GbyE: an integrated tool for genome widely association study and genome selection based on genetic by environmental interaction.

BACKGROUND: The growth and development of organism were dependent on the effect of genetic, environment, and their interaction. In recent decades, lots of candidate additive genetic markers and genes had been detected by using genome-widely association study (GWAS). However, restricted to computing power and practical tool, the interactive effect of markers and genes were not revealed clearly. And utilization of these interactive markers is difficult in the breeding and prediction, such as genome selection (GS). RESULTS: Through the Power-FDR curve, the GbyE algorithm can detect more significant genetic loci at different levels of genetic correlation and heritability, especially at low heritability levels. The additive effect of GbyE exhibits high significance on certain chromosomes, while the interactive effect detects more significant sites on other chromosomes, which were not detected in the first two parts. In prediction accuracy testing, in most cases of heritability and genetic correlation, the majority of prediction accuracy of GbyE is significantly higher than that of the mean method, regardless of whether the rrBLUP model or BGLR model is used for statistics. The GbyE algorithm improves the prediction accuracy of the three Bayesian models BRR, BayesA, and BayesLASSO using information from genetic by environmental interaction (G × E) and increases the prediction accuracy by 9.4%, 9.1%, and 11%, respectively, relative to the Mean value method. The GbyE algorithm is significantly superior to the mean method in the absence of a single environment, regardless of the combination of heritability and genetic correlation, especially in the case of high genetic correlation and heritability. CONCLUSIONS: Therefore, this study constructed a new genotype design model program (GbyE) for GWAS and GS using Kronecker product. which was able to clearly estimate the additive and interactive effects separately. The results showed that GbyE can provide higher statistical power for the GWAS and more prediction accuracy of the GS models. In addition, GbyE gives varying degrees of improvement of prediction accuracy in three Bayesian models (BRR, BayesA, and BayesCpi). Whatever the phenotype were missed in the single environment or multiple environments, the GbyE also makes better prediction for inference population set. This study helps us understand the interactive relationship between genomic and environment in the complex traits. The GbyE source code is available at the GitHub website ( https://github.com/liu-xinrui/GbyE ).

Transcriptomic analysis of yak longissimus dorsi muscle identifies genes associated with tenderness.

Meat tenderness is an important sensory index when consumers choose meat products, which determines the value of meat products and consumers' buying intentions. Yak meat is rich in nutrition and unique in flavor, which is favored by consumers. However, its meat has the deficiencies of low tenderness and poor taste, which has a negative impact on the value of its meat products and customer satisfaction. To identify the genes affecting the yak meat tenderness, we used RNA-seq to analyze the longissimus dorsi muscle of yaks with different tenderness, screened a total of 1120 differentially expressed genes (DEGs). Meanwhile, 23 pathways were significantly enriched. By further analysis, we identified eight genes related to yak meat tenderness (WNT5A, ARID5B, SERPINE1 KLHL40, RUNX1, MAFF, RFX7 and ARID5A). Notably, SERPINE1 was involved in the significant enrichment pathways of 'complement and coagulation cascade pathway', 'HIF-1 signaling pathway' and 'AGE-RAGE signaling pathway in diabetic complications' which can regulate meat tenderness. This implies that SERPINE1 may play an important regulatory role among them. The DEGs associated with yak meat quality screened in this work will be helpful to identify potential biomarkers related to meat tenderness.

Risk factors associated with the prevalence of neck and shoulder pain among high school students: a cross-sectional survey in China.

BACKGROUND: After the COVID-19 outbreak, many Chinese high school students have increased their dependence on electronic devices for studying and life, which may affect the incidence of neck and shoulder pain (NSP) in Chinese adolescents. METHODS: To evaluate the prevalence of NSP in high school students and its associated risk factors during COVID-19, a survey was conducted among 5,046 high school students in Shanghai, Qinghai, Henan and Macao during the second semester and summer vacation of the 2019-2020 academic year. The questionnaire included questions regarding demographic characteristics, the prevalence of NSP and lifestyle factors such as sedentary behavior, poor posture and electronic device usage. Univariable and multivariable logistic regression was used to analyze the possible influencing factors for neck and shoulder pain. RESULTS: A total of 4793 valid questionnaires (95.0%) were collected. The results indicated that the prevalence of NSP was 23.7% among high school students. Binary logistic regression analysis revealed that female gender (P < 0.05, OR = 1.82), grade (P < 0.05, range OR 1.40-1.51) and subject selection (P < 0.05, range OR 0.49-0.68) were risk factors for NSP in high school students. Sedentary behavior (P < 0.05, range OR 1.74-2.36), poor posture (P < 0.05, range OR 1.19-2.56), backpack weight (P < 0.05, range OR 1.17-1.88), exercise style and frequency (P < 0.05, range OR 1.18-1.31; P < 0.05, range OR 0.76-0.79, respectively), and the time spent using electronic devices (P < 0.05, range OR 1.23-1.38)had a significant correlation with NSP in high school students. CONCLUSIONS: NSP is currently very common among high school students during the outbreak of COVID-19. Sedentary behavior, poor posture and other factors have a great impact on the occurrence of NSP in high school students. Education regarding healthy lifestyle choices should be advocated for to decrease NSP among high school students, such as more physical activity, changing poor postures and reducing the amount of time spent using electronic devices.

Identification and validation of a major quantitative trait locus for spike length and compactness in the wheat (Triticum aestivum L.) line Chuanyu12D7.

Spike length (SL) and spike compactness (SC) are crucial traits related to wheat (Triticum aestivum L.) yield potential. In this study, a backcrossed inbred lines (BILs) population segregating for SL/SC was developed by using a commercial variety chuanyu25 as recurrent parent and a backbone parent Chuanyu12D7. Bulked segregant analysis (BSA) combined with the Wheat 660K SNP array was performed to conduct quantitative trait locus (QTL) mapping. A major and stable SL/SC QTL (designated as QSl/Sc.cib-2D.1) was identified on chromosome 2DS, explaining 45.63-59.72% of the phenotypic variation. QSl/Sc.cib-2D.1 was mapped to a 102.29-Kb interval by flanking SNPs AX-110276364 and AX-111593853 using a BC4F2:3 population. Since QSl/Sc.cib-2D.1 is linked to the Rht8 gene, their additive effects on plant type and spike type were analysed. Remarkably, the superior allele of QSl/Sc.cib-2D.1 combined with Rht8 can increase SL and TGW, and decrese SC without any apparent trade-offs in other yield-related traits. In addition, the closely linked kompetitive allele-specific PCR (KASP) markers of this locus were developed for marker-assisted selection (MAS) breeding. Four genes within the physical interval were considered as potential candidates based on expression patterns as well as orthologous gene functions. These results laid the foundation for map-based cloning of the gene(s) underlying QSl/Sc.cib-2D.1 and its potential application in wheat ideotype breeding.

Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information.

Yaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, including FXYD6, SOHLH2, ADGRB2, and OSBPL6, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds.

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

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

Single-cell transcriptome analysis and in vitro differentiation of testicular cells reveal novel insights into male sterility of the interspecific hybrid cattle-yak.

BACKGROUND: Interspecific hybridization plays vital roles in enriching animal diversity, while male hybrid sterility (MHS) of the offspring commonly suffered from spermatogenic arrest constitutes the postzygotic reproductive isolation. Cattle-yak, the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens) can serve as an ideal MHS animal model. Although meiotic arrest was found to contribute to MHS of cattle-yak, yet the cellular characteristics and developmental potentials of male germline cell in pubertal cattle-yak remain to be systematically investigated. RESULTS: Single-cell RNA-seq analysis of germline and niche cell types in pubertal testis of cattle-yak and yak indicated that dynamic gene expression of developmental germ cells was terminated at late primary spermatocyte (meiotic arrest) and abnormal components of niche cell in pubertal cattle-yak. Further in vitro proliferation and differentially expressed gene (DEG) analysis of specific type of cells revealed that undifferentiated spermatogonia of cattle-yak exhibited defects in viability and proliferation/differentiation potentials. CONCLUSION: Comparative scRNA-seq and in vitro proliferation analysis of testicular cells indicated that not only meiotic arrest contributed to MHS of cattle-yak. Spermatogenic arrest of cattle-yak may originate from the differentiation stage of undifferentiated spermatogonia and niche cells of cattle-yak may provide an adverse microenvironment for spermatogenesis.

A Benzil- and BODIPY-Based Turn-On Fluorescent Probe for Detection of Hydrogen Peroxide.

Faced with rising threats of terrorism, environmental and health risks, achieving sensitive and selective detection of peroxide-based explosives (PEs) has become a global focus. In this study, a turn-on fluorescent probe (BOD) based on benzil (H2O2-recognition element) and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) derivative (fluorophore) was developed to sensitively and specifically detect hydrogen peroxide (H2O2). The synthesized BOD had a very weak fluorescence due to intramolecular donor-excited photo-induced electron transfer (d-PET) effect; however, it could emit a strong fluorescence since H2O2 selectively oxidized the benzil moiety and released free BODIPY fluorophore (BOD-COOH). As a result, the proposed BOD detected H2O2 in linear detection ranged from 25 to 125 µM with a detection limit of 4.41 µM. Meanwhile, the proposed BOD showed good selectivity toward H2O2, which is not affected by other common reactive oxygen species (ROS) and ions from explosive residues. In addition, a blue shift from 508 to 498 nm was observed in the absorption spectra upon addition of H2O2. More importantly, the BOD was successfully applied for rapid detection of H2O2 vapor with good sensitivity (down to 7 ppb), which holds great potential for practical use in public safety, forensic analysis and environmental monitoring.

Correction of multi-scale sunglint reflections from the water surface in airborne high-spatial resolution optical images.

Airborne optical images (AOI) are often with complex sunglint reflections, which brings a certain influence to watercolor retrieval. This includes the sunglint reflection with water surface statistical distribution characteristics caused by imaging viewing angles differences, with high spatial resolution surface discrete characteristics sharing similar viewing angles, and the surface Fresnel reflection sunglint differences caused by the skylight difference during the flight of unmanned aerial vehicles. Aiming at the multiscale optical characteristics of sunglint reflection in high spatial resolution AOI, based on multi-path optical radiation transmission, the sunglint reflection interference from three different imaging processes is clarified. We developed a correction method to eliminate these different sunglint reflections on water surfaces and improve the reflectivity accuracy. The comparison with the in situ measured remote sensing reflectance of water indicated that the root mean square error (RMSE) was reduced from 0.0009 sr-1 to 0.0004 sr-1, and the mean relative error (MRE) decreased from 21.8% to 15.7%. This method has also been applied to correct the Airborne Visible Infrared Imaging Spectrometer (AVIRIS) images, showing good applicability. The method is fast, effective, and without auxiliary parameters, which provides a correction reference for different surface sunglint corrections of various AOI.

Dysregulated genes in undifferentiated spermatogonia and Sertoli cells are associated with the spermatogenic arrest in cattleyak.

Hybrid male sterility (HMS) is a reproductive isolation mechanism limiting the formation of fertile offspring through interspecific fertilization. Cattleyak is the interspecific hybrid presenting significant heterosis in several economic traits, but HMS restricted its wide reproduction in cettleyak breeding. In this study, we detected the specifically expressed genes of a variety of cells (undifferentiated spermatogonia, primary spermatocytes, secondary spermatocytes, haploid spermatids, sperm, Sertoli cells, Leydig cells, and macrophages) in the testis of yak and cattleyak, and found that the spermatogenesis of cattleyak might be blocked at meiosis I, and the expression of niche factors (NR5A1, GATA4, STAR, CYP11A1, CD68, TNF, and CX3CR1) in undifferentiated spermatogonia niche was abnormal. Then we isolated the undifferentiated spermatogonia and Sertoli cells from yak and cattleyak by enzyme digestion, and detected the specific genes in the two bovid testicular cells as well as the proliferation capacity of the undifferentiated spermatogonia. These results indicated that weak proliferation ability and scarce number of undifferentiated spermatogonia and abnormal gene expressions in Sertoli cells may contribute to male sterility of cattleyak.

Target-Binding Accelerated Response for Sensitive Detection of Basal H2O2 in Tumor Cells and Tissues via a Dual-Functional Fluorescence Probe.

Aberrant production of H2O2 is involved in cancer. The levels of H2O2 are significantly higher in tumor cells than in normal cells. It is important to develop fluorescent probes to image basal H2O2 selectively in tumor cells. So far, a cancer cell-targeting probe to image basal H2O2 has not been reported. Thus, we developed a fluorescent probe, BBHP, which contains benzil as a H2O2-recognition site and biotin as a target binding motif for the selective and sufficient detection of H2O2 in tumor cells. BBHP enables a selective fluorescence turn-on response to H2O2. The binding of the probe with biotin receptors can greatly accelerate the fluorescence response to H2O2. As a result, BBHP can sufficiently image basal H2O2 in biotin receptor-positive cancer cells and tumor tissues. Finally, BBHP was successfully applied to discriminate between cancerous and normal tissues.

Characterization of Various Subunit Combinations of ADP-Glucose Pyrophosphorylase in Duckweed (Landoltia punctata).

Background: Landoltia punctata can be used as renewable and sustainable biofuel feedstock because it can quickly accumulate high starch levels. ADP-glucose pyrophosphorylase (AGPase) catalyzes the first committed step during starch biosynthesis in higher plants. The heterotetrameric structure of plant AGPases comprises pairs of large subunits (LSs) and small subunits (SSs). Although several studies have reported on the high starch accumulation capacity of duckweed, no study has explored the underlying molecular accumulation mechanisms and their linkage with AGPase. Therefore, this study focused on characterizing the roles of different L. punctate AGPases. Methodology. Expression patterns of LpAGPs were determined through comparative transcriptome analyses, followed by coexpressing their coding sequences in Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana tabacum. Results: Comparative transcriptome analyses showed that there are five AGPase subunits encoding cDNAs in L. punctata (LpAGPS1, LpAGPS2, LpAGPL1, LpAGPL2, and LpAGPL3). Nutrient starvation (distilled water treatment) significantly upregulated the expression of LpAGPS1, LpAGPL2, and LpAGPL3. Coexpression of LpAGPSs and LpAGPLs in Escherichia coli generated six heterotetramers, but only four (LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3) exhibited AGPase activities and displayed a brownish coloration upon exposure to iodine staining. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays validated the interactions between LpAGPS1/LpAGPL2, LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3. All the five LpAGPs were fusion-expressed with hGFP in Arabidopsis protoplasts, and their green fluorescence signals were uniformly localized in the chloroplast, indicating that they are plastid proteins. Conclusions: This study uncovered the cDNA sequences, structures, subunit interactions, expression patterns, and subcellular localization of AGPase. Collectively, these findings provide new insights into the molecular mechanism of fast starch accumulation in L. punctata.

Electrochemical Sensor for the Detection of 1-Hydroxypyrene Based on Composites of PAMAM-Regulated Chromium-Centered Metal-Organic Framework Nanoparticles and Graphene Oxide.

A nanocomposite was formed by combining graphene oxide (GO) with chromium-centered metal-organic framework (Cr-MOF) nanoparticles regulated by the dendrimer polyamidoamine (PAMAM). PAMAM can successfully regulate the synthesis of Cr-MOF; in doing so, the size of Cr-MOF is reduced, its original morphology is maintained, and it has good crystallinity. A simple ultrasonication method was used to make the Cr-MOF/GO hybrid nanocomposite. Various characterization methods confirmed the successful synthesis of PAMAM/Cr-MOF/GO nanocomposites. The PAMAM/Cr-MOF/ERGO modified electrode could be used with cyclic voltammetry (CV) and differential pulse voltammetry (DPV) to study the electrochemical behaviors of 1-hydroxypyrene (1-OHPyr). The results indicated that the constructed PAMAM/Cr-MOF/ERGO electrochemical sensor had a significantly enhanced electrocatalytic effect on the electrochemical reduction of 1-OHPyr compared with the sensors with no PAMAM and the ERGO sensor, which could be ascribed to the synergetic effect from the high porosity of Cr-MOF and the high conductivity of ERGO, as well as the further electron transport action of the nanocomposite. Under the optimal conditions, the reduction peak current and concentration of 1-OHPyr showed a good linear relationship in the range of 0.1-1.0 and 1.0-6.0 µM, and the detection limit of 1-OHPyr was calculated to be 0.075 µM. Moreover, the PAMAM/Cr-MOF/ERGO electrochemical sensor constructed in this paper can be expected to provide some instructions for the construction of electrochemical sensing platforms and wider potential applications.

Cu-MOF/hemin: a bionic enzyme with excellent dispersity for the determination of hydrogen peroxide released from living cells.

The stability, repeatability and sensitivity of an electrochemical biosensor material are closely connected with the dispersibility of metal organic frameworks (MOFs) in aqueous media. Herein, a nanocomposite based on Cu-MOF/hemin, which is not only highly water-soluble but also simple and efficient in synthesis, was used for the construction of a non-enzymatic sensor to detect hydrogen peroxide (H2O2). The Cu-MOF/hemin was characterized via scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS)-mapping, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS) and thermal gravimetric analysis (TGA), which indicate that hemin and the Cu-MOF were successfully combined. As a H2O2 electrochemical biomimetic enzyme, the Cu-MOF/hemin exhibited excellent electrocatalytic performance, which was confirmed by the electrochemical experiments and chromogenic reactions, and the possible mechanism of the reactions has been deduced. The electrochemical sensor based on the biomimetic enzyme exhibited an extended linear detection range from 0.01-5.0 mM (R = 0.998), low detection limit of 4.14 µM, and high selectivity and stability under the optimized conditions. More importantly, the practical application ability of the sensor was verified by the test of H2O2 in human serum samples and it could be used for the real-time detection of H2O2 released from living cells with satisfactory results. Therefore, this novel nanocomposite has certain potential in preparing electrochemical sensing platforms for nonenzymatic biosensing and provides a new method for clinical diagnosis and real-time monitoring.

Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema.

Polygonatum cyrtonema Hua (Huangjing, HJ) has medicinal and edible value in China. However, the seeds of this plant are naturally difficult to germinate. Therefore, to elucidate the mechanism underlying the germination of this plant in order to meet the market demand, the metabolomic and transcriptomic analyses were performed in this study. We observed that plant hormones and α-amylase activity were differentially regulated when comparing germinated and un-germinated seeds. In addition, the metabolites related to phenylpropanoid and flavonoid biosynthesis were significantly up-accumulated in germinated seeds. Hydroxycinnamoyl derivatives and organic acids were observed to be significantly decreased during germination. The results of this study suggested that compared to un-germinated seeds, germinated seeds promote flavonoid synthesis and inhibit lignin synthesis which could be beneficial to the germination of HJ seeds. Furthermore, these results suggested that starch if hydrolyzed into glucose, which could provide the necessary energy for germination. Our results may help to establish a foundation for further research investigating the regulatory networks of seed germination and may facilitate the propagation of HJ seeds.

Evidences for a role of two Y-specific genes in sex determination in Populus deltoides.

Almost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene's expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera.

Correction to: Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.

We request that the following corrections be made in our article.

Quantitatively estimating main soil water-soluble salt ions content based on Visible-near infrared wavelength selected using GC, SR and VIP.

Soil salinization is the primary obstacle to the sustainable development of agriculture and eco-environment in arid regions. The accurate inversion of the major water-soluble salt ions in the soil using visible-near infrared (VIS-NIR) spectroscopy technique can enhance the effectiveness of saline soil management. However, the accuracy of spectral models of soil salt ions turns out to be affected by high dimensionality and noise information of spectral data. This study aims to improve the model accuracy by optimizing the spectral models based on the exploration of the sensitive spectral intervals of different salt ions. To this end, 120 soil samples were collected from Shahaoqu Irrigation Area in Inner Mongolia, China. After determining the raw reflectance spectrum and content of salt ions in the lab, the spectral data were pre-treated by standard normal variable (SNV). Subsequently the sensitive spectral intervals of each ion were selected using methods of gray correlation (GC), stepwise regression (SR) and variable importance in projection (VIP). Finally, the performance of both models of partial least squares regression (PLSR) and support vector regression (SVR) was investigated on the basis of the sensitive spectral intervals. The results indicated that the model accuracy based on the sensitive spectral intervals selected using different analytical methods turned out to be different: VIP was the highest, SR came next and GC was the lowest. The optimal inversion models of different ions were different. In general, both PLSR and SVR had achieved satisfactory model accuracy, but PLSR outperformed SVR in the forecasting effects. Great difference existed among the optimal inversion accuracy of different ions: the predicative accuracy of Ca2+, Na+, Cl-, Mg2+ and SO4 2- was very high, that of CO3 2- was high and K+ was relatively lower, but HCO3 - failed to have any predicative power. These findings provide a new approach for the optimization of the spectral model of water-soluble salt ions and improvement of its predicative precision.

Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.

Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group. High-throughput sequencing was used to determine the sequences of 16S rRNA gene V3-V4 variable regions of the vase solutions to analyze bacterial species, their average proportions, and absolute abundance. The results showed that the titanium ions reduced the entire bacterial counts as well as altered the absolute abundance of different bacterial species in the vase solution. The most prevalent bacteria were mainly Enterobacteriaceae, Pseudomonas veronii, Pseudomonas sp., Delftia sp., Agrobacterium sp., Sphingobacterium multivorum, Acinetobacter johnsonii, and Clostridiaceae. In combination with plate colony counts, we demonstrated that all the bacterial growths were significantly inhibited by titanium ions, regardless of their average proportions increased or decreased. These results showed that titanium ions could extend effectively the longevity of gerberas and possess the broad-spectrum antibacterial properties. This study provides a basis for further mechanism exploration of titanium ions action and its applications in cut flower preservation and agricultural production.

Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3'-RACE and High-Throughput Sequencing.

Detection of complex splice sites (SSs) and polyadenylation sites (PASs) of eukaryotic genes is essential for the elucidation of gene regulatory mechanisms. Transcriptome-wide studies using high-throughput sequencing (HTS) have revealed prevalent alternative splicing (AS) and alternative polyadenylation (APA) in plants. However, small-scale and high-depth HTS aimed at detecting genes or gene families are very few and limited. We explored a convenient and flexible method for profiling SSs and PASs, which combines rapid amplification of 3'-cDNA ends (3'-RACE) and HTS. Fourteen NAC (NAM, ATAF1/2, CUC2) transcription factor genes of Populus trichocarpa were analyzed by 3'-RACE-seq. Based on experimental reproducibility, boundary sequence analysis and reverse transcription PCR (RT-PCR) verification, only canonical SSs were considered to be authentic. Based on stringent criteria, candidate PASs without any internal priming features were chosen as authentic PASs and assumed to be PAS-rich markers. Thirty-four novel canonical SSs, six intronic/internal exons and thirty 3'-UTR PAS-rich markers were revealed by 3'-RACE-seq. Using 3'-RACE and real-time PCR, we confirmed that three APA transcripts ending in/around PAS-rich markers were differentially regulated in response to plant hormones. Our results indicate that 3'-RACE-seq is a robust and cost-effective method to discover SSs and label active regions subjected to APA for genes or gene families. The method is suitable for small-scale AS and APA research in the initial stage.