Differentially expressed genes in Populus simonii x Populus nigra in response to NaCl stress using cDNA-AFLP

Optimization of preparation and transformation of protoplasts from Populus simonii × P. nigra leaves and subcellular localization of the major latex protein 328 (MLP328)

BACKGROUND

Populus simonii × P. nigra is an ideal material for studying the molecular mechanisms of woody plants. In recent years, research on Populus simonii × P. nigra has increasingly focused on the application of transgenic technology to improve salt tolerance. However, the rapid characterization of gene functions has been hampered by the long growth cycle and exceedingly poor transformation efficiency. Protoplasts are an important tool for plant gene engineering, which can assist with challenging genetic transformation and the protracted growth cycle of Populus simonii × P. nigra. This study established an optimized system for the preparation and transformation of protoplasts from Populus simonii × P. nigra leaves, making genetic research on Populus simonii × P. nigra faster and more convenient. Major Latex Protein (MLP) family genes play a crucial role in plant salt stress response. In the previous study, we discovered that PsnMLP328 can be induced by salt treatment, which suggested that this gene may be involved in response to salt stress. Protein localization is a suggestion for its function. Therefore, we conducted subcellular localization analysis using protoplasts of Populus simonii × P. nigra to study the function of the PsnMLP328 gene preliminarily.

RESULTS

This study established an optimized system for the preparation and transformation of Populus simonii × P. nigra protoplasts. The research results indicate that the optimal separation scheme for the protoplasts of Populus simonii × P. nigra leaves included 2.5% cellulase R-10, 0.6% macerozyme R-10, 0.3% pectolyase Y-23, and 0.8 M mannitol. After enzymatic digestion for 5 h, the yield of obtained protoplasts could reach up to 2 × 107 protoplasts/gFW, with a high viability of 98%. We carried out the subcellular localization analysis based on the optimized transient transformation system, and the results indicated that the MLP328 protein is localized in the nucleus and cytoplasm; thereby proving the effectiveness of the transformation system.

CONCLUSION

In summary, this study successfully established an efficient system for preparing and transforming leaf protoplasts of Populus simonii × P. nigra, laying the foundation for future research on gene function and expression of Populus simonii × P. nigra.

Study on the differences of phyllosphere microorganisms between poplar hybrid offspring and their parents

The females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microorganism of dioecious plants between parents and hybrid offspring remain largely unexplored. Here, the phyllosphere bacterial and fungal community diversity and composition of female (Populus nigra 'DH5' (PNDH5)), male (P. simonii 'DH4' (PSDH4)), and the hybrid offspring (P. simonii × P. nigra 'DH1' (PSPNDH1), P. simonii × P. nigra 'DH2' (PSPNDH2), P. simonii × P. nigra 'DH3' (PSPNDH3)) were investigated using 16S rDNA/ITS rDNA gene-based Illumina NovaSeq 6000 sequencing. There was considerable variation of plant height, diameter at breast height, leaf area, length of petioles, leaf moisture content, and starch among different samples, and PSDH2 owned the highest plant height, diameter at breast height, and length of petioles. No distinct differences of phyllosphere bacterial community diversity were observed among PSDH4, PNDH5, PSPNDH1, PSPNDH2, and PSPNDH3; while, PSPNDH2 owned the highest fungal Pielou_e index, Shannon index, and Simpson index. Firmicutes and Ascomycota were the predominant phyllosphere bacterial and fungal community at the phylum level, respectively. Bacilli and Gammaproteobacteria were the two most dominant bacterial classes regardless of parent and the hybrid offspring. The predominant phyllosphere fungal community was Dothideomycetes at the class level. The NMDS demonstrated that phyllosphere microbial community obviously differed between parents and offspring, while the phyllosphere microbial community presented some similarities under different hybrid progeny. Also, leaf characteristics contributed to the differentiation of phyllosphere bacterial and fungal communities between parents and hybrid offspring. These results highlighted the discrimination of phyllosphere microorganisms on parent and hybrid offspring, which provided clues to potential host-related species in the phyllosphere environment.

Association of transcription factor WRKY56 gene from Populus simonii × P. nigra with salt tolerance in Arabidopsis thaliana

The WRKY transcription factor family is one of the largest groups of transcription factor in plants, playing important roles in growth, development, and biotic and abiotic stress responses. Many WRKY genes have been cloned from a variety of plant species and their functions have been analyzed. However, the studies on WRKY transcription factors in tree species under abiotic stress are still not well characterized. To understand the effects of the WRKY gene in response to abiotic stress, mRNA abundances of 102 WRKY genes in Populus simonii × P. nigra were identified by RNA sequencing under normal and salt stress conditions. The expression of 23 WRKY genes varied remarkably, in a tissue-specific manner, under salt stress. Since the WRKY56 was one of the genes significantly induced by NaCl treatment, its cDNA fragment containing an open reading frame from P. simonii × P. nigra was then cloned and transferred into Arabidopsis using the floral dip method. Under salt stress, the transgenic Arabidopsis over-expressed the WRKY56 gene, showing an increase in fresh weight, germination rate, proline content, and peroxidase and superoxide dismutase activity, when compared with the wild type. In contrast, transgenic Arabidopsis displayed a decrease in malondialdehyde content under salt stress. Overall, these results indicated that the WRKY56 gene played an important role in regulating salt tolerance in transgenic Arabidopsis.

Hydrogen Peroxide Response in Leaves of Poplar (Populus simonii × Populus nigra) Revealed from Physiological and Proteomic Analyses

Hydrogen peroxide (H₂O₂) is one of the most abundant reactive oxygen species (ROS), which plays dual roles as a toxic byproduct of cell metabolism and a regulatory signal molecule in plant development and stress response. Populus simonii × Populus nigra is an important cultivated forest species with resistance to cold, drought, insect and disease, and also a key model plant for forest genetic engineering. In this study, H₂O₂ response in P. simonii × P. nigra leaves was investigated using physiological and proteomics approaches. The seedlings of 50-day-old P. simonii × P. nigra under H₂O₂ stress exhibited stressful phenotypes, such as increase of in vivo H₂O₂ content, decrease of photosynthetic rate, elevated osmolytes, antioxidant accumulation, as well as increased activities of several ROS scavenging enzymes. Besides, 81 H₂O₂-responsive proteins were identified in the poplar leaves. The diverse abundant patterns of these proteins highlight the H₂O₂-responsive pathways in leaves, including 14-3-3 protein and nucleoside diphosphate kinase (NDPK)-mediated signaling, modulation of thylakoid membrane structure, enhancement of various ROS scavenging pathways, decrease of photosynthesis, dynamics of proteins conformation, and changes in carbohydrate and other metabolisms. This study provides valuable information for understanding H₂O₂-responsive mechanisms in leaves of P. simonii × P. nigra.

Transgenic poplar overexpressing the endogenous transcription factor ERF76 gene improves salinity tolerance

The ethylene response factor (ERF) family is one of the largest plant-specific transcription factor families, playing an important role in plant development and response to stresses. The ERF76 gene is a member of the poplar ERF transcription factor gene family. First, we validated that the ERF76 gene expressed in leaf and root tissues is responsive to salinity stress. We then successfully cloned the ERF76 cDNA fragment containing an open reading frame from di-haploid Populus simonii × Populus nigra and proved that ERF76 protein is targeted to the nucleus. Finally, we transferred the gene into the same poplar clone by the Agrobacterium-mediated leaf disc method. Using both RNA-Seq and reverse transcription-quantitative polymerase chain reaction, we validated that expression level of ERF76 is significantly higher in transgenic plants than that in the nontransgenic control. Using RNA-Seq data, we have identified 375 genes that are differentially expressed between the transgenic plants and the control under salt treatment. Among the differentially expressed genes, 16 are transcription factor genes and 45 are stress-related genes, both of which are upregulated significantly in transgenic plants, compared with the control. Under salt stress, the transgenic plants showed significant increases in plant height, root length, fresh weight, and abscisic acid (ABA) and gibberellin (GA) concentration compared with the control, suggesting that overexpression of ERF76 in transgenic poplar upregulated the expression of stress-related genes and increased the ability of ABA and GA biosynthesis, which resulted in stronger tolerance to salt stress.

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

RNA-SEQ Reveals Transcriptional Level Changes of Poplar Roots in Different Forms of Nitrogen Treatments

Poplar has emerged as a model plant for better understanding cellular and molecular changes accompanying tree growth, development, and response to environment. Long-term application of different forms of nitrogen (such as [Formula: see text]-N and [Formula: see text]-N) may cause morphological changes of poplar roots; however, the molecular level changes are still not well-known. In this study, we analyzed the expression profiling of poplar roots treated by three forms of nitrogen: S1 ([Formula: see text]), S2 (NH4NO3), and S3 ([Formula: see text]) by using RNA-SEQ technique. We found 463 genes significantly differentially expressed in roots by different N treatments, of which a total of 112 genes were found to differentially express between S1 and S2, 171 genes between S2 and S3, and 319 genes between S1 and S3. A cluster analysis shows significant difference in many transcription factor families and functional genes family under different N forms. Through an analysis of Mapman metabolic pathway, we found that the significantly differentially expressed genes are associated with fermentation, glycolysis, and tricarboxylic acid cycle (TCA), secondary metabolism, hormone metabolism, and transport processing. Interestingly, we did not find significantly differentially expressed genes in N metabolism pathway, mitochondrial electron transport/ATP synthesis and mineral nutrition. We also found abundant candidate genes (20 transcription factors and 30 functional genes) regulating morphology changes of poplar roots under the three N forms. The results obtained are beneficial to a better understanding of the potential molecular and cellular mechanisms regulating root morphology changes under different N treatments.

Identification of Differentially Expressed Genes by cDNA-AFLP Technique in Response to Drought Stress in Triticum durum

Drought is the single largest abiotic stress factor leading to reduced crop yields. The identification of differentially expressed genes and the understanding of their functions in environmentally stressful conditions are essential to improve drought tolerance. Transcriptomics is a powerful approach for the global analysis of molecular mechanisms under abiotic stress. To identify genes that are important for drought tolerance, we analyzed mRNA populations from untreated and drought-stressed leaves of Triticum durum by cDNA- -amplified fragment length polymorphism (cDNA-AFLP) technique. Overall, 76 transcript- -derived fragments corresponding to differentially induced transcripts were successfully sequenced. Most of the transcripts identified here, using basic local alignment search tool (BLAST) database, were genes belonging to different functional categories related to metabolism, energy, cellular biosynthesis, cell defense, signal transduction, transcription regulation, protein degradation and transport. The expression patterns of these genes were confirmed by quantitative reverse transcriptase real-time polymerase chain reaction (qRT- -PCR) based on ten selected genes representing different patterns. These results could facilitate the understanding of cellular mechanisms involving groups of genes that act in coordination in response to stimuli of water deficit. The identification of novel stress-responsive genes will provide useful data that could help develop breeding strategies aimed at improving durum wheat tolerance to field stress.

Oligo-dT anchored cDNA-SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.)

Differential display is a powerful technique for analyzing differences in gene expression. Oligo-dT cDNAstart codon targeted marker (cDNA-SCoT) technique is a novel, simple, cheap, rapid, and efficient method for differential gene expression research. In the present study, the oligo-dT anchored cDNA-SCoT technique was exploited to identify differentially expressed genes during several stress treatments in mango. A total of 37 primers combined with oligo-dT anchor primers 3side amplified approximately 150 fragments of 150 bp to 1500 bp in length. Up to 100 fragments were differentially expressed among the stress treatments and control samples, among which 92 were obtained and sequenced. Out of the 92 transcript derived fragments (TDFs), 70% were highly homologous to known genes, and 30% encoded unclassified proteins with unknown functions. The expression pattern of nine genes with known functions involved in several abiotic stresses in other species was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) under cold (4 °C), salinity (NaCl), polyethylene glycol (PEG, MW 6000), and heavy metal treatments in leaves and stems at different time points (0, 24, 48, and 72 h). The expression patterns of the genes (TDF4, TDF7, TDF23, TDF45, TDF49, TDF50, TDF57, TDF91 and TDF92) that had direct or indirect relationships with cold, salinity, drought and heavy metal stress response were analyzed through qRT-PCR. The possible roles of these genes are discussed. This study suggests that the oligo-dT anchored cDNA-SCoT differential display method is a useful tool to serve as an initial step for characterizing transcriptional changes induced by abiotic stresses and provide gene information for further study and application in genetic improvement and breeding in mango.

Cadmium treatment alters the expression of five genes at the Cda1 locus in two soybean cultivars [Glycine max (L.) Merr]

Westag 97 has larger capacity of Cd accumulation in roots which prevents Cd from translocating into stems and leaves; conversely, AC Hime has smaller capacity of Cd accumulation in roots; more Cd is transported into stems and leaves. The different capacity of Cd in roots between Westag 97 and AC Hime causes the different Cd concentration in seeds. Meanwhile, according to the different expression levels of RSTK, ISCP, and H(+)-ATPase between Westag 97 and AC Hime, RSTK may be involved in transporting Cd into stems and leaves; H(+)-ATPase may be correlated to the capacity of Cd accumulation in roots; and Cd caused some changes of fundamental life process which leaded to the different expression patterns of ISCP between Westag 97 and AC Hime.

Identification of candidate genes related to rice grain weight under high-temperature stress

The rise of global warming presents a problem for all living organisms, including rice and other staple plants. High temperatures impair rice grain weight by inhibiting the filling of the caryopses during the milky stage. The molecular mechanism behind this process, however, is poorly understood. Identifying candidate genes involved in responses to high-temperature stress may provide a basis for the improvement of heat tolerance in rice. Using paired, genetically similar heat-tolerant and heat-sensitive rice lines as plant materials, cDNA-AFLP analysis revealed a total of 54 transcript derived fragments (TDFs), mainly from the heat-tolerant lines. This clearly indicated variations in gene expression between the two rice lines. BLAST results showed that 28 of the 54 TDFs were homologous sequences. These homologous genes were found to encode proteins involved in signal transduction, oxidation, transcriptional regulation, transport, and metabolism. The functions and differential expression patterns of some important genes are further discussed. High temperature stress may trigger a wide range of changes in gene expression in rice caryopses, in turn affecting functions ranging from signal transduction to cellular metabolism. Forty-five of the 54 TDFs were mapped to rice chromosomes. The genes identified in the present study would make good candidates for further study into the molecular mechanisms underlying rice adaptation to high-temperature stress.