Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing

<p>Abstract</p> <p>Background</p> <p>Tumourous stem mustard (<it>Brassica juncea </it>var. <it>tumida </it>Tsen et Lee) is an economically and nutritionally important vegetable crop of the <it>Cruciferae </it>family that also provides the raw material for <it>Fuling </it>mustard. The genetics breeding, physiology, biochemistry and classification of mustards have been extensively studied, but little information is available on tumourous stem mustard at the molecular level. To gain greater insight into the molecular mechanisms underlying stem swelling in this vegetable and to provide additional information for molecular research and breeding, we sequenced the transcriptome of tumourous stem mustard at various stem developmental stages and compared it with that of a mutant variety lacking swollen stems.</p> <p>Results</p> <p>Using Illumina short-read technology with a tag-based digital gene expression (DGE) system, we performed <it>de novo </it>transcriptome assembly and gene expression analysis. In our analysis, we assembled genetic information for tumourous stem mustard at various stem developmental stages. In addition, we constructed five DGE libraries, which covered the strains <it>Yong'an </it>and <it>Dayejie </it>at various development stages. Illumina sequencing identified 146,265 unigenes, including 11,245 clusters and 135,020 singletons. The unigenes were subjected to a BLAST search and annotated using the GO and KO databases. We also compared the gene expression profiles of three swollen stem samples with those of two non-swollen stem samples. A total of 1,042 genes with significantly different expression levels occurring simultaneously in the six comparison groups were screened out. Finally, the altered expression levels of a number of randomly selected genes were confirmed by quantitative real-time PCR.</p> <p>Conclusions</p> <p>Our data provide comprehensive gene expression information at the transcriptional level and the first insight into the understanding of the molecular mechanisms and regulatory pathways of stem swelling and development in this plant, and will help define new mechanisms of stem development in non-model plant organisms.</p

Selective modes affect gene feature and function differentiation of tetraploid Brassica species in their evolution and domestication

The genus Brassica contains a diverse group of important vegetables and oilseed crops. Genome sequencing has been completed for the six species (B. rapa, B. oleracea, B. nigra, B. carinata, B. napus, and B. juncea) in U’s triangle model. The purpose of the study is to investigate whether positively and negatively selected genes (PSGs and NSGs) affect gene feature and function differentiation of Brassica tetraploids in their evolution and domestication. A total of 9,701 PSGs were found in the A, B and C subgenomes of the three tetraploids, of which, a higher number of PSGs were identified in the C subgenome as comparing to the A and B subgenomes. The PSGs of the three tetraploids had more tandem duplicated genes, higher single copy, lower multi-copy, shorter exon length and fewer exon number than the NSGs, suggesting that the selective modes affected the gene feature of Brassica tetraploids. The PSGs of all the three tetraploids enriched in a few common KEGG pathways relating to environmental adaption (such as Phenylpropanoid biosynthesis, Riboflavin metabolism, Isoflavonoid biosynthesis, Plant-pathogen interaction and Tropane, piperidine and pyridine alkaloid biosynthesis) and reproduction (Homologous recombination). Whereas, the NSGs of the three tetraploids significantly enriched in dozens of biologic processes and pathways without clear relationships with evolution. Moreover, the PSGs of B. carinata were found specifically enriched in lipid biosynthesis and metabolism which possibly contributed to the domestication of B. carinata as an oil crop. Our data suggest that selective modes affected the gene feature of Brassica tetraploids, and PSGs contributed in not only the evolution but also the domestication of Brassica tetraploids

Genomic prediction of drought tolerance during seedling stage in maize using low-cost molecular markers

Drought tolerance in maize is a complex and polygenic trait, especially in the seedling stage. In plant breeding, complex genetic traits can be improved by genomic selection (GS), which has become a practical and effective breeding tool. In the present study, a natural maize population named Northeast China core population (NCCP) consisting of 379 inbred lines were genotyped with diversity arrays technology (DArT) and genotyping-by-sequencing (GBS) platforms. Target traits of seedling emergence rate (ER), seedling plant height (SPH), and grain yield (GY) were evaluated under two natural drought stress environments in northeast China. Adequate genetic variations were observed for all the target traits, but they were divergent across environments. Similarly, the heritability of the target trait also varied across years and environments, the heritabilities in 2019 (0.88, 0.82, 0.85 for ER, SPH, GY) were higher than those in 2020 (0.65, 0.53, 0.33) and cross-2-years (0.32, 0.26, 0.33). In total, three marker datasets, 11,865 SilicoDArT markers obtained from the DArT-seq platform, 7837 SNPs obtained from the DArT-seq platform, and 91,003 SNPs obtained from the GBS platform, were used for GS analysis after quality control. The results of phylogenetic trees showed that broad genetic diversity existed in the NCCP population. Genomic prediction results showed that the average prediction accuracies estimated using the DArT SNP dataset under the two-fold cross-validation scheme were 0.27, 0.19, and 0.33, for ER, SPH, and GY, respectively. The result of SilicoDArT is close to the SNPs from DArT-seq, those were 0.26, 0.22, and 0.33. For the trait with lower heritability, the prediction accuracy can be improved using the dataset filtered by linkage disequilibrium. For the same trait, the prediction accuracies estimated with two DArT marker datasets were consistently higher than that estimated with the GBS SNP dataset under the same genotyping cost. The prediction accuracy was improved by controlling population structure and marker quality, even though the marker density was reduced. The prediction accuracies were improved by more than 30% using the significant-associated SNPs. Due to the complexity of drought tolerance under the natural stress environments, multiple years of data need to be accumulated to improve prediction accuracy by reducing genotype-by-environment interaction. Modeling genotype-by-environment interaction into genomic prediction needs to be further developed for improving drought tolerance in maize. The results obtained from the present study provides valuable pathway for improving drought tolerance in maize using GS

Changes in sucrose metabolism in maize varieties with different cadmium sensitivities under cadmium stress.

Sucrose metabolism contributes to the growth and development of plants and helps plants cope with abiotic stresses, including stress from Cd. Many of these processes are not well-defined, including the mechanism underlying the response of sucrose metabolism to Cd stress. In this study, we investigated how sucrose metabolism in maize varieties with low (FY9) and high (SY33) sensitivities to Cd changed in response to different levels of Cd (0 (control), 5, 10, and 20 mg L-1 Cd). The results showed that photosynthesis was impaired, and the biomass decreased, in both varieties of maize at different Cd concentrations. Cd inhibited the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SS) (sucrose synthesis), and stimulated the activities of acid invertase (AI) and SS (sucrose hydrolysis). The total soluble sugar contents were higher in the Cd-treated seedlings than in the control. Also, Cd concentrations in the shoots were higher in SY33 than in FY9, and in the roots were lower in SY33 than in FY9. The decreases in the photosynthetic rate, synthesis of photosynthetic products, enzyme activity in sucrose synthesis direction, and increases in activity in hydrolysis direction were more obvious in SY33 (the sensitive variety) than in FY9 (the tolerant variety), and more photosynthetic products were converted into soluble sugar in SY33 than in FY9 as the Cd stress increased. The transcript levels of the sugar transporter genes also differed between the two varieties at different concentrations of Cd. These results suggest that sucrose metabolism may be a secondary response to Cd additions, and that the Cd-sensitive variety used more carbohydrates to defend against Cd stress rather than to support growth than the Cd-tolerant variety

Research Progress in Characterization Methods of Anti-corrosion and Wear-resistant Polyurethane Coatings

Polyurethane is a coating material widely used in the field of anti-corrosion and wear resistance. At present, a lot of research work has been carried out in the research and development of polyurethane materials and process improvement. However, there are few researches on the characterization methods of polyurethane coatings, and suitable characterization methods are selected. Conducive to the improvement and application of materials. This article summarizes the characterization methods of polyurethane coatings from the aspects of morphology, structure, mechanical properties, electrochemical properties and thermodynamic properties. It is found that there is no standardized and unified evaluation standard for the electrochemical characterization methods of polyurethane; polyurethane as a high molecular polymer has a certain sensitivity to the service environment. Humidity and temperature have a great influence on its physical and chemical properties. Conventional characterization methods cannot perform microstructure characterization under the stress state of the material and the service environment. The establishment of standardized and unified electrochemical evaluation standards for polyurethane; the ability to characterize polyurethane under service conditions is an important research direction for improving the characterization method

Cost effectiveness analysis of total laparoscopic hysterectomy versus total abdominal hysterectomy for uterine fibroids in Western China:a societal perspective

BACKGROUND: As a common female pelvic tumor, uterine fibroids remain the leading cause for hysterectomy in China. Hysterectomy provides a good surgical treatment of uterine fibroids, and it guarantees the removal of all uterine fibroids without lower risk of recurrence. This study compares the cost effectiveness of total laparoscopic hysterectomy (TLH) versus total abdominal hysterectomy (TAH) for women with uterine fibroids from a societal perspective. METHODS: An economic analysis was conducted in 392 patients (TLH n = 75; TAH n = 317), including all relevant costs over a 12-month time horizon. Primary outcome was major surgical complications; secondary outcomes were postoperative discomfort symptoms and time of return to normal activities. Clinical, outcomes and costs data were collected from medical records, telephone survey and financial information system. Generalized linear models were used to assess costs and outcomes differences between the two groups. Incremental cost effectiveness ratio (ICER) was used to estimate the cost effectiveness. RESULTS: Mean direct costs were $2,925.71 for TLH,$2,436.24 for TAH, respectively. Mean indirect costs were $1,133.22 for TLH,$1,394.85 for TAH, respectively. Incremental societal costs were $256.86 (95$5,669.16 (95%CI: 5,384.76–5,955.56) per complication averted, $3,801.54 (95$202.96 (95%CI: 194.97–210.95) per week saved to return to normal activities. CONCLUSIONS: TLH is cost effective compared with TAH in preventing additional complications based on our estimated conservative threshold in China. The findings provide useful information for researchers to conduct further cost effectiveness analysis based on prospective study which can provide stronger and more evidence, in China. In addition, the data may be useful for Chinese health care policy-makers and medical insurance payers to make related health care decisions

Genome-Wide Investigation and Characterization of SWEET Gene Family with Focus on Their Evolution and Expression during Hormone and Abiotic Stress Response in Maize

The sugar will eventually be exported transporters (SWEET) family is an important group of transport carriers for carbon partitioning in plants and has important functions in growth, development, and abiotic stress tolerance. Although the SWEET family is an important sugar transporter, little is known of the functions of the SWEET family in maize (Zea mays), especially in response to abiotic stresses. To further explore the response pattern of maize SWEET to abiotic stress, a bioinformatics-based approach was used to predict and identify the maize SWEET gene (ZmSWEET) family. Twenty-four ZmSWEET genes were identified using the MaizeGDB database. Phylogenetic analysis resolved these twenty-four genes into four clades. One tandem and five segmental duplication events were identified, which played a major role in ZmSWEET family expansion. Synteny analysis provided insight into the evolutionary characteristics of the ZmSWEET genes with those of three graminaceous crop species. A heatmap showed that most ZmSWEET genes responded to at least one type of abiotic stress. By an abscisic acid signaling pathway, among which five genes were significantly induced under NaCl treatment, eight were obviously up-regulated under PEG treatment and five were up-regulated under Cd stress, revealing their potential functions in response to abiotic stress. These findings will help to explain the evolutionary links of the ZmSWEET family and contribute to future studies on the functional characteristics of ZmSWEET genes, and then improve abiotic stress tolerance in maize through molecular breeding

Enhanced P-Type GaN Conductivity by Mg Delta Doped AlGaN/GaN Superlattice Structure

A method of combining the AlGaN/GaN superlattices and Mg delta doping was proposed to achieve a high conductivity p-type GaN layer. The experimental results provided the evidence that the novel doping technique achieves superior p-conductivity. The Hall-effect measurement indicated that the hole concentration was increased by 2.06 times while the sheet resistivity was reduced by 48%. The fabricated green-yellow light-emitting diodes using the achieved high conductivity p-type GaN layer showed an 8- and 10-times enhancement of light output power and external quantum efficiency, respectively. The subsequent numerical calculation was conducted by using an Advanced Physical Model of Semiconductor Device to reveal the mechanism of enhanced device performance. This new doping technique offers an attractive solution to the p-type doping problems in wide-bandgap GaN or AlGaN materials

Genome-Wide Identification and Characterization of the CCT Gene Family in Foxtail Millet (Setaria italica) Response to Diurnal Rhythm and Abiotic Stress

The CCT gene family plays important roles in diurnal rhythm and abiotic stress response, affecting crop growth and development, and thus yield. However, little information is available on the CCT family in foxtail millet (Setaria italica). In the present study, we identified 37 putative SiCCT genes from the foxtail millet genome. A phylogenetic tree was constructed from the predicted full-length SiCCT amino acid sequences, together with CCT proteins from rice and Arabidopsis as representatives of monocotyledonous and dicotyledonous plants, respectively. Based on the conserved structure and phylogenetic relationships, 13, 5, and 19 SiCCT proteins were classified in the COL, PRR, and CMF subfamilies, respectively. The gene structure and protein conserved motifs analysis exhibited highly similar compositions within the same subfamily. Whole-genome duplication analysis indicated that segmental duplication events played an important role in the expansion of the CCT gene family in foxtail millet. Analysis of transcriptome data showed that 16 SiCCT genes had significant diurnal rhythm oscillations. Under abiotic stress and exogenous hormonal treatment, the expression of many CMF subfamily genes was significantly changed. Especially after drought treatment, the expression of CMF subfamily genes except SiCCT32 was significantly up-regulated. This work provides valuable information for further study of the molecular mechanism of diurnal rhythm regulation, abiotic stress responses, and the identification of candidate genes for foxtail millet molecular breeding