The cotton transcription factor TCP14 functions in auxin-mediated epidermal cell differentiation and elongation

RNA-Seq analysis unveils gene regulation of fruit size cooperatively determined by velocity and duration of fruit swelling in peach

Fruit swelling determines fruit size and usually occurs in two distinct time periods in peach. However, little is known about the gene regulation of fruit swelling. In this study, measurements of longitudinal and transverse diameters in developing and ripening peach fruits unveiled two periods of fruit swelling: the first swelling ends at approximately 65 days after flower blooming (DAFB) and the second swelling starts at approximately 75 DAFB. Comparisons of diameters sizes and development periods among cultivars and accessions revealed a cooperative regulation of swelling velocity and swelling duration, which leads to final determination of fruit size. Furthermore, RNA-sequencing was conducted for fruits at the initial swelling, non-swelling interval between the two swellings (hereafter, 'the interval'), second swelling and ripening stages. A total of 110 and 128 differentially expressed genes were screened from fruits in the first and second swelling, respectively. Besides, the nine most differentially expressed genes located within the reported quantitative trait locations (QTLs) of fruit size in peach were detected in both the first and second swelling stages. Those genes have been reported to be involved in mediating cell size, which indicates the occurrence of both cell proliferation and cell expansion in each of the two major periods of fruit swelling. In addition, a potential gene regulation network is proposed herein and could be used to elucidate the molecular mechanism of peach fruit swellings mediated by multiple key genes.

Transcriptome analysis of the genes regulating phytohormone and cellular patterning in Lagerstroemia plant architecture

Plant architecture is a popular research topic because plants with different growth habits that may generate economic or ornamental value are in great demand by orchards and nurseries. However, the molecular basis of the architecture of woody perennial plants is poorly understood due to the complexity of the phenotypic and regulatory relationships. Here, transcriptional profiling of dwarf and non-dwarf crapemyrtles was performed, and potential target genes were identified based on the phenotype, histology and phytohormone metabolite levels. An integrated analysis demonstrated that the internode length was explained mainly by cell number and secondarily by cell length and revealed important hormones in regulatory pathway of Lagerstroemia architecture. Differentially expressed genes (DEGs) involved in phytohormone pathways and cellular patterning regulation were analysed, and the regulatory relationships between these parameters were evaluated at the transcriptional level. Exogenous indole-3-acetic acid (IAA) and gibberellin A₄ (GA₄) treatments further indicated the pivotal role of auxin in cell division within the shoot apical meristem (SAM) and suggested an interaction between auxin and GA₄ in regulating the internode length of Lagerstroemia. These results provide insights for further functional genomic studies on the regulatory mechanisms underlying Lagerstroemia plant architecture and may improve the efficiency of woody plant molecular breeding.

Comparative transcriptome study of hairy and hairless tea plant (Camellia sinensis) shoots

Trichome (also referred to as 'háo' in tea) is a key feature in both tea products and tea plant (Camellia sinensis) selection breeding. Although trichomes are used as a model for studying cell differentiation and have been well studied in many plant species, the regulation of trichome formation at the molecular level is poorly understood in tea plants. In the present study, the hairy and hairless tea plant cultivars Fudingdabaicha (FDDB) and Rongchunzao (RCZ), respectively, were used to study this mechanism. We characterised tea plant trichomes as unicellular and unbranched structures. High-throughput Illumina sequencing yielded approximately 277.0 million high-quality clean reads from the FDDB and RCZ cultivars. After de novo assembly, 161,444 unigenes were generated, with an average length of 937 bp. Among these unigenes, 81,425 were annotated using public databases, and 55,201 coding sequences and 4004 transcription factors (TFs) were identified. In total, 21,599 differentially expressed genes (DEGs) were identified between RCZ and FDDB, of which 10,785 DEGs were up-regulated and 10,814 DEGs were down-regulated. Genes involved in the DNA replication pathway were significantly enriched. Furthermore, between FDDB and RCZ, DEGs related to TFs, phytohormone signals, and cellulose synthesis were identified, suggesting that certain genes involved in these pathways are crucial for trichome initiation in tea plants. Together, the results of this study provide novel data to improve our understanding of the potential molecular mechanisms of trichome formation and lay a foundation for additional trichome studies in tea plants.

Genome-wide identification and expression analyses of TCP transcription factor genes in Gossypium barbadense

Sea-island cotton (Gossypium barbadense) has drawn great attention in the textile industry for its comprehensive resistance and superior fiber properties. However, the mechanisms involved in fiber growth and development are unclear. As TCP transcription factors play important roles in plant growth and development, this study investigated the TCP family genes in G. barbadense (GbTCP). We identified 75 GbTCP genes, of which 68 had no introns. Phylogenetic analyses categorized the GbTCP transcription factors into 11 groups. Genomic analyses showed that 66 genes are located on 21 chromosomes. Phylogenetic analyses of G. arboreum, G. raimondii, G. hirsutum, G. barbadense, Theobroma cacao, Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, and Zea mays, Picea abies, Sphagnum fallax and Physcomitrella patens, categorized 373 TCP genes into two classes (Classes I and II). By studying the structures of TCP genes in sea-island cotton, we identified genes from the same evolutionary branches that showed similar motif patterns. qRT-PCR results suggested that the GbTCPs had different expression patterns in fibers at various developmental stages of cotton, with several showing specific expression patterns during development. This report helps lay the foundation for future investigations of TCP functions and molecular mechanisms in sea-island cotton fiber development.

The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana

Trichomes are the first cell type to be differentiated during the morphogenesis of leaf epidermis and serve as an ideal model to study cellular differentiation. Many genes involved in the patterning and differentiation of trichome cells have been studied over the past decades, and the majority of these genes encode transcription factors that specifically regulate epidermal cell development. However, the upstream regulators of these genes that link early leaf morphogenesis with cell type differentiation are less studied. The TCP proteins are the plant-specific transcription factors involved in regulating diverse aspects of plant development including lateral organ morphogenesis by modulating cell proliferation and differentiation. Here, we show that the miR319-regulated class II TCP proteins, notably TCP4, suppress trichome branching in Arabidopsis leaves and inflorescence stem by direct transcriptional activation of GLABROUS INFLORESCENCE STEMS (GIS), a known negative regulator of trichome branching. The trichome branch number is increased in plants with reduced TCP activity and decreased in the gain-of-function lines of TCP4. Biochemical analyses show that TCP4 binds to the upstream regulatory region of GIS and activates its expression. Detailed genetic analyses show that GIS and TCP4 work in same pathway and GIS function is required for TCP4-mediated regulation of trichome differentiation. Taken together, these results identify a role for the class II TCP genes in trichome differentiation, thus providing a connection between organ morphogenesis and cellular differentiation.

Hairy Leaf 6, an AP2/ERF Transcription Factor, Interacts with OsWOX3B and Regulates Trichome Formation in Rice

Trichome formation has been extensively studied as a mechanistic model for epidermal cell differentiation and cell morphogenesis in plants. However, the genetic and molecular mechanisms underlying trichome formation (i.e., initiation and elongation) in rice remain largely unclear. Here, we report an AP2/ERF transcription factor, Hairy Leaf 6 (HL6), which controls trichome formation in rice. Functional analyses revealed that HL6 transcriptionally regulates trichome elongation in rice, which is dependent on functional OsWOX3B, a homeodomain-containing protein that acts as a key regulator in trichome initiation. Biochemical and molecular genetic analyses demonstrated that HL6 physically interacts with OsWOX3B, and both of them regulate the expression of some auxin-related genes during trichome formation, in which OsWOX3B likely enhances the binding ability of HL6 with one of its direct target gene, OsYUCCA5. Population genetic analysis indicated that HL6 was under negative selection during rice domestication. Taken together, our findings provide new insights into the molecular regulatory network of trichome formation in rice.

Genome-wide identification and characterization of TCP transcription factor genes in upland cotton (Gossypium hirsutum)

TCP proteins are plant-specific transcription factors (TFs), and perform a variety of physiological functions in plant growth and development. In this study, 74 non-redundant TCP genes were identified in upland cotton (Gossypium hirsutum L.) genome. Cotton TCP family can be classified into two classes (class I and class II) that can be further divided into 11 types (groups) based on their motif composition. Quantitative RT-PCR analysis indicated that GhTCPs display different expression patterns in cotton tissues. The majority of these genes are preferentially or specifically expressed in cotton leaves, while some GhTCP genes are highly expressed in initiating fibers and/or elongating fibers of cotton. Yeast two-hybrid results indicated that GhTCPs can interact with each other to form homodimers or heterodimers. In addition, GhTCP14a and GhTCP22 can interact with some transcription factors which are involved in fiber development. These results lay solid foundation for further study on the functions of TCP genes during cotton fiber development.

The heterologous expression of a chrysanthemum TCP-P transcription factor CmTCP14 suppresses organ size and delays senescence in Arabidopsis thaliana

TCP transcription factors are important for plant growth and development, but their activity in chrysanthemum (Chrysanthemum morifolium) has not been thoroughly explored. Here, a chrysanthemum TCP-P sequence, which encodes a protein harboring the conserved basic helix-loop-helix (bHLH) motif, was shown to be related phylogenetically to the Arabidopsis thaliana gene AtTCP14. A yeast-one hybrid assay showed that the encoding protein had no transcriptional activation ability, and a localization experiment indicated that it was localized in the nucleus. Transcription profiling established that the gene was most active in the stem and leaf. Its heterologous expression in A. thaliana down-regulated certain cell cycle-related genes, reduced the size of various organs and increased the chlorophyll and carotenoid contents of the leaf which led to delayed senescence and a prolonged flowering period. Moreover, by screening the cDNA library of chrysanthemum, we found that the CmTCP14 can interact with CmFTL2 and some CmDELLAs.

PIN-formed protein, a door to reveal the mechanism for auxin-triggered initiation of cotton fiber

Cotton fibers are differentiated ovule epidermal cells that provide an ideal model to study cell differentiation and elongation. Establishment of auxin maximum in fiber cells is crucial for cotton-fiber protrusion from ovule surface. However, it is unclear where the auxin originates from and how the auxin accumulates in fiber cells. Our recent results indicate that the auxin is mainly imported from the outside of ovules, and transported to fiber cells through GhPIN (homolog of PIN-formed proteins in cotton) -mediated polar auxin transport, rather than in situ synthesis. Based on our finding in GhPINs, we discuss here briefly how auxin flow to fiber cells and auxin gradient in ovule epidermis is established mainly by GhPIN3a protein.

Evolving Tale of TCPs: New Paradigms and Old Lacunae

Teosinte Branched1/Cycloidea/Proliferating cell factors (TCP) genes are key mediators of genetic innovations underlying morphological novelties, stress adaptation, and evolution of immune response in plants. They have a remarkable ability to integrate and translate diverse endogenous, and environmental signals with high fidelity. Compilation of studies, aimed at elucidating the mechanism of TCP functions, shows that it takes an amalgamation and interplay of several different factors, regulatory processes and pathways, instead of individual components, to achieve the incredible functional diversity and specificity, demonstrated by TCP proteins. Through this minireview, we provide a brief description of key structural features and molecular components, known so far, that operate this conglomerate, and highlight the important conceptual challenges and lacunae in TCP research.

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

Background

Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.

Results

We resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species. Phylogenetic analysis shows two divergent groups for G. hirsutum and G. barbadense, suggesting a dual domestication processes in tetraploid cottons. In spite of the strong genetic divergence, a small number of interspecific reciprocal introgression events are found between these species and the introgression pattern is significantly biased towards the gene flow from G. hirsutum into G. barbadense. We identify selective sweeps, some of which are associated with relatively highly expressed genes for fiber development and seed germination.

Conclusions

We report a comprehensive analysis of the evolution and domestication history of allotetraploid cottons based on the whole genomic variation between G. hirsutum and G. barbadense and between wild accessions and modern cultivars. These results provide genomic bases for improving cotton production and for further evolution analysis of polyploid crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1167-5) contains supplementary material, which is available to authorized users.

Auxin Regulates Cotton Fiber Initiation via GhPIN-Mediated Auxin Transport

Cotton fibers are seed trichomes that make cotton unique compared with other plants. At anthesis, IAA, a major auxin in plants, accumulates in the fiber cell to promote cell initiation. However, many important aspects of this process are not clear. Here, auxin distribution patterns indicated by auxin-dependent DR5::GUS (β-glucuronidase) expression in cotton ovules were studied during fiber cell differentiation and cell initiation [-2 to 2 DPA (days post-anthesis)]. The nucellus and fiber cell were two major sites where auxin accumulates. The accumulation in the nucellus started from -1 DPA, and that in fiber cells from 0 DPA. Immunolocalization analysis further suggests that the IAA accumulation in fiber initials began before flower opening. Furthermore, we demonstrate that accumulated IAA in fiber initials was mainly from efflux transport and not from in situ synthesis. Eleven auxin efflux carrier (GhPIN) genes were identified, and their expression during ovule and fiber development was investigated. Ovule-specific suppression of multiple GhPIN genes in transgenic cotton inhibited both fiber initiation and elongation. In 0 DPA ovules, GhPIN3a, unlike other GhPIN genes, showed additional localization of the transcript in the outer integument. Collectively, these results demonstrate the important role of GhPIN-mediated auxin transport in fiber-specific auxin accumulation for fiber initiation.

Genome-Wide Identification and Characterization of BrrTCP Transcription Factors in Brassica rapa ssp. rapa

The teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family is a plant-specific transcription factor that participates in the control of plant development by regulating cell proliferation. However, no report is currently available about this gene family in turnips (Brassica rapa ssp. rapa). In this study, a genome-wide analysis of TCP genes was performed in turnips. Thirty-nine TCP genes in turnip genome were identified and distributed on 10 chromosomes. Phylogenetic analysis clearly showed that the family was classified as two clades: class I and class II. Gene structure and conserved motif analysis showed that the same clade genes have similar gene structures and conserved motifs. The expression profiles of 39 TCP genes were determined through quantitative real-time PCR. Most CIN-type BrrTCP genes were highly expressed in leaf. The members of CYC/TB1 subclade are highly expressed in flower bud and weakly expressed in root. By contrast, class I clade showed more widespread but less tissue-specific expression patterns. Yeast two-hybrid data show that BrrTCP proteins preferentially formed heterodimers. The function of BrrTCP2 was confirmed through ectopic expression of BrrTCP2 in wild-type and loss-of-function ortholog mutant of Arabidopsis. Overexpression of BrrTCP2 in wild-type Arabidopsis resulted in the diminished leaf size. Overexpression of BrrTCP2 in triple mutants of tcp2/4/10 restored the leaf phenotype of tcp2/4/10 to the phenotype of wild type. The comprehensive analysis of turnip TCP gene family provided the foundation to further study the roles of TCP genes in turnips.

Genome-wide identification and characterization of TCP genes involved in ovule development of Phalaenopsis equestris

TEOSINTE-BRANCHED/CYCLOIDEA/PCF (TCP) proteins are plant-specific transcription factors known to have a role in multiple aspects of plant growth and development at the cellular, organ and tissue levels. However, there has been no related study of TCPs in orchids. Here we identified 23 TCP genes from the genome sequence of Phalaenopsis equestris Phylogenetic analysis distinguished two homology classes of PeTCP transcription factor families: classes I and II. Class II was further divided into two subclasses, CIN and CYC/TB1. Spatial and temporal expression analysis showed that PePCF10 was predominantly expressed in ovules at early developmental stages and PeCIN8 had high expression at late developmental stages in ovules, with overlapping expression at day 16 after pollination. Subcellular localization and protein-protein interaction analyses revealed that PePCF10 and PeCIN8 could form homodimers and localize in the nucleus. However, PePCF10 and PeCIN8 could not form heterodimers. In transgenic Arabidopsis thaliana plants (overexpression and SRDX, a super repression motif derived from the EAR-motif of the repression domain of tobacco ETHYLENE-RESPONSIVE ELEMENT-BINDING FACTOR 3 and SUPERMAN, dominantly repressed), the two genes helped regulate cell proliferation. Together, these results suggest that PePCF10 and PeCIN8 play important roles in orchid ovule development by modulating cell division.

Apoplastic H2 O2 plays a critical role in axillary bud outgrowth by altering auxin and cytokinin homeostasis in tomato plants

Although phytohormones such as indole-3-acetic acid (IAA), cytokinin (CK) and strigolactone are important modulators of plant architecture, it remains unclear whether reactive oxygen species are involved in the regulation of phytohormone-dependent axillary bud outgrowth in plants. We used diverse techniques, including transcriptional suppression, HPLC-MS, biochemical methodologies and gene transcript analysis to investigate the signaling pathway for apoplastic hydrogen peroxide (H2 O2 )-induced axillary bud outgrowth. Silencing of tomato RESPIRATORY BURST OXIDASE HOMOLOG 1 (RBOH1) and WHITEFLY INDUCED 1 (WFI1), two important genes involved in H2 O2 production in the apoplast, enhanced bud outgrowth, decreased transcript of FZY - a rate-limiting gene in IAA biosynthesis and IAA accumulation in the apex - and increased the transcript of IPT2 involved in CK biosynthesis and CK accumulation in the stem node. These effects were fully abolished by the application of exogenous H2 O2 . Both decapitation and the silencing of FZY promoted bud outgrowth, and downregulated and upregulated the transcripts for IAA3 and IAA15, and IPT2, respectively. However, these effects were not blocked by treatment with exogenous H2 O2 but by napthaleneacetic acid (NAA) treatment. These results suggest that RBOHs-dependent apoplastic H2 O2 promotes IAA biosynthesis in the apex, which, in turn, inhibits CK biosynthesis and subsequent bud outgrowth in tomato plants.

Phytoplasma SAP11 alters 3-isobutyl-2-methoxypyrazine biosynthesis in Nicotiana benthamiana by suppressing NbOMT1

Phytoplasmas are bacterial phytopathogens that release virulence effectors into sieve cells and act systemically to affect the physiological and morphological state of host plants to promote successful pathogenesis. We show here that transgenic Nicotiana benthamiana lines expressing the secreted effector SAP11 from Candidatus Phytoplasma mali exhibit an altered aroma phenotype. This phenomenon is correlated with defects in the development of glandular trichomes and the biosynthesis of 3-isobutyl-2-methoxypyrazine (IBMP). IBMP is a volatile organic compound (VOC) synthesized by an O-methyltransferase, via a methylation step, from a non-volatile precursor, 3-isobutyl-2-hydroxypyrazine (IBHP). Based on comparative and functional genomics analyses, NbOMT1, which encodes an O-methyltransferase, was found to be highly suppressed in SAP11-transgenic plants. We further silenced NbOMT1 through virus-induced gene silencing and demonstrated that this enzyme influenced the accumulation of IBMP in N. benthamiana In vitro biochemical analyses also showed that NbOMT1 can catalyse IBHP O-methylation in the presence of S-adenosyl-L-methionine. Our study suggests that the phytoplasma effector SAP11 has the ability to modulate host VOC emissions. In addition, we also demonstrated that SAP11 destabilized TCP transcription factors and suppressed jasmonic acid responses in N. benthamiana These findings provide valuable insights into understanding how phytoplasma effectors influence plant volatiles.

Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses

Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.

Comprehensive analysis of TCP transcription factors and their expression during cotton (Gossypium arboreum) fiber early development

TCP proteins are plant-specific transcription factors implicated to perform a variety of physiological functions during plant growth and development. In the current study, we performed for the first time the comprehensive analysis of TCP gene family in a diploid cotton species, Gossypium arboreum, including phylogenetic analysis, chromosome location, gene duplication status, gene structure and conserved motif analysis, as well as expression profiles in fiber at different developmental stages. Our results showed that G. arboreum contains 36 TCP genes, distributing across all of the thirteen chromosomes. GaTCPs within the same subclade of the phylogenetic tree shared similar exon/intron organization and motif composition. In addition, both segmental duplication and whole-genome duplication contributed significantly to the expansion of GaTCPs. Many these TCP transcription factor genes are specifically expressed in cotton fiber during different developmental stages, including cotton fiber initiation and early development. This suggests that TCP genes may play important roles in cotton fiber development.

Transposable elements play an important role during cotton genome evolution and fiber cell development

Transposable elements (TEs) usually occupy largest fractions of plant genome and are also the most variable part of the structure. Although traditionally it is hallmarked as "junk and selfish DNA", today more and more evidence points out TE's participation in gene regulations including gene mutation, duplication, movement and novel gene creation via genetic and epigenetic mechanisms. The recently sequenced genomes of diploid cottons Gossypium arboreum (AA) and Gossypium raimondii (DD) together with their allotetraploid progeny Gossypium hirsutum (AtAtDtDt) provides a unique opportunity to compare genome variations in the Gossypium genus and to analyze the functions of TEs during its evolution. TEs accounted for 57%, 68.5% and 67.2%, respectively in DD, AA and AtAtDtDt genomes. The 1,694 Mb A-genome was found to harbor more LTR(long terminal repeat)-type retrotransposons that made cardinal contributions to the twofold increase in its genome size after evolution from the 775.2 Mb D-genome. Although the 2,173 Mb AtAtDtDt genome showed similar TE content to the A-genome, the total numbers of LTR-gypsy and LTR-copia type TEs varied significantly between these two genomes. Considering their roles on rewiring gene regulatory networks, we believe that TEs may somehow be involved in cotton fiber cell development. Indeed, the insertion or deletion of different TEs in the upstream region of two important transcription factor genes in At or Dt subgenomes resulted in qualitative differences in target gene expression. We suggest that our findings may open a window for improving cotton agronomic traits by editing TE activities.

AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering

There is a longstanding problem of an inverse relationship between cotton fiber qualities versus high yields. To better understand drought stress signaling and adaptation in cotton (Gossypium hirsutum) fiber development, we expressed the Arabidopsis transcription factors RELATED_TO_ABA-INSENSITIVE3/VIVIPAROUS1/(RAV1) and AtRAV2, which encode APETALA2-Basic3 domain proteins shown to repress transcription of FLOWERING_LOCUS_T (FT) and to promote stomatal opening cell-autonomously. In three years of field trials, we show that AtRAV1 and AtRAV2-overexpressing cotton had ∼5% significantly longer fibers with only marginal decreases in yields under well-watered or drought stress conditions that resulted in 40-60% yield penalties and 3-7% fiber length penalties in control plants. The longer transgenic fibers from drought-stressed transgenics could be spun into yarn which was measurably stronger and more uniform than that from well-watered control fibers. The transgenic AtRAV1 and AtRAV2 lines flowered later and retained bolls at higher nodes, which correlated with repression of endogenous GhFT-Like (FTL) transcript accumulation. Elevated expression early in development of ovules was observed for GhRAV2L, GhMYB25-Like (MYB25L) involved in fiber initiation, and GhMYB2 and GhMYB25 involved in fiber elongation. Altered expression of RAVs controlling critical nodes in developmental and environmental signaling hierarchies has the potential for phenotypic modification of crops.

Expression of Brassica napus TTG2, a regulator of trichome development, increases plant sensitivity to salt stress by suppressing the expression of auxin biosynthesis genes

WRKY transcription factors (TFs) are plant specific and play important roles in regulating diverse biological processes. To identify TFs with broad-spectrum effects on various stress responses in Brassica napus, an important oil crop grown across diverse ecological regions worldwide, we functionally characterized Bna.TTG2 genes, which are homologous to the Arabidopsis AtTTG2 (WRKY44) gene. Four Bna.TTG2 genes were capable of rescuing the trichome phenotypes of Arabidopsis ttg2 mutants. Overexpressing one Bna.TTG2 family member, BnaA.TTG2.a.1, remarkably increased trichome numbers in Arabidopsis and B. napus plants. Interestingly, the BnaA.TTG2.a.1-overexpressing plants of both species exhibited increased sensitivity to salt stress. In BnaA.TTG2.a.1-overexpressing Arabidopsis under salt stress, the endogenous indole-3-acetic acid (IAA) content was reduced, and the expression of two auxin biosynthesis genes, TRYPTOPHAN BIOSYNTHESIS 5 (TRP5) and YUCCA2 (YUC2), was downregulated. The results from yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase reporter assays revealed that BnaA.TTG2.a.1 is able to bind to the promoters of TRP5 and YUC2. These data indicated that BnaA.TTG2.a.1 confers salt sensitivity to overexpressing plants by suppressing the expression of IAA synthesis genes and thus lowering IAA levels. Transgenic Arabidopsis plants with an N-terminus-deleted BnaA.TTG2.a.1 no longer showed hypersensitivity to salt stress, suggesting that the N terminus of BnaA.TTG2.a.1 plays a critical role in salt stress responses. Therefore, in addition to its classical function in trichome development, our study reveals a novel role for Bna.TTG2 genes in salt stress responses.

Mapping-by-sequencing of Ligon-lintless-1 (Li 1 ) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.)

Mapping-by-sequencing and SNP marker analysis were used to fine map the Ligon-lintless-1 ( Li 1 ) short fiber mutation in tetraploid cotton to a 255-kb region that contains 16 annotated proteins. The Ligon-lintless-1 (Li 1 ) mutant of cotton (Gossypium hirsutum L.) has been studied as a model for cotton fiber development since its identification in 1929; however, the causative mutation has not been identified yet. Here we report the fine genetic mapping of the mutation to a 255-kb region that contains only 16 annotated genes in the reference Gossypium raimondii genome. We took advantage of the incompletely dominant dwarf vegetative phenotype to identify 100 mutants (Li 1 /Li 1 ) and 100 wild-type (li 1 /li 1 ) homozygotes from a mapping population of 2567 F2 plants, which we bulked and deep sequenced. Since only homozygotes were sequenced, we were able to use a high stringency in SNP calling to rapidly narrow down the region harboring the Li 1 locus, and designed subgenome-specific SNP markers to test the population. We characterized the expression of all sixteen genes in the region by RNA sequencing of elongating fibers and by RT-qPCR at seven time points spanning fiber development. One of the most highly expressed genes found in this interval in wild-type fiber cells is 40-fold under-expressed at the day of anthesis (DOA) in the mutant fiber cells.  This gene is a major facilitator superfamily protein, part of the large family of proteins that includes auxin and sugar transporters. Interestingly, nearly all genes in this region were most highly expressed at DOA and showed a high degree of co-expression. Further characterization is required to determine if transport of hormones or carbohydrates is involved in both the dwarf and lintless phenotypes of Li 1 plants.

GmWRKY27 interacts with GmMYB174 to reduce expression of GmNAC29 for stress tolerance in soybean plants

Soybean (Glycine max) is an important crop for oil and protein resources worldwide. The molecular mechanism of the abiotic stress response in soybean is largely unclear. We previously identified multiple stress-responsive WRKY genes from soybean. Here, we further characterized the roles of one of these genes, GmWRKY27, in abiotic stress tolerance using a transgenic hairy root assay. GmWRKY27 expression was increased by various abiotic stresses. Over-expression and RNAi analysis demonstrated that GmWRKY27 improves salt and drought tolerance in transgenic soybean hairy roots. Measurement of physiological parameters, including reactive oxygen species and proline contents, supported this conclusion. GmWRKY27 inhibits expression of a downstream gene GmNAC29 by binding to the W-boxes in its promoter region. The GmNAC29 is a negative factor of stress tolerance as indicated by the performance of transgenic hairy roots under stress. GmWRKY27 interacts with GmMYB174, which also suppresses GmNAC29 expression and enhances drought stress tolerance. The GmWRKY27 and GmMYB174 may have evolved to bind to neighbouring cis elements in the GmNAC29 promoter to co-reduce promoter activity and gene expression. Our study discloses a valuable mechanism in soybean for regulation of the stress response by two associated transcription factors. Manipulation of these genes should facilitate improvements in stress tolerance in soybean and other crops.

Phytohormonal networks promote differentiation of fiber initials on pre-anthesis cotton ovules grown in vitro and in planta

The number of cotton (Gossypium sp.) ovule epidermal cells differentiating into fiber initials is an important factor affecting cotton yield and fiber quality. Despite extensive efforts in determining the molecular mechanisms regulating fiber initial differentiation, only a few genes responsible for fiber initial differentiation have been discovered. To identify putative genes directly involved in the fiber initiation process, we used a cotton ovule culture technique that controls the timing of fiber initial differentiation by exogenous phytohormone application in combination with comparative expression analyses between wild type and three fiberless mutants. The addition of exogenous auxin and gibberellins to pre-anthesis wild type ovules that did not have visible fiber initials increased the expression of genes affecting auxin, ethylene, ABA and jasmonic acid signaling pathways within 1 h after treatment. Most transcripts expressed differentially by the phytohormone treatment in vitro were also differentially expressed in the ovules of wild type and fiberless mutants that were grown in planta. In addition to MYB25-like, a gene that was previously shown to be associated with the differentiation of fiber initials, several other differentially expressed genes, including auxin/indole-3-acetic acid (AUX/IAA) involved in auxin signaling, ACC oxidase involved in ethylene biosynthesis, and abscisic acid (ABA) 8'-hydroxylase an enzyme that controls the rate of ABA catabolism, were co-regulated in the pre-anthesis ovules of both wild type and fiberless mutants. These results support the hypothesis that phytohormonal signaling networks regulate the temporal expression of genes responsible for differentiation of cotton fiber initials in vitro and in planta.

Ethylene and pollination decrease transcript abundance of an ethylene receptor gene in Dendrobium petals

We studied the expression of a gene encoding an ethylene receptor, called Ethylene Response Sensor 1 (Den-ERS1), in the petals of Dendrobium orchid flowers. Transcripts accumulated during the young floral bud stage and declined by the time the flowers had been open for several days. Pollination or exposure to exogenous ethylene resulted in earlier flower senescence, an increase in ethylene production and a lower Den-ERS1 transcript abundance. Treatment with 1-methylcyclopropene (1-MCP), an inhibitor of the ethylene receptor, decreased ethylene production and resulted in high transcript abundance. The literature indicates two kinds of ethylene receptor genes with regard to the effects of ethylene. One group shows ethylene-induced down-regulated transcription, while the other has ethylene-induced up-regulation. The present gene is an example of the first group. The 5' flanking region showed binding sites for Myb and myb-like, homeodomain, MADS domain, NAC, TCP, bHLH and EIN3-like transcription factors. The binding site for the EIN3-like factor might explain the ethylene effect on transcription. A few other transcription factors (RAV1 and NAC) seem also related to ethylene effects.

Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis

BACKGROUND

Trihelix transcription factor family is plant-specific and plays important roles in developmental processes. However, their function in abiotic stress response is largely unclear.

RESULTS

We studied one member GT-4 from Arabidopsis in relation to salt stress response. GT-4 expression is induced by salt stress and GT-4 protein is localized in nucleus and cytoplasm. GT-4 acts as a transcriptional activator and its C-terminal end is the activation domain. The protein can bind to the cis-elements GT-3 box, GT-3b box and MRE4. GT-4 confers enhanced salt tolerance in Arabidopsis likely through direct binding to the promoter and activation of Cor15A, in addition to possible regulation of other relevant genes. The gt-4 mutant shows salt sensitivity. TEM2, a member of AP2/ERF family was identified to interact with GT-4 in yeast two-hybrid, BiFC and Co-IP assays. Loss-of-function of TEM2 exerts no significant difference on salt tolerance or Cor15A expression in Arabidopsis. However, double mutant gt-4/tem2 shows greater sensitivity to salt stress and lower transcript level of Cor15A than gt-4 single mutant. GT-4 plus TEM2 can synergistically increase the promoter activity of Cor15A.

CONCLUSIONS

GT-4 interacts with TEM2 and then co-regulates the salt responsive gene Cor15A to improve salt stress tolerance.

CINCINNATA in Antirrhinum majus directly modulates genes involved in cytokinin and auxin signaling

Mutations in the CINCINNATA (CIN) gene in Antirrhinum majus and its orthologs in Arabidopsis result in crinkly leaves as a result of excess growth towards the leaf margin. CIN homologs code for TCP (TEOSINTE-BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 AND 2) transcription factors and are expressed in a broad zone in a growing leaf distal to the proliferation zone where they accelerate cell maturation. Although a few TCP targets are known, the functional basis of CIN-mediated leaf morphogenesis remains unclear. We compared the global transcription profiles of wild-type and the cin mutant of A. majus to identify the targets of CIN. We cloned and studied the direct targets using RNA in situ hybridization, DNA-protein interaction, chromatin immunoprecipitation and reporter gene analysis. Many of the genes involved in the auxin and cytokinin signaling pathways showed altered expression in the cin mutant. Further, we showed that CIN binds to genomic regions and directly promotes the transcription of a cytokinin receptor homolog HISTIDINE KINASE 4 (AmHK4) and an IAA3/SHY2 (INDOLE-3-ACETIC ACID INDUCIBLE 3/SHORT HYPOCOTYL 2) homolog in A. majus. Our results suggest that CIN limits excess cell proliferation and maintains the flatness of the leaf surface by directly modulating the hormone pathways involved in patterning cell proliferation and differentiation during leaf growth.

Flower opening and closure: an update

This review is an update of a 2003 review (Journal of Experimental Botany 54,1801-1812) by the same corresponding author. Many examples of flower opening have been recorded using time-lapse photography, showing its velocity and the required elongation growth. Ethylene regulates flower opening, together with at least gibberellins and auxin. Ethylene and gibberellic acid often promote and inhibit, respectively, the expression of DELLA genes and the stability of DELLA proteins. DELLA results in growth inhibition. Both hormones also inhibited and promoted, respectively, the expression of aquaporin genes required for cell elongation. Arabidopsis miRNA319a mutants exhibited narrow and short petals, whereby miRNA319a indirectly regulates auxin effects. Flower opening in roses was controlled by a NAC transcription factor, acting through miRNA164. The regulatory role of light and temperature, in interaction with the circadian clock, has been further elucidated. The end of the life span in many flowers is determined by floral closure. In some species pollination resulted in earlier closure of turgid flowers, compared with unpollinated flowers. It is hypothesized that this pollination-induced effect is only found in flowers in which closure is regulated by ethylene.

Genome-wide identification and expression analysis of TCP transcription factors in Gossypium raimondii

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play versatile functions in multiple aspects of plant growth and development. However, no systematical study has been performed in cotton. In this study, we performed for the first time the genome-wide identification and expression analysis of the TCP transcription factor family in Gossypium raimondii. A total of 38 non-redundant cotton TCP encoding genes were identified. The TCP transcription factors were divided into eleven subgroups based on phylogenetic analysis. Most TCP genes within the same subfamily demonstrated similar exon and intron organization and the motif structures were highly conserved among the subfamilies. Additionally, the chromosomal distribution pattern revealed that TCP genes were unevenly distributed across 11 out of the 13 chromosomes; segmental duplication is a predominant duplication event for TCP genes and the major contributor to the expansion of TCP gene family in G. raimondii. Moreover, the expression profiles of TCP genes shed light on their functional divergence.

Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome

The single-celled cotton (Gossypium hirsutum) fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ∼5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution.

Ever since Darwin biologists have recognized that comparative study of crop plants and their wild relatives offers a powerful framework for generating insights into the mechanisms that underlie evolutionary change. Here, we study the domestication process in cotton, Gossypium hirsutum, an allopolyploid species (containing two different genomes) which initially was domesticated approximately 5000 years ago, and which primarily is grown for its single-celled seed fibers. Strong directional selection over the millennia was accompanied by transformation of the short, coarse, and brown fibers of wild plants into the long, strong, and fine white fibers of the modern cotton crop plant. To explore the evolutionary genetics of cotton domestication, we conducted transcriptome profiling of developing cotton fibers from multiple accessions of wild and domesticated cottons. Comparative analysis revealed that the domestication process dramatically rewired the transcriptome, affecting more than 5,000 genes, and with a more evenly balanced usage of the duplicated copies arising from genome doubling. We identify many different biological processes that were involved in this transformation, including those leading to a prolongation of fiber elongation and a reallocation of resources toward increased fiber growth in modern forms. The data provide a rich resource for future functional analyses targeting crop improvement and evolutionary objectives.