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We studied the surface potentials of hybrid photosensitive organic/inorganic systems to correlate the surface–adsorbate interplay with their surface properties and provide theoretical guidance.

Monolayer GeP3 and InP3 exhibit different polarization-resolved and helicity-resolved Raman spectra and Raman-active phonons are categorized as a guidance for experiment.

Sediment erosion of Pelton turbines seriously damage the economic benefits and safe operation of the power station under the high head. The gas-liquid-solid three-phase unsteady flow calculation was carried out using the Eulerian-Lagrangian method to study the influence of velocity and nozzle opening on buckets torque and erosion. Experimental research were carried out under the condition of clear water and sediment-laden flow, the experimental results are in good agreement with the numerical simulation results, which proves the reliability of the calculation model and calculation method. The conclusions obtained from the numerical simulation are as follows: after adding the sediment particles, there is a slight delay of the bucket torque curve. Compared to clear water, the maximum torque of a single bucket will increase by about 2% in sediment-laden flow under different scenarios (the particle concentration is 1%, the particle size is 0.1 mm, the velocity range is 28–32 m/s, and the nozzle opening range is 50%–100%). For particles with strong flowability, the erosion region is highly consistent with the high-pressure zone. The increase in the velocity will increase the erosion rate on buckets. The nozzle opening change has little effect on the erosion region and maximum erosion rate. Meanwhile, the number of eroded buckets is three at the same moment, which is not affected by the nozzle opening change. This paper could provide some theoretical assistance for runner manufacturing, optimization design, and maintenance.

As the progenitor of durum wheat (Triticum durum Desf.) and common wheat (T. aestivum L.), wild emmer wheat (T. turgidum L. subsp. dicoccoides, TTD) has many valuable alleles for enlarging the genetic pool of common wheat. Chromosome arm substitution lines (CASLs) are useful genetic resources producing genome‐wide variations in the background of certain cultivars, with each CASL containing a pair of an individual chromosome arms from the donor parent. Therefore, CASLs can be used to identify a broad range of phenotypes that are usually different from the parental lines, to map causal genes or quantitative trait loci and to broaden the genetic pools of existing cultivars as prebreeding materials. In this review we summarize recent progress in wheat genetic studies and breeding using two sets of CASLs of the wild emmer accession TTD140 in two common wheat backgrounds of ‘Chinese Spring’ and ‘Bethlehem’. We report the production of CASLs, confirmation of their chromosome structure using molecular markers, and their application in discovering and mapping agronomically important genes. We propose that, together with the release of high‐quality reference genomes of wild emmer and common wheat, wild emmer CASLs are useful resources for genetic study and breeding of wheat.

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement., Sequencing and genomic diversification of five allopolyploid cotton species provide insights into polyploid genome evolution and epigenetic landscapes for cotton improvement.

Cotton fibers are initiated from the epidermal cells of the ovule before or on the day of anthesis. Gossypium arboreum SMA-4 mutant contains recessive mutation (sma-4(ha)) and has the phenotypes of fibreless seeds and glabrous stems. In this study, fine mapping and alternative splicing analysis indicated a nucleotide substitution (AG → AC) at splicing site in a homeodomain-leucine zipper IV family gene (GaHD1) might cause gene A3S (Alternative 3′ splicing) mistake, suggested that GaHD1 was the candidate gene of sma-4(ha). Many genes related to the fiber initiation are identified to be differentially expressed in the mutant which could result in the blocked fiber initiation signals such as H2O2, or Ca in the mutant. Further comparative physiological analysis of H2O2 production and Ca2+ flux in the SMA-4 and wide type cotton confirmed that H2O2 and Ca were important fiber initiation signals and regulated by GaHD1. The in vitro ovule culture of the mutant with hormones recovered the fibered phenotype coupled with the restoration of these signals. Overexpressing of GaHD1 in Arabidopsis increased trichome densities on the sepal, leaf, and stem tissues while transient silencing of the GaHD1 gene in G. arboreum reduced the trichome densities. These phenotypes indicated that GaHD1 is the candidate gene of SMA-4 with a crucial role in acting upstream molecular switch of signal transductions for cotton trichome and fiber initiations.

Bamboo is one of the most important non-timber forest resources worldwide. It has considerable economic value and unique flowering characteristics. The long juvenile phase in bamboo and unpredictable flowering time limit breeding and genetic improvement and seriously affect the productivity and application of bamboo forests. Members of SQUA-like subfamily genes play an essential role in controlling flowering time and floral organ identity. A comprehensive study was conducted to explain the functions of five SQUA-like subfamily genes in Phyllostachys edulis. Expression analysis revealed that all PeSQUAs have higher transcript levels in the reproductive period than in the juvenile phase. However, PeSQUAs showed divergent expression patterns during inflorescence development. The protein–protein interaction (PPI) patterns among PeSQUAs and other MADS-box members were analyzed by yeast two-hybrid (Y2H) experiments. Consistent with amino acid sequence similarity and phylogenetic analysis, the PPI patterns clustered into two groups. PeMADS2, 13, and 41 interacted with multiple PeMADS proteins, whereas PeMADS3 and 28 hardly interacted with other proteins. Based on our results, PeSQUA might possess different functions by forming protein complexes with other MADS-box proteins at different flowering stages. Furthermore, we chose PeMADS2 for functional analysis. Ectopic expression of PeMADS2 in Arabidopsis and rice caused early flowering, and abnormal phenotype was observed in transgenic Arabidopsis lines. RNA-seq analysis indicated that PeMADS2 integrated multiple pathways regulating floral transition to trigger early flowering time in rice. This function might be due to the interaction between PeMADS2 and homologous in rice. Therefore, we concluded that the five SQUA-like genes showed functional conservation and divergence based on sequence differences and were involved in floral transitions by forming protein complexes in P. edulis. The MADS-box protein complex model obtained in the current study will provide crucial insights into the molecular mechanisms of bamboo’s unique flowering characteristics.

LEACH algorithm is a key technology that restricts the life cycle of wireless sensor network (Wireless Sensor Network, WSN). Aiming at the unreasonable problem of LEACH algorithm cluster head election and clustering method, the fuzzy logic (FLS) method is adopted to adaptively select the best cluster head node considering the remaining energy of the node, the relative density of the node and the relative distance from the node to the sink node. According to the distance from the sink node to the cluster head node, a three-layer ring monitoring area is divided. Communicating with sink node in single-hop multi-hop mode. Simulation results show that the algorithm has extended the life cycle of the network.

Dynamic remodeling of the actin cytoskeleton plays a central role in the elongation of cotton fibers, which are the most important natural fibers in the global textile industry. Here, a high-resolution mapping approach combined with comparative sequencing and a transgenic method revealed that a G65V substitution in the cotton actin Gh_D04G0865 (GhACT17D in the wild-type) is responsible for the Gossypium hirsutum Ligon lintless-1 (Li1) mutant (GhACT17DM). In the mutant GhACT17DM from Li1 plant, Gly65 is substituted with valine on the lip of the nucleotide-binding domain of GhACT17D, which probably affects the polymerization of F-actin. Over-expression of GhACT17DM, but not GhACT17D, driven by either a CaMV35 promoter or a fiber-specific promoter in cotton produced a Li1-like phenotype. Compared with the wild-type control, actin filaments in Li1 fibers showed higher growth and shrinkage rates, decreased filament skewness and parallelness, and increased filament density. Taken together, our results indicate that the incorporation of GhACT17DM during actin polymerization disrupts the establishment and dynamics of the actin cytoskeleton, resulting in defective fiber elongation and the overall dwarf and twisted phenotype of the Li1 mutant.

BackgroundCotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood.ResultsIn this study,Gossypium hirsutum(Gh) andG. barbadense(Gb)were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore.Ghvarieties normally had long singular and clustered trichomes, whileGbvarieties had short clustered trichomes. Genetic mapping using five F2populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F1generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion ofGhwild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion ofGbprimitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in bothGhandGbprimitive accessions and modern varieties.ConclusionBased on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.

Additional file 1: Supplementary Figs. S1 to S5 (Fig. S1. Observations of cotton stem trichome phenotypes; Fig. S2. Stem trichome grading; Fig. S3. Seeds having different fuzzy fiber density levels grouped into five grades from 0 to 4 (from left to right); Fig. S4. Stem trichome phenotypes of the G. hirsutum wild accessions showing the different lengths and density levels; Fig. S5. Stem trichome phenotypes of parents and their F1 hybrids from crosses between G. hirsutum and G. babradense varieties with different types of trichomes.

Background: Cotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism . Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood. Results: In this study, Gossypium hirsutum (Gh ) and G . barbadense ( Gb ) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F2 populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr.06 and Chr.24. The twenty six F1 generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties. Conclusion: Based on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.

With the development of intelligent, flexible, interactive, and renewable energy power generation systems with higher penetration rates, the short-term load forecasting of individual power users plays an increasingly important role in future grid planning and operation scheduling. Due to the high volatility and uncertainty of the power load sequence, the power load prediction of individual energy users is quite challenging. Considering the impact of historical information and future information that affects the current state on the prediction results, this paper proposes a short-term load forecasting model by Seq2seq-LSTM based on Long-short-term Memory (LSTM) recurrent neural network to solve this difficult problem. In this framework, residual LSTM and Scaled Dot-Product (SDP) Attention are integrated to improve the accuracy of short-term forecasting of single-user power consumption. In order to verify the effectiveness and efficiency of the method, the actual measured single-user load data is used as an example and the model is compared with three state of the art. Experimental results show that the model proposed in this paper is superior to other models in terms of prediction accuracy and algorithm robustness.

Dynamic remodeling of the actin cytoskeleton plays a central role in the elongation of cotton fibers, which are the most important natural fibers in the global textile industry. Here, a high-resolution mapping approach combined with comparative sequencing and a transgenic method revealed that a G65V substitution in the cotton actin Gh_D04G0865 (GhACT17D in the wild-type) is responsible for the Gossypium hirsutum Ligon lintless-1 (Li1) mutant (GhACT17DM). In the mutant GhACT17DM from Li1 plant, Gly65 is substituted with valine on the lip of the nucleotide-binding domain of GhACT17D, which probably affects the polymerization of F-actin. Over-expression of GhACT17DM, but not GhACT17D, driven by either a CaMV35 promoter or a fiber-specific promoter in cotton produced a Li1-like phenotype. Compared with the wild-type control, actin filaments in Li1 fibers showed higher growth and shrinkage rates, decreased filament skewness and parallelness, and increased filament density. Taken together, our results indicate that the incorporation of GhACT17DM during actin polymerization disrupts the establishment and dynamics of the actin cytoskeleton, resulting in defective fiber elongation and the overall dwarf and twisted phenotype of the Li1 mutant.

To uncover the role of LINC01980 in aggravating the progression of hepatocellular carcinoma (HCC) via targeting caspase 9.The expression levels of LINC01980 and caspase 9 in HCC tissues and paracancer tissues were determined by qRT-PCR. The prognostic potentials of LINC01980 and caspase 9 in HCC were assessed by Kaplan-Meier method. The regulatory effects of LINC01980 and caspase 9 on the viability, clonality and apoptosis of Huh7 and Hep3B cells were examined. Finally, the interaction between LINC01980 and caspase 9 was evaluated by performing dual-luciferase reporter gene assay and rescue experiments.LINC01980 was upregulated in HCC tissues and cells. High level of LINC01980 indicated worse prognosis in HCC patients. Knockdown of LINC01980 could attenuate viability and clonality, but induced apoptosis in Huh7 and Hep3B cells. Caspase 9 was downregulated in HCC, and its high level predicted a better prognosis in HCC patients. Overexpression of caspase 9 achieved the same regulatory effects as LINC01980 knockdown on HCC cells. Caspase 9 was the downstream target for LINC01980, and its level was negatively regulated by LINC01980. In HCC, LINC01980 regulated HCC cell behaviors by downregulating caspase 9.Upregulation of LINC01980 in HCC predicts a poor prognosis. LINC01980 aggravates the progression of HCC via downregulating caspase 9.

Background: Cotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism . Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood. Results: In this study, Gossypium hirsutum (Gh ) and G . barbadense ( Gb ) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F2 populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr.06 and Chr.24. The twenty six F1 generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties. Conclusion: Based on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.

Background MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Bamboo is an important non-timber forest product worldwide, but previous studies on the moso bamboo (Phyllostachys edulis) MADS-box gene family were not accurate nor sufficiently detailed. Results Here, a complete genome-wide identification and characterization of the MADS-box genes in moso bamboo was conducted. There was an unusual lack of type-I MADS-box genes in the bamboo genome database (http://202.127.18.221/bamboo/index.php), and some of the PeMADS sequences are fragmented and/or inaccurate. We performed several bioinformatics techniques to obtain more precise sequences using transcriptome assembly. In total, 42 MADS-box genes, including six new type-I MADS-box genes, were identified in bamboo, and their structures, phylogenetic relationships, predicted conserved motifs and promoter cis-elements were systematically investigated. An expression analysis of the bamboo MADS-box genes in floral organs and leaves revealed that several key members are involved in bamboo inflorescence development, like their orthologous genes in Oryza. The ectopic overexpression of one MADS-box gene, PeMADS5, in Arabidopsis triggered an earlier flowering time and the development of an aberrant flower phenotype, suggesting that PeMADS5 acts as a floral activator and is involved in bamboo flowering. Conclusion We produced the most comprehensive information on MADS-box genes in moso bamboo. Additionally, a critical PeMADS gene (PeMADS5) responsible for the transition from vegetative to reproductive growth was identified and shown to be related to bamboo floral development. Electronic supplementary material The online version of this article (10.1186/s12870-018-1394-2) contains supplementary material, which is available to authorized users.

Cotton fibers are initiated from the epidermal cells of the ovule before or on the day of anthesis. Gossypium arboreum SMA-4 mutant contains recessive mutation (sma-4(ha)) and has the phenotypes of fibreless seeds and glabrous stems. In this study, fine mapping and alternative splicing analysis indicated a nucleotide substitution (AG → AC) at splicing site in a homeodomain-leucine zipper IV family gene (GaHD1) might cause gene A3S (Alternative 3' splicing) mistake, suggested that GaHD1 was the candidate gene of sma-4(ha). Many genes related to the fiber initiation are identified to be differentially expressed in the mutant which could result in the blocked fiber initiation signals such as H

Heading date (HD) is an important agronomic trait, influencing directly or indirectly yield and quality traits. Previous experiments showed that the chromosome arm substitution line (CASL) 4AL of wild emmer in the background of Chinese Spring (CS) was about 18–22 days later in HD than CS. In this study, CASL4AL flowered roughly 20 days earlier than CS grown under long day (LD) with short day (SD) vernalization, but failed to flower when planted under controlled SD conditions. The above results suggest CASL4AL carries an extremely sensitive photoperiod response gene. CASL4AL showed a major difference from CS in restricted young spike development, remaining at the double-ridge stage and floret-primordium differentiation stage much longer than CS under SD. To map this gene, the F2 population from cross between CS and CASL4AL were explored in two consecutive years. In 2016, a HD related QTL flanked by M576 and wmc468 with a LOD score (8.5) was detected. In 2017, this QTL was repeatedly detected with a higher LOD score (10.03), and therefore named as QPpd.zafu-4A. A total of 27 genes were annotated and possible candidate was discussed. This work lays a foundation for map-based cloning of QPpd.zafu-4A and elucidating its molecular mechanism in affecting HD.

Stem trichomes and seed fibers originate from epidermal cells and partially share a regulatory pathway at the molecular level. In Gossypium barbadense, two insertions of a Ty1 long-terminal repeat-retrotransposon [transposable element TE1 and TE2] in a homeodomain-leucine zipper gene (HD1) result in glabrous stems. The primers used to identify the TE insertions in G. barbadense were applied to screen for the same events in 81 modern G. hirsutum varieties and 31 wild races. Three wild races were found carrying the same TEs as G. barbadense. However, the TE insertions in two of these wild races occurred at different sites (4th exon), therefore, named TE3, while the TE in the other wild race occurred at the same site as TE2. An RNA sequencing and qRT-PCR analysis indicated that the loss of HD1 function was caused by the TE insertion. Genetic mapping revealed a strong association between glabrous stems and TE3 insertions, confirming that HD1 is a critical gene for stem trichome initiation in G. hirsutum, as in G. barbadense. Using the long-terminal repeat sequence as a query to search against the Texas Marker-1 reference genome sequence, we found that the TE occurred after tetraploid cotton formation and evolved at different rates in G. hirsutum and G. barbadense. Interestingly, at least three independent insertion events of the same retrotransposon occurred preferentially in the A sub-genome's HD1 gene, but not in the D sub-genome of G. hirsutum or G. barbadense, suggesting that an unknown TE insertion mechanism and resultant gene function changes may have hastened cotton speciation.

To create recombinant substitution lines from chromosome arm substitution lines (CASLs) of wild emmer, the common wheat cultivar ‘Bethlehem’ (BLH) was crossed with 4 CASLs of group 1 and the resulting F1s were backcrossed with corresponding BLH ditelosomic (DT) lines to produce monotelosomic plants (BC1F1, 2n = 6x = 41 + t). For each cross combination, about 100 BC1F2 plants derived from 47 to 49 BC1F1 plants were analyzed for their chromosome number and constitution. The frequencies of plants with 42 or 41 + t chromosomes in [DT1BS × (BLH × CASL1BL)] progenies were much lower than in crosses involving CASLs 1AS, 1AL and 1BS; while the frequency of [DT1BS × (BLH × CASL1BL)] progeny plants with 41 chromosomes was high. A total of 49 (BLH × CASL1BL) BC1F1 plants could be clearly classified into three types based on chromosome constitution of their 461 BC1F2 progenies. In type I (21 BC1F1 plants), 95 % of BC1F2 plants possessed 42 chromosomes (counting the telosomic chromosome as an entire chromosome). In type III (24 BC1F1 plants), most BC1F2 plants (75.6 %) had 41 chromosomes and no telosomic chromosome. In type II (4 BC1F1 plants), the expected number of ~48 % of BC1F2 plants had the telosomic chromosome, but about 70 % had fewer than the expected 42 chromosomes. All type III BC1F1 plants were confirmed to have experienced elimination of telosomic chromosome 1BS. Observation of BC1F1 seedling mitosis revealed that the elimination of 1BS occurred most probably during embryogenesis. However, type II BC1F1 plants experienced the elimination of different chromosomes, which was deduced to occur during meiosis. Reciprocal crosses indicated that both types of chromosome elimination occurred only when BLH DT1BS, which has Chinese Spring cytoplasm, was used as female parent. Collectively, these results reveal a genetic system on chromosome arm 1BL of wild emmer that interacts with the CS cytoplasm to cause chromosome elimination.

Apyrase and extracellular ATP play crucial roles in mediating plant growth and defense responses. In the cold-tolerant poplar, Populus euphratica, low temperatures up-regulate APYRASE2 (PeAPY2) expression in callus cells. We investigated the biochemical characteristics of PeAPY2 and its role in cold tolerance. We found that PeAPY2 predominantly localized to the plasma membrane, but punctate signals also appeared in the endoplasmic reticulum and Golgi apparatus. PeAPY2 exhibited broad substrate specificity, but it most efficiently hydrolyzed purine nucleotides, particularly ATP. PeAPY2 preferred Mg(2+) as a cofactor, and it was insensitive to various, specific ATPase inhibitors. When PeAPY2 was ectopically expressed in Arabidopsis (Arabidopsis thaliana), cold tolerance was enhanced, based on root growth measurements and survival rates. Moreover, under cold stress, PeAPY2-transgenic plants maintained plasma membrane integrity and showed reduced cold-elicited electrolyte leakage compared with wild-type plants. These responses probably resulted from efficient plasma membrane repair via vesicular trafficking. Indeed, transgenic plants showed accelerated endocytosis and exocytosis during cold stress and recovery. We found that low doses of extracellular ATP accelerated vesicular trafficking, but high extracellular ATP inhibited trafficking and reduced cell viability. Cold stress caused significant increases in root medium extracellular ATP. However, under these conditions, PeAPY2-transgenic lines showed greater control of extracellular ATP levels than wild-type plants. We conclude that Arabidopsis plants that overexpressed PeAPY2 could increase membrane repair by accelerating vesicular trafficking and hydrolyzing extracellular ATP to avoid excessive, cold-elicited ATP accumulation in the root medium and, thus, reduced ATP-induced inhibition of vesicular trafficking.

Virus-induced gene silencing (VIGS) has been shown to be an effective tool for investigating gene functions in herbaceous plant species, but has rarely been tested in trees. The establishment of a fast and reliable transformation system is especially important for woody plants, many of which are recalcitrant to transformation. In this study, we established a tobacco rattle virus (TRV)-based VIGS system for two Populus species, Populus euphratica and P. × canescens. Here, TRV constructs carrying a 266 bp or a 558 bp fragment of the phytoene desaturase (PDS) gene were Agrobacterium-infiltrated into leaves of the two poplar species. Agrobacterium-mediated delivery of the shorter insert, TRV2-PePDS266, into the host poplars resulted in expected photobleaching in both tree species, but not the longer insert, PePDS558. The efficiency of VIGS was temperature-dependent, increasing by raising the temperature from 18 to 28 °C. The optimized TRV-VIGS system at 28 °C resulted in a high silencing frequency and efficiency up to 65-73 and 83-94%, respectively, in the two tested poplars. Moreover, syringe inoculation of Agrobacterium in 100 mM acetosyringone induced a more efficient silencing in the two poplar species, compared with other agroinfiltration methods, e.g., direct injection, misting and agrodrench. There were plant species-related differences in the response to VIGS because the photobleaching symptoms were more severe in P. × canescens than in P. euphratica. Furthermore, VIGS-treated P. euphratica exhibited a higher recovery rate (50%) after several weeks of the virus infection, compared with TRV-infected P. × canescens plants (20%). Expression stability of reference genes was screened to assess the relative abundance of PePDS mRNA in VIGS-treated P. euphratica and P. × canescens. PeACT7 was stably expressed in P. euphratica and UBQ-L was selected as the most suitable reference gene for P. × canescens using three different statistical approaches, geNorm, NormFinder and BestKeeper. Quantitative real-time PCR showed significant reductions in PDS transcripts (55-64%) in the photobleached leaves of both VIGS-treated poplar species. Our results demonstrate that the TRV-based VIGS provides a practical tool for gene functional analysis in Populus sp., especially in those poplar species which are otherwise recalcitrant to transformation.

Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. In this study, a homeodomain-leucine zipper gene (HD1) was found to cosegregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern Gossypium barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in the At subgenome HD1 gene (At-GbHD1). In both the At and Dt subgenomes, reduced transcription of GbHD1 genes is caused by this insertion. The disruption of At-HD1 further affects the expression of downstream GbMYB25 and GbHOX3 genes. Analyses of primitive cultivated accessions identified another retrotransposon insertion event in the sixth exon of At-GbHD1 that might predate the previously identified retrotransposon in modern varieties. Although both retrotransposon insertions results in similar phenotypic changes, the timing of these two retrotransposon insertion events fits well with our current understanding of the history of cotton speciation and dispersal. Taken together, the results of genetics mapping, gene expression and association analyses suggest that GbHD1 is an important component that controls stem trichome development and is a promising candidate gene for the T1 locus. The interspecific phenotypic difference in stem trichome traits also may be attributable to HD1 inactivation associated with retrotransposon insertion.

Poplar species increase expressions of transcription factors to deal with salt environments. We assessed the salt-induced transcriptional responses of heat-shock transcription factor (HSF) and WRKY1 in Populus euphratica, and their roles in salt tolerance. High NaCl (200mM) induced PeHSF and PeWRKY1 expressions in P. euphratica, with a rapid rise in roots than in leaves. Moreover, the salt-elicited PeHSF reached its peak level 6h earlier than PeWRKY1 in leaves. PeWRKY1 was down-regulated in salinized P. euphratica when PeHSF was silenced by tobacco rattle virus-based gene silencing. Subcellular assays in onion epidermal cells and Arabidopsis protoplasts revealed that PeHSF and PeWRKY1 were restricted to the nucleus. Transgenic tobacco plants overexpressing PeWRKY1 showed improved salt tolerance in terms of survival rate, root growth, photosynthesis, and ion fluxes. We further isolated an 1182-bp promoter fragment upstream of the translational start of PeWRKY1 from P. euphratica. Promoter sequence analysis revealed that PeWRKY1 harbours four tandem repeats of heat shock element (HSE) in the upstream regulatory region. Yeast one-hybrid assay showed that PeHSF directly binds the cis-acting HSE. To determine whether the HSE cluster was important for salt-induced PeWRKY1 expression, the promoter-reporter construct PeWRKY1-pro::GUS was transferred to tobacco plants. β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. Therefore, we conclude that salinity increased PeHSF transcription in P. euphratica, and that PeHSF binds the cis-acting HSE of the PeWRKY1 promoter, thus activating PeWRKY1 expression.

A transcriptionally active Ty1/ copia -like retrotransposon was identified in the genome of Gossypium barbadense . The different heat activation of this element was observed in two tetraploid cotton species. Most retrotransposons from plants are transcriptionally silent, or activated under certain conditions. Only a small portion of elements are transcriptionally active under regular condition. A long terminal repeat (LTR) retrotransposon was isolated from the cultivated Sea Island cotton (H7124) genome during the investigation of the function of a homeodomain leucine zipper gene (HD1) in trichome growth. Insertion of this element in HD1 gene of At sub-genome was related to the trichomeless stem in Gossypium barbadense. The element, named as GBRE-1, had all features of a typical Ty1/copia retrotransposon and possessed high similarity to the members of ONSEN retrotransposon family. It was 4997 bp long, comprising a single 4110 bp open reading frame, which encoded 1369 amino acids including the conserved domains of gag and pol. The expression of GBRE-1 was detected under regular condition in G. barbadense and G. hirsutum, and its expression level was increased under heat-stress condition in G. hirsutum. Besides, its expression pattern was similar to that of the ONSEN retrotransposon. Abundant cis-regulatory motifs related to stress-response and transcriptional regulation were found in the LTR sequence. These results suggested that GBRE-1 was a transcriptionally active retrotransposon in Gossypium. To our knowledge, this is the first report of the isolation of a complete Ty1/copia-type retrotransposon with present-day transcriptional activity in cotton.

Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.

Tanshinones and phenolic acids are crucial bioactive compounds biosynthesized in Salvia miltiorrhiza. Methyl jasmonate (MeJA) is an effective elicitor to enhance the production of phenolic acids and tanshinones simultaneously, while yeast extract (YE) is used as a biotic elicitor that only induce tanshinones accumulation. However, little was known about the different molecular mechanism. To identify the downstream and regulatory genes involved in tanshinone and phenolic acid biosynthesis, we conducted comprehensive transcriptome profiling of S. miltiorrhiza hairy roots treated with either MeJA or YE. Total 55588 unigenes were assembled from about 1.72 billion clean reads, of which 42458 unigenes (76.4%) were successfully annotated. The expression patterns of 19 selected genes in the significantly upregulated unigenes were verified by quantitative real-time PCR. The candidate downstream genes and other cytochrome P450s involved in the late steps of tanshinone and phenolic acid biosynthesis pathways were screened from the RNA-seq dataset based on co-expression pattern analysis with specific biosynthetic genes. Additionally, 375 transcription factors were identified to exhibit a significant up-regulated expression pattern in response to induction. This study can provide us a valuable gene resource for elucidating the molecular mechanism of tanshinones and phenolic acids biosynthesis in hairy roots of S. miltiorrhiza.

WRKY transcription factors play important roles in various stress responses in diverse plant species. In cotton, this family has not been well studied, especially in relation to fiber development. Here, the genomes and transcriptomes of Gossypium raimondii and Gossypium arboreum were investigated to identify fiber development related WRKY genes. This represents the first comprehensive comparative study of WRKY transcription factors in both diploid A and D cotton species. In total, 112 G. raimondii and 109 G. arboreum WRKY genes were identified. No significant gene structure or domain alterations were detected between the two species, but many SNPs distributed unequally in exon and intron regions. Physical mapping revealed that the WRKY genes in G. arboreum were not located in the corresponding chromosomes of G. raimondii, suggesting great chromosome rearrangement in the diploid cotton genomes. The cotton WRKY genes, especially subgroups I and II, have expanded through multiple whole genome duplications and tandem duplications compared with other plant species. Sequence comparison showed many functionally divergent sites between WRKY subgroups, while the genes within each group are under strong purifying selection. Transcriptome analysis suggested that many WRKY genes participate in specific fiber development processes such as fiber initiation, elongation and maturation with different expression patterns between species. Complex WRKY gene expression such as differential Dt and At allelic gene expression in G. hirsutum and alternative splicing events were also observed in both diploid and tetraploid cottons during fiber development process. In conclusion, this study provides important information on the evolution and function of WRKY gene family in cotton species.

Cadmium (Cd2+) is a toxic heavy metal impairing plant growth and development. Xyloglucan endotransglucosylase/hydrolase gene (XTH) is involved in the plant response to heavy metal toxicity, in addition to controlling cell wall extensibility. However, the link between XTH and Cd2+ stress has not yet been established in higher plants. PeXTH expression was up-regulated by 1.2–2.1-fold in Populus euphratica roots and leaves upon Cd2+ exposure (40–80 μM CdCl2). Cellular Cd2+ analysis and flux data showed that the cadmium-elicited expression of PeXTH markedly restricted Cd2+ uptake and accumulation in P. euphratica roots. Moreover, tobacco plants overexpressing PeXTH were more tolerant to Cd2+ stress (80 μM CdCl2) than wild-type tobacco in terms of root and shoot growth. Transgenic lines accumulated 49–58% less Cd2+ in root apical and mature regions, as compared to the wild type. The less buildup of Cd2+ in roots of transgenic lines was the result of lower influx of Cd2+ under Cd2+ stress. It is noting that transgenic plants displayed 56–87% higher xyloglucan degradation activity (XDA) than the wild type, leading to a 25–27% decline of xyloglucan content in the root cell walls. Therefore, overexpression of PeXTH increased the activity of XDA in transgenic plants, which enhanced the degradation of xyloglucan in the wall. The down-regulated amount of xyloglucan led to less binding sites for Cd2+ and thus reduced the root Cd2+ uptake and buildup in transgenic plants. Consequently, the Cd2+ toxicity was eventually alleviated in transgenic tobacco.

Transcriptional responses of a heat-shock transcription factor from the salt-resistant Populus euphratica, PeHSF, were assessed in transgenic tobacco seedlings subjected to salinity stress. Moreover, their relevance to NaCl-induced anti-oxidative defense responses in higher plants was also explored. Expression of PeHSF was induced by high-salinity (150 mM NaCl) in leaves and callus cultures of P. euphratica. The salt-stimulated PeHSF expression in P. euphratica callus cultures was markedly inhibited by DPI (an inhibitor of plasma membrane NADPH oxidase) and LaCl3 (an inhibitor of plasma membrane Ca2+-permeable channels), indicating the involvement of reactive oxygen species (ROS) and Ca2+ in HSF activation under NaCl stress. Sequence analysis showed that PeHSF is a typical class A HSF in higher plants. PeHSF overexpression in tobacco significantly improved the salt tolerance of transgenic plants, in term of seed germination and root growth. Compared to the wild-type plants, the PeHSF-transgenic lines exhibited an increased capacity to control ROS homeostasis, but not an enhanced capacity to retain ionic homeostasis under salt stress. PeHSF expression in tobacco enhanced the activities of ascorbate peroxidase, glutathione peroxidase, and glutathione reductase, due to upregulated transcriptional levels. We conclude that PeHSF plays a crucial role in ROS detoxification under salt stress, rather than in maintenance of the K+/Na+. It is likely that the salt-induced H2O2 and cytosolic Ca2+ led to transcriptional activation of HSF, which initiated the transcription of genes encoding antioxidant enzymes in P. euphratica, thus contributing to ROS homeostasis control under saline conditions.

A well-characterized and systematically organized collection of genetic markers is crucial in the study of any crop species. It is the basis of map-based gene cloning and crop improvements through marker-assisted selections. Single-strand conformation polymorphism (SSCP) has been a robust way of discovering new polymorphisms in marker development without the requirement of sequencing. Here, we report the first approach of applying SSCP marker discovery methods in the genetic map construction and gene mapping of cotton species. A total of 80 restriction fragment length polymorphism (RFLP) markers were selected from a region on published cotton genetic maps around the T1 gene related to cotton trichome. Among the 80 RFLPs, 28 showed polymorphisms through SSCP, showing a polymorphic rate of approximately 35%, which is much higher than that of simple sequence repeat (SSR) markers in the same region (7.8%). By integrating these newly generated SSCP markers, a detailed genetic map was reconstructed around this region using an F2 population derived from a cross between Gossypium arboreum and G. herboceum. The reconstructed region comprises 22 SSCP markers, eight SSR markers and the T1 gene, spanning 21.6 cM. The marker order of the new map agrees well with published reference RFLP maps. The above results suggest that SSCP method can be applied very efficiently and reliably to the marker development of cotton genomes. It will prove to be even more valuable and robust after the public release of cotton whole-genome sequences.

Wheat heading date is an important agronomic trait determining maturation time and yield. A set of common wheat (Triticum aestivum var. Chinese Spring; CS)-wild emmer (T. turgidum L. subsp. dicoccoides (TDIC)) chromosome arm substitution lines (CASLs) was used to identify and allocate QTLs conferring late or early spike emergence by examining heading date. Genetic loci accelerating heading were found on TDIC chromosome arms 3AL and 7BS, while loci delaying heading were located on 4AL and 2BS. To map QTLs conferring late heading on 2BS, F2 populations derived from two cross combinations of CASL2BS × CS and CASL3AL × CASL2BS were developed and each planted at two times, constituting four F2 mapping populations. Heading date varied continuously among individuals of these four populations, suggesting quantitative characteristics. A genetic map of 2BS, consisting of 23 SSR and one single-stranded conformation polymorphism (SSCP) marker(s), was constructed using these F2 populations. This map spanned a genetic length of 53.2 cM with average marker density of 2.3 cM. The photoperiod-sensitivity gene Ppd-B1 was mapped to chromosome arm 2BS as a SSCP molecular marker, and was validated as tightly linked to a major QTL governing late heading of CASL2BS in all mapping populations. A significant dominance by additive effect of Ppd-B1 with the LUX gene located on 3AL was also detected. CS had more copies of Ppd-B1 than CASL2BS, implying that increased copy number could elevate the expression of Ppd-1 in CS, also increasing expression of LUX and FT genes and causing CS to have an earlier heading date than CASL2BS in long days.

Using callus cells of a salt-tolerant Populus euphratica Oliver and a salt-sensitive P. popularis 35–44 (P. popularis), the effects of NaCl stress on hydrogen peroxide (H2O2) and nitric oxide (NO) production and the relevance to ionic homeostasis and antioxidant defense were investigated. Results show that P. euphratica exhibited a greater capacity to tolerate NaCl stress in terms of cell viability, membrane permeability and K+/Na+ relations. NaCl salinity (150 mM) caused a rapid increase of H2O2 and NO in P. euphratica cells, but not in P. popularis. Moreover, salinised P. euphratica cells retained a high and stable level of H2O2 and NO during the period of 24-h salt stress. Noteworthy, P. eupratica cells increased activities of superoxide dismutase, ascorbate peroxidase, catalase and glutathione reductase under salinity stress, but these antioxidant enzymes were significantly inhibited by the salt treatment in P. popularis cells. Pharmacological experiments proved that the NaCl-induced H2O2 and NO was interdependent and contributed to the mediation of K+/Na+ homeostasis and antioxidant defense in P. euphratica cells. Given these results, we conclude that the increased H2O2 and NO enable P. euphratica cells to regulate ionic and ROS (reactive oxygen species) homeostasis under salinity stress in the longer term.

Using confocal microscopy, X-ray microanalysis and the scanning ion-selective electrode technique, we investigated the signalling of H(2)O(2), cytosolic Ca(2+) ([Ca(2+)](cyt)) and the PM H(+)-coupled transport system in K(+)/Na(+) homeostasis control in NaCl-stressed calluses of Populus euphratica. An obvious Na(+)/H(+) antiport was seen in salinized cells; however, NaCl stress caused a net K(+) efflux, because of the salt-induced membrane depolarization. H(2)O(2) levels, regulated upwards by salinity, contributed to ionic homeostasis, because H(2)O(2) restrictions by DPI or DMTU caused enhanced K(+) efflux and decreased Na(+)/H(+) antiport activity. NaCl induced a net Ca(2+) influx and a subsequent rise of [Ca(2+)](cyt), which is involved in H(2)O(2)-mediated K(+)/Na(+) homeostasis in salinized P. euphratica cells. When callus cells were pretreated with inhibitors of the Na(+)/H(+) antiport system, the NaCl-induced elevation of H(2)O(2) and [Ca(2+)](cyt) was correspondingly restricted, leading to a greater K(+) efflux and a more pronounced reduction in Na(+)/H(+) antiport activity. Results suggest that the PM H(+)-coupled transport system mediates H(+) translocation and triggers the stress signalling of H(2)O(2) and Ca(2+), which results in a K(+)/Na(+) homeostasis via mediations of K(+) channels and the Na(+)/H(+) antiport system in the PM of NaCl-stressed cells. Accordingly, a salt stress signalling pathway of P. euphratica cells is proposed.

Ligon lintless-1 (Li1) is a Gossypium hirsutum mutant that is controlled by a dominant gene that arrests the development of cotton fiber after anthesis. Two F2 mapping populations were developed from mutant (Li1 × H7124) F1 plants in 2012 and 2013; each was composed of 142 and 1024 plants, respectively. Using these populations, Li1 was mapped to a 0.3-cM region in which nine single-strand conformation polymorphism markers co-segregated with the Li1 locus. In the published G. raimondii genome, these markers were mapped to a region of about 1.2 Mb (the Li1 region) and were separated by markers that flanked the Li1 locus in the genetic map, dividing the Li1 region into three segments. Thirty-six genes were annotated by the gene prediction software FGENESH (Softberry) in the Li1 region. Twelve genes were candidates of Li1, while the remaining 24 genes were identified as transposable elements, DNA/RNA polymerase superfamily or unknown function genes. Among the 12 candidate genes, those encoding ribosomal protein s10, actin protein, ATP synthase, and beta-tubulin 5 were the most-promising candidates of the Li1 mutant because the function of these genes is closely related to fiber development. High-throughput RNA sequencing and quantitative PCR revealed that these candidate genes had obvious differential gene expression between mutant and wild-type plants at the fiber elongation stage, strengthening the inference that they could be the most likely candidate gene of the Li1 mutant phenotype.