Dataset Information

Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture.

ABSTRACT: Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (Triticum aestivum L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and somatic embryogenesis were identified through deep sequencing of small RNAs (sRNAs) and analyzed with bioinformatics tools. Six sRNA libraries derived from calli of IMEs and MEs after 3, 6, or 15 d of culture (DC) were constructed and sequenced. A total of 85 known miRNAs were identified, of which 30, 33, and 18 were differentially expressed (P < 0.05) between the IME and ME libraries at 3, 6, and 15 DC, respectively. Additionally, 171 novel and 41 candidate miRNAs were also identified, of the novel miRNA, 69, 67, and 37 were differentially expressed (P < 0.05) between the two types of libraries at 3, 6, and 15 DC, respectively. The expression patterns of eight known and eight novel miRNAs were validated using quantitative real-time polymerase chain reaction. Gene ontology annotation of differentially expressed miRNA targets provided information regarding the underlying molecular functions, biological processes, and cellular components involved in embryogenic callus development. Functional miRNAs, such as miR156, miR164, miR1432, miR398, and miR397, differentially expressed in IMEs and MEs might be related to embryogenic callus formation and somatic embryogenesis. This study suggests that miRNA plays an important role in embryogenic callus formation and somatic embryogenesis in wheat, and our data provide a useful resource for further research.

SUBMITTER: Chu Z

PROVIDER: S-EPMC5003897 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture.

Chu Zongli Z Chen Junying J Xu Haixia H Dong Zhongdong Z Chen Feng F Cui Dangqun D

Frontiers in plant science 20160830

Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (Triticum aestivum L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and ...[more]

PMID: 27625667

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Project description:BackgroundDuring asexual reproduction the embryogenic callus can differentiate into a new plantlet, offering great potential for fostering in vitro culture efficiency in plants. The immature embryos (IMEs) of wheat (Triticum aestivum L.) are more easily able to generate embryogenic callus than mature embryos (MEs). To understand the molecular process of embryogenic callus formation in wheat, de novo transcriptome sequencing was used to generate transcriptome sequences from calli derived from IMEs and MEs after 3d, 6d, or 15d of culture (DC).ResultsIn total, 155 million high quality paired-end reads were obtained from the 6 cDNA libraries. Our de novo assembly generated 142,221 unigenes, of which 59,976 (42.17%) were annotated with a significant Blastx against nr, Pfam, Swissprot, KOG, KEGG, GO and COG/KOG databases. Comparative transcriptome analysis indicated that a total of 5194 differentially expressed genes (DEGs) were identified in the comparisons of IME vs. ME at the three stages, including 3181, 2085 and 1468 DEGs at 3, 6 and 15 DC, respectively. Of them, 283 overlapped in all the three comparisons. Furthermore, 4731 DEGs were identified in the comparisons between stages in IMEs and MEs. Functional analysis revealed that 271transcription factor (TF) genes (10 overlapped in all 3 comparisons of IME vs. ME) and 346 somatic embryogenesis related genes (SSEGs; 35 overlapped in all 3 comparisons of IME vs. ME) were differentially expressed in at least one comparison of IME vs. ME. In addition, of the 283 overlapped DEGs in the 3 comparisons of IME vs. ME, excluding the SSEGs and TFs, 39 possessed a higher rate of involvement in biological processes relating to response to stimuli, in multi-organism processes, reproductive processes and reproduction. Furthermore, 7 were simultaneously differentially expressed in the 2 comparisons between the stages in IMEs, but not MEs, suggesting that they may be related to embryogenic callus formation. The expression levels of genes, which were validated by qRT-PCR, showed a high correlation with the RNA-seq value.ConclusionsThis study provides new insights into the role of the transcriptome in embryogenic callus formation in wheat, and will serve as a valuable resource for further studies addressing embryogenic callus formation in plants.

Project description:Wheat is an important cereal crop, which is adversely affected by water deficit stress. The effect of induced stress can be reduced by the application of salicylic acid (SA). With the objective to combat drought stress in wheat, an experiment was conducted in greenhouse under hydroponic conditions. The treatments consisted of (a) no drought (DD0 = 0 MPa), mild drought (DD1 = -0.40 MPa) and severe drought (DD2 = -0.60 MPa) by applying PEG-8000, (b) two contrasting wheat varieties Barani-17 (drought tolerant) and Anaj-17 (drought-sensitive), and (c) foliar treatments of salicylic acid (0, 50 mM, 75 mM, and 100 mM). Evaluation of wheat plants regarding biochemical, physiological, and morphological attributes were rendered after harvesting of plants. Statistically, maximum shoot and root fresh and dry weights (18.77, 11.15 and 1.99, 1.81 g, respectively) were recorded in cultivar Barani-17 under no drought condition with the application of SA (100 mM). While, minimum shoot and root fresh and dry weights (6.65, 3.14 and 0.73, 0.61 g, respectively) were recorded in cultivar Anaj-2017 under mild drought stress without SA application. The maximum shoot length (68.0 cm) was observed in cultivar Barani-2017 under no drought condition with the application of SA (100 mM). While, maximum root length (59.67 cm) was recorded in cultivar Anaj-17 under moderate drought stress without application of SA. Further, minimum shoot length (28.67 cm) was recorded in Anaj-17 under moderate drought stress without SA application. Minimum root length (38.67 cm) was recorded in cultivar Barani-17 under no drought condition without SA application. Furthermore, maximum physio-biochemical traits, including membrane stability index (MSI), chlorophyl content, photosynthetic rates, stomatal conductance, antioxidant enzymatic activities and relative water content (RWC) were found highest in cultivar Barani-17 under no drought stress and SA application at 100 mM. However, minimum values of these traits were recorded in cultivar Anaj-17 under severe drought stress without SA application. Our results also demonstrated that under severe drought, application of SA at 100 mM significantly increased leaf nitrogen (N), phosphrus (P) and potassium (K) contents and cultivar Barani-17 demonstrated significantly higher values than Anaj-17. The obtained results also indicated that the cultivation of wheat under drought stress conditions noticeably declines the morphological, physiological, and biochemical attributes of the plants. However, the exogenous application of SA had a positive impact on wheat crop for enhancing its productivity.

Dataset Information

Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture.

Publications

Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture.

Similar Datasets

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