladder-based salinity tolerance in Chenopodium quinoa

Chenopodium quinoa uses epidermal bladder cells (EBCs) to sequester excess salt. Each EBC complex consists of a leaf epidermal cell, a stalk cell, and the bladder. Under salt stress, sodium (Na⁺ ), chloride (Cl^- ), potassium (K⁺ ) and various metabolites are shuttled from the leaf lamina to the bladders. Stalk cells operate as both a selectivity filter and a flux controller. In line with the nature of a transfer cell, advanced transmission electron tomography, electrophysiology, and fluorescent tracer flux studies revealed the stalk cell's polar organization and bladder-directed solute flow. RNA sequencing and cluster analysis revealed the gene expression profiles of the stalk cells. Among the stalk cell enriched genes, ion channels and carriers as well as sugar transporters were most pronounced. Based on their electrophysiological fingerprint and thermodynamic considerations, a model for stalk cell transcellular transport was derived.

Identification and characterization of a novel gene involved in glandular trichome development in Nepeta tenuifolia

Nepeta tenuifolia is a medicinal plant rich in terpenoids and flavonoids with antiviral, immunoregulatory, and anti-inflammatory activities. The peltate glandular trichome (PGT) is a multicellular structure considered to be the primary storage organ for monoterpenes; it may serve as an ideal model for studying cell differentiation and the development of glandular trichomes (GTs). The genes that regulate the development of GTs have not yet been well studied. In this study, we identified NtMIXTA1, a GT development-associated gene from the R2R3 MYB SBG9 family. NtMIXTA1 overexpression in tobacco resulted in the production of longer and denser GTs. Virus-induced gene silencing of NtMIXTA1 resulted in lower PGT density, a significant reduction in monoterpene concentration, and the decreased expression of genes related to monoterpene biosynthesis. Comparative transcriptome and widely targeted metabolic analyses revealed that silencing NtMIXTA1 significantly influenced the expression of genes, and the production of metabolites involved in the biosynthesis of terpenoids, flavonoids, and lipids. This study provides a solid foundation describing a mechanism underlying the regulation of GT development. In addition, this study further deepens our understanding of the regulatory networks involved in GT development and GT development-associated metabolite flux, as well as provides valuable reference data for studying plants with a high medicinal value without genetic transformation.

The genomic basis of the plant island syndrome in Darwin's giant daisies

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies.

Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.

Genome-wide identification and expression analysis of the R2R3-MYB gene family in tobacco (Nicotiana tabacum L.)

BACKGROUND

The R2R3-MYB transcription factor is one of the largest gene families in plants and involved in the regulation of plant development, hormone signal transduction, biotic and abiotic stresses. Tobacco is one of the most important model plants. Therefore, it will be of great significance to investigate the R2R3-MYB gene family and their expression patterns under abiotic stress and senescence in tobacco.

RESULTS

A total of 174 R2R3-MYB genes were identified from tobacco (Nicotiana tabacum L.) genome and were divided into 24 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were especially conserved among the NtR2R3-MYB genes, especially members within the same subgroup. The NtR2R3-MYB genes were distributed on 24 tobacco chromosomes. Analysis of gene duplication events obtained 3 pairs of tandem duplication genes and 62 pairs of segmental duplication genes, suggesting that segmental duplications is the major pattern for R2R3-MYB gene family expansion in tobacco. Cis-regulatory elements of the NtR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponsive. Expression profile analysis showed that NtR2R3-MYB genes were widely expressed in different maturity tobacco leaves, and however, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 15 NtR2R3-MYBs confirmed their differential expression under different abiotic stresses (cold, salt and drought), and notably, NtMYB46 was significantly up-regulated under three treatments.

CONCLUSIONS

In summary, a genome-wide identification, evolutionary and expression analysis of R2R3-MYB gene family in tobacco were conducted. Our results provided a solid foundation for further biological functional study of NtR2R3-MYB genes in tobacco.

Molecular Mechanisms of Plant Trichome Development

Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.

Characterisation of the Mentha canadensis R2R3-MYB transcription factor gene McMIXTA and its involvement in peltate glandular trichome development

BACKGROUND

Mentha canadensis L. has important economic value for the production of essential oils, which are synthesised, secreted and stored in peltate glandular trichomes. As a typical multicellular secretory trichome, glandular trichomes are important biological factories for the synthesis of some specialised metabolites. However, little is known about the molecular mechanism of glandular trichome development in M. canadensis.

RESULTS

In this study, the R2R3-MYB transcription factor gene McMIXTA was isolated to investigate its function in glandular trichome development. Bioinformatics analysis indicated that McMIXTA belonged to the subgroup 9 R2R3-MYB, with a R2R3 DNA-binding domain and conserved subgroup 9 motifs. A subcellular localisation assay indicated that McMIXTA was localised in the nucleus. Transactivation analysis indicated that McMIXTA was a positive regulator, with transactivation regions located between positions N253 and N307. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that McMIXTA formed a complex with McHD-Zip3, a trichome development-related HD-ZIP IV transcription factor. Overexpression of McMIXTA in Mentha × piperita L. caused an increase in peltate glandular trichomes density of approximately 25% on the leaf abaxial surface.

CONCLUSIONS

Our results demonstrated that the subgroup 9 R2R3-MYB transcription factor McMIXTA has a positive effect on regulating peltate glandular trichome development and the MIXTA/HD-ZIP IV complexes might be conserved regulators for glandular trichome initiation. These results provide useful information for revealing the regulatory mechanism of multicellular glandular trichome development.

Non-autonomous stomatal control by pavement cell turgor via the K+ channel subunit AtKC1

Stomata optimize land plants' photosynthetic requirements and limit water vapor loss. So far, all of the molecular and electrical components identified as regulating stomatal aperture are produced, and operate, directly within the guard cells. However, a completely autonomous function of guard cells is inconsistent with anatomical and biophysical observations hinting at mechanical contributions of epidermal origins. Here, potassium (K+) assays, membrane potential measurements, microindentation, and plasmolysis experiments provide evidence that disruption of the Arabidopsis thaliana K+ channel subunit gene AtKC1 reduces pavement cell turgor, due to decreased K+ accumulation, without affecting guard cell turgor. This results in an impaired back pressure of pavement cells onto guard cells, leading to larger stomatal apertures. Poorly rectifying membrane conductances to K+ were consistently observed in pavement cells. This plasmalemma property is likely to play an essential role in K+ shuttling within the epidermis. Functional complementation reveals that restoration of the wild-type stomatal functioning requires the expression of the transgenic AtKC1 at least in the pavement cells and trichomes. Altogether, the data suggest that AtKC1 activity contributes to the building of the back pressure that pavement cells exert onto guard cells by tuning K+ distribution throughout the leaf epidermis.

Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton

Plant trichomes are specialized epidermal cells that are widely distributed on plant aerial tissues. The initiation and progression of trichomes are controlled in a coordinated sequence of multiple molecular events. During the past decade, major breakthroughs in the molecular understanding of trichome development were achieved through the characterization of various trichomes defective mutants and trichome-associated genes, which revealed a highly complex molecular regulatory network underlying plant trichome development. This review focuses on the recent millstone in plant trichomes research obtained using genetic and molecular studies, as well as 'omics' analyses in model plant Arabidopsis and fiber crop cotton. In particular, we discuss the latest understanding and insights into the underlying molecular mechanisms of trichomes formation at multiple dimensions, including at the chromatin, transcriptional, post-transcriptional, and post-translational levels. We summarize that the integration of multi-dimensional trichome-associated genes will enable us to systematically understand the molecular regulation network that landscapes the development of the plant trichomes. These advances will enable us to address the unresolved questions regarding the molecular crosstalk that coordinate concurrent and ordered the changes in cotton fiber initiation and progression, together with their possible implications for genetic improvement of cotton fiber.

Two R2R3-MYB genes cooperatively control trichome development and cuticular wax biosynthesis in Prunus persica

The fruit surface has an enormous impact on the external appearance and postharvest shelf-life of fruit. Here, we report two functionally redundant genes, PpMYB25 and PpMYB26, involved in regulation of fruit skin texture in peach. PpMYB25 can activate transcription of PpMYB26 and they both induce trichome development and cuticular wax accumulation, resulting in peach fruit with a fuzzy and dull appearance. By contrast, nonfunctional mutation of PpMYB25 caused by an insertional retrotransposon in the last exon in nectarine fails to activate transcription of PpMYB26, resulting in nectarine fruit with a smooth and shiny appearance due to loss of trichome initiation and decreased cuticular wax accumulation. Secondary cell wall biosynthesis in peach fruit pubescence is controlled by a transcriptional regulatory network, including the master regulator PpNAC43 and its downstream MYB transcription factors such as PpMYB42, PpMYB46 and PpMYB83. Our results show that PpMYB25 and PpMYB26 coordinately regulate fruit pubescence and cuticular wax accumulation and their simultaneous perturbation results in the origin of nectarine, which is botanically classified as a subspecies of peach.

Subtle interplay between trichome development and cuticle formation in plants

Trichomes and cuticles are key protective epidermal specializations. This review highlights the genetic interplay existing between trichome and cuticle formation in a variety of species. Controlling trichome development, the biosynthesis of trichome-derived specialized metabolites as well as cuticle biosynthesis and deposition can be viewed as different aspects of a common defensive strategy adopted by plants to protect themselves from environmental stresses. Existence of such interplay is based on the mining of published transcriptomic data as well as on phenotypic observations in trichome or cuticle mutants where the morphology of both structures often appear to be concomitantly altered. Given the existence of several trichome developmental pathways depending on the plant species and the types of trichomes, genetic interactions between cuticle formation and trichome development are complex to decipher and not easy to generalize. Based on our review of the literature, a schematic overview of the gene network mediating this transcriptional interplay is presented for two model plant species: Arabidopsis thaliana and Solanum lycopersicum. In addition to fundamental new insights on the regulation of these processes, identifying key transcriptional switches controlling both processes could also facilitate more applied investigations aiming at improving much desired agronomical traits in plants.

An advanced method for the release, enrichment and purification of high-quality Arabidopsis thaliana rosette leaf trichomes enables profound insights into the trichome proteome

BACKGROUND

Rosette leaf trichomes of Arabidopsis thaliana have been broadly used to study cell development, cell differentiation and, more recently, cell wall biogenesis. However, trichome-specific biochemical or -omics analyses require a proper separation of trichomes from residual plant tissue. Thus, different strategies were proposed in the past for trichome isolation, which mostly rely on harsh conditions and suffer from low yield, thereby limiting the spectrum of downstream analyses.

RESULTS

To take trichome-leaf separation to the next level, we revised a previously proposed method for isolating A. thaliana trichomes by optimizing the mechanical and biochemical specifications for trichome release. We additionally introduced a density gradient centrifugation step to remove residual plant debris. We found that prolonged, yet mild seedling agitation increases the overall trichome yield by more than 60% compared to the original protocol. We noticed that subsequent density gradient centrifugation further visually enhances trichome purity, which may be advantageous for downstream analyses. Gene expression analysis by quantitative reverse transcriptase-polymerase chain reaction validated a substantial enrichment upon purification of trichomes by density gradient centrifugation. Histochemical and biochemical investigation of trichome cell wall composition indicated that unlike the original protocol gentle agitation during trichome release largely preserves trichome integrity. We used enriched and density gradient-purified trichomes for proteomic analysis in comparison to trichome-depleted leaf samples and present a comprehensive reference data set of trichome-resident and -enriched proteins. Collectively we identified 223 proteins that are highly enriched in trichomes as compared to trichome-depleted leaves. We further demonstrate that the procedure can be applied to retrieve diverse glandular and non-glandular trichome types from other plant species.

CONCLUSIONS

We provide an advanced method for the isolation of A. thaliana leaf trichomes that outcompetes previous procedures regarding yield and purity. Due to the large amount of high-quality trichomes our method enabled profound insights into the so far largely unexplored A. thaliana trichome proteome. We anticipate that our protocol will be of use for a variety of downstream analyses, which are expected to shed further light on the biology of leaf trichomes in A. thaliana and possibly other plant species.

Trichome Transcripts as Efficiency Control for Synthetic Biology and Molecular Farming

A variety of methods for studying glandular leaf hairs (trichomes) as multicellular micro-organs are well established for synthetic biology platforms like tobacco or tomato but rather rare for nonglandular and usually single-celled trichomes of the model plant Arabidopsis thaliana. A thorough isolation of-ideally intact-trichomes is decisive for further biochemical and genomic analyses of primary and secondary metabolic compounds, enzymes, and especially transcripts to monitor initial success of an engineering approach. While isolation of tomato or tobacco trichomes is rather easy, by simply freezing whole plants in liquid nitrogen and brushing off trichomes, this approach does not work for Arabidopsis. This is mainly due to damage of trichome cells during the collection procedure and very low yield. Here, we provide a robust method for a virtually epithelial cell-free isolation of Arabidopsis trichomes. This method is then joined with an RNA isolation protocol to perform mRNA analysis on extracts of the isolated trichomes using a semi-quantitative RT-PCR setup.

Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Nonglandular prickle formation is associated with development and secondary metabolism-related genes in Rosa multiflora

Roses are among the most economically important ornamental plants worldwide. But prickles on the stem and leaves cause difficulties for cultivation or inconveniences during harvest and transportation, thus are an undesirable horticultural character. However, little is known about the molecular mechanisms of prickle development. In this study, we sought to develop Rosa multiflora (in the family Rosaceae) as a model plant to study prickle formation. The morphology, structure, and ontogeny of prickles were characterized, and transcriptome analysis of prickly and prickleless R. multiflora genotypes was performed. Morphological observation and microscopic analyses revealed that prickles of R. multiflora were non-glandular prickles (NGPs) and their maturation went through five developmental stages, which was accompanied by the accumulation of secondary metabolites such as lignin and anthocyanins. Comparative transcriptome analysis identified key pathways and hub genes potentially involved in prickle formation. Interestingly, among the differentially expressed genes (DEGs), several notable development and secondary metabolism-related transcription factors (TFs) including NAC, TCP, MYB, homeobox, and WRKY were up-regulated in prickly internodes. KEGG enrichment analysis indicated that DEGs were enriched in the pathways related to biosynthesis of secondary metabolites, flavonoids, and phenylpropanoids in the prickly R. multiflora. Our study provides novel insights into the molecular network underlying the regulation of prickle morphogenesis in R. multiflora, and the identified candidates might be applied to the genetic improvement of roses.

Molecular research progress and improvement approach of fruit quality traits in cucumber

Recent molecular studies revealed new opportunities to improve cucumber fruit quality. However, the fruit color and spine traits molecular basis remain vague despite the vast sources of genetic diversity. Cucumber is agriculturally, economically and nutritionally important vegetable crop. China produces three-fourths of the world's total cucumber production. Cucumber fruit quality depends on a number of traits such as the fruit color (peel and flesh color), spine (density, size and color), fruit shape, fruit size, defects, texture, firmness, taste, maturity stage and nutritional composition. Fruit color and spine traits determine critical quality attributes and have been the interest of researchers at the molecular level. Evaluating the molecular mechanisms of fruit quality traits is important to improve production and quality of cucumber varieties. Genes and qualitative trait locus (QTL) that are responsible for cucumber fruit color and fruit spine have been identified. The purpose of this paper is to reveal the molecular research progress of fruit color and spines as key quality traits of cucumber. The markers and genes identified so far could help for marker-assisted selection of the fruit color and spine trait in cucumber breeding and its associated nutritional improvement. Based on the previous studies, peel color and spine density as examples, we proposed a comprehensive approach for cucumber fruit quality traits improvement. Moreover, the markers and genes can be useful to facilitate cloning-mediated genetic breeding in cucumber. However, in the era of climate change, increased human population and high-quality demand of consumers, studies on molecular mechanisms of cucumber fruit quality traits are limited.

Comparative genomic analysis of MYB transcription factors for cuticular wax biosynthesis and drought stress tolerance in Helianthus annuus L

Sunflower is an important oil-seed crop in Pakistan, it is mainly cultivated in the spring season. It is severely affected by drought stress resulting in lower yield. Cuticular wax acts as the first defense line to protect plants from drought stress condition. It seals the aerial parts of plants and reduce the water loss from leaf surfaces. Various myeloblastosis (MYB) transcription factors (TFs) are involved in biosynthesis of epicuticular waxes under drought-stress. However, less information is available for MYB, TFs in drought stress and wax biosynthesis in sunflower. We used different computational tools to compare the Arabidopsis MYB, TFs involved in cuticular wax biosynthesis and drought stress tolerance with sunflower genome. We identified three putative MYB genes (MYB16, MYB94 and MYB96) in sunflower along with their seven homologs in Arabidopsis. Phylogenetic association of MYB TFs in Arabidopsis and sunflower indicated strong conservation of TFs in plant species. From gene structure analysis, it was observed that intron and exon organization was family-specific. MYB TFs were unevenly distributed on sunflower chromosomes. Evolutionary analysis indicated the segmental duplication of the MYB gene family in sunflower. Quantitative Real-Time PCR revealed the up-regulation of three MYB genes under drought stress. The gene expression of MYB16, MYB94 and MYB96 were found many folds higher in experimental plants than control. The present study provided the first insight into MYB TFs family's characterization in sunflower under drought stress conditions and wax biosynthesis TFs.

Transcriptome profiling reveals key genes in regulation of the tepal trichome development in Lilium pumilum D.C

A number of potential genes and pathways involved in tepal trichome development were identified in a natural lily mutant by transcriptome analysis and were confirmed with trichome and trichomeless species. Trichome is a specialized structure found on the surface of the plant with an important function in survival against abiotic and biotic stress. It is also an important economic trait in crop breeding. Extensive research has investigated the foliar trichome in model plants (Arabidopsis and tomato). However, the developmental mechanism of tepal trichome remains elusive. Lilium pumilum is an edible ornamental bulb and a good breeding parent possessing cold and salt-alkali resistance. Here, we found a natural mutant of Lilium pumilum grown on a highland whose tepals are covered by trichomes. Our data indicate that trichomes of the mutant are multicellular and branchless. Notably, stomata are also developed on the tepal of the mutant as well, suggesting there may be a correlation between trichome and stomata regulation. Furthermore, we isolated 27 differentially expressed genes (DEGs) by comparing the transcriptome profiling between the natural mutant and the wild type. These 27 genes belong to 4 groups: epidermal cell cycle and division, trichome morphogenesis, stress response, and transcription factors. Quantitative real-time PCR in Lilium pumilum (natural mutant and the wild type) and other lily species (Lilium leichtlinii var. maximowiczii/trichome; Lilium davidii var. willmottiae/, trichomeless) confirmed the validation of RNA-seq data and identified several trichome-related genes.

Organic nitrogen nutrition: LHT1.2 protein from hybrid aspen (Populus tremula L. x tremuloides Michx) is a functional amino acid transporter and a homolog of Arabidopsis LHT1

The contribution of amino acids (AAs) to soil nitrogen (N) fluxes is higher than previously thought. The fact that AA uptake is pivotal for N nutrition in boreal ecosystems highlights plant AA transporters as key components of the N cycle. At the same time, very little is known about AA transport and respective transporters in trees. Tree genomes may contain 13 or more genes encoding the lysine histidine transporter (LHT) family proteins, and this complicates the study of their significance for tree N-use efficiency. With the strategy of obtaining a tool to study N-use efficiency, our aim was to identify and characterize a relevant AA transporter in hybrid aspen (Populus tremula L. x tremuloides Michx.). We identified PtrLHT1.2, the closest homolog of Arabidopsis thaliana (L.) Heynh AtLHT1, which is expressed in leaves, stems and roots. Complementation of a yeast AA uptake mutant verified the function of PtrLHT1.2 as an AA transporter. Furthermore, PtrLHT1.2 was able to fully complement the phenotypes of the Arabidopsis AA uptake mutant lht1 aap5, including early leaf senescence-like phenotype, reduced growth, decreased plant N levels and reduced root AA uptake. Amino acid uptake studies finally showed that PtrLHT1.2 is a high affinity transporter for neutral and acidic AAs. Thus, we identified a functional AtLHT1 homolog in hybrid aspen, which harbors the potential to enhance overall plant N levels and hence increase biomass production. This finding provides a valuable tool for N nutrition studies in trees and opens new avenues to optimizing tree N-use efficiency.

VvMYB114 mediated by miR828 negatively regulates trichome development of Arabidopsis

Trichome is a specialized structure differentiated during the morphogenesis of plant leaf epidermal cells. In recent years, with the continuous researches on trichome development of Arabidopsis and other plants, more and more genes related to trichome morphogenesis have been discovered, including R2R3-type MYB genes. In this study, we cloned a R2R3-type MYB family gene from grape, VvMYB114, a target gene of vvi-miR828. qRT-PCR showed that VvMYB114 mRNA accumulated during grape fruit ripening, and VvMYB114 protein had transcriptional activation activity. Heterologous overexpression of VvMYB114 in Arabidopsis reduced the number of trichome on leaves and stems. Mutating the miR828-binding site in VvMYB114 without altering amino-acid sequence had no effect on trichome development in Arabidopsis. The results showed a different role of the regulation of miR828 to VvMYB114 in Arabidopsis from in grape, which indicated the functional divergence of miRNA targeting homoeologous genes in different species played an important roles in evolution and useful trait selection.

Effect of gene mutation of plants on their mechano-sensibility: the mutant of EXO70H4 influences the buckling of Arabidopsis trichomes

With the development of molecular biology, more and more mutants of plants have been constructed, where gene mutants have been found to influence not only the biological processes but also biophysical behaviors of plant cells. Trichomes are an important appendage, which has been found to act as an active mechanosensory switch transducing mechanical signals into physiology changes, where the mechanical property of trichomes is vital for such functions. Up to now, over 40 different genes have been found with the function of regulating trichome cell morphogenesis; however, the effect of gene mutants on trichome mechanosensory function remains elusive. In this study, we found that EXO70H4, one of the most up-regulated genes in the mature trichome, not only affects the thickness of the trichome cell wall but also the mechanical property (i.e., the Young's modulus) of trichomes. Finite element method simulation results show that the buckling instability and stress concentration (e.g., exerted by insects) cannot occur on the base of the mutant exo70H4 trichome, which might further interrupt the mechanical signal transduction from branches to the base of trichomes. These results indicated that the mutant exo70H4 trichome might lack the ability to act as an active mechanosensory switch against chewing insect herbivores. Our findings provide new information about the effect of gene mutation (like crop mutants) on the mechano-sensibility and capability to resist the agricultural pests or lodging, which could be of great significance to the development of agriculture.

A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae)

The karst environment is characterized by low soil water content, periodic water deficiency, and poor nutrient availability, which provides an ideal natural laboratory for studying the adaptive evolution of its inhabitants. However, how species adapt to such a special karst environment remains poorly understood. Here, transcriptome sequences of two Urophysa species (Urophysa rockii and Urophysa henryi), which are Chinese endemics with karst-specific distribution, and allied species in Semiaquilegia and Aquilegia (living in non-karst habitat) were collected. Single-copy genes (SCGs) were extracted to perform the phylogenetic analysis using concatenation and coalescent methods. Positively selected genes (PSGs) and clusters of paralogous genes (Mul_genes) were detected and subsequently used to conduct gene function annotation. We filtered 2,271 SCGs and the coalescent analysis revealed that 1,930 SCGs shared the same tree topology, which was consistent with the topology detected from the concatenated tree. Total of 335 PSGs and 243 Mul_genes were detected, and many were enriched in stress and stimulus resistance, transmembrane transport, cellular ion homeostasis, calcium ion transport, calcium signaling regulation, and water retention. Both molecular and morphological evidences indicated that Urophysa species evolved complex strategies for adapting to hostile karst environments. Our findings will contribute to a new understanding of genetic and phenotypic adaptive mechanisms of karst adaptation in plants.

MYB106 is a negative regulator and a substrate for CRL3BPM E3 ligase in regulating flowering time in Arabidopsis thaliana

Flowering time is crucial for successful reproduction in plants, the onset and progression of which are strictly controlled. However, flowering time is a complex and environmentally responsive history trait and the underlying mechanisms still need to be fully characterized. Post-translational regulation of the activities of transcription factors (TFs) is a dynamic and essential mechanism for plant growth and development. CRL3^BPM E3 ligase is a CULLIN3-based E3 ligase involved in orchestrating protein stability via the ubiquitin proteasome pathway. Our study shows that the mutation of MYB106 induced early flowering phenotype while over-expression of MYB106 delayed Arabidopsis flowering. Transcriptome analysis of myb106 mutants reveals 257 differentially expressed genes between wild type and myb106-1 mutants, including Flowering Locus T (FT) which is related to flowering time. Moreover, in vitro electrophoretic mobility shift assays (EMSA), in vivo chromatin immunoprecipitation quantitative polymerase chain reaction (ChIP-qPCR) assays and dual luciferase assays demonstrate that MYB106 directly binds to the promoter of FT to suppress its expression. Furthermore, we confirm that MYB106 interacts with BPM proteins which are further identified by CRL3^BPM E3 ligases as the substrate. Taken together, we have identified MYB106 as a negative regulator in the control of flowering time and a new substrate for CRL3^BPM E3 ligases in Arabidopsis.

Gene expression underlying floral epidermal specialization in Aristolochia fimbriata (Aristolochiaceae)

BACKGROUND AND AIMS

The epidermis constitutes the outermost tissue of the plant body. Although it plays major structural, physiological and ecological roles in embryophytes, the molecular mechanisms controlling epidermal cell fate, differentiation and trichome development have been scarcely studied across angiosperms, and remain almost unexplored in floral organs.

METHODS

In this study, we assess the spatio-temporal expression patterns of GL2, GL3, TTG1, TRY, MYB5, MYB6, HDG2, MYB106-like, WIN1 and RAV1-like homologues in the magnoliid Aristolochia fimbriata (Aristolochiaceae) by using comparative RNA-sequencing and in situ hybridization assays.

KEY RESULTS

Genes involved in Aristolochia fimbriata trichome development vary depending on the organ where they are formed. Stem, leaf and pedicel trichomes recruit most of the transcription factors (TFs) described above. Conversely, floral trichomes only use a small subset of genes including AfimGL2, AfimRAV1-like, AfimWIN1, AfimMYB106-like and AfimHDG2. The remaining TFs, AfimTTG1, AfimGL3, AfimTRY, AfimMYB5 and AfimMYB6, are restricted to the abaxial (outer) and the adaxial (inner) pavement epidermal cells.

CONCLUSIONS

We re-evaluate the core genetic network shaping trichome fate in flowers of an early-divergent angiosperm lineage and show a morphologically diverse output with a simpler genetic mechanism in place when compared to the models Arabidopsis thaliana and Cucumis sativus. In turn, our results strongly suggest that the canonical trichome gene expression appears to be more conserved in vegetative than in floral tissues across angiosperms.

MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.