Analysis of expression profile of selected genes expressed during auxin-induced somatic embryogenesis in leaf base system of wheat (Triticum aestivum) and their possible interactions

Abstract

Somatic embryogenesis is a notable illustration of plant totipotency and involves reprogramming of development in somatic cells toward the embryogenic pathway. Auxins are key components as their exogenous application recuperates the embryogenic potential of the mitotically quiescent somatic cells. In order to unravel the molecular basis of somatic embryogenesis, cDNA library was made from the regeneration proficient wheat leaf base segments treated with auxin. In total, 1440 clones were sequenced and among these 1,196 good quality sequences were assembled into 270 contigs and 425 were singletons. By reverse northern analysis, a total of 57 clones were found to be upregulated during somatic embryogenesis, 64 during 2,4-D treatment, and 170 were common to 2,4-D treatment and somatic embryogenesis. A substantial number of genes involved in hormone response, signal transduction cascades, defense, anti-oxidation, programmed cell death/senescence and cell division were identified and characterized partially. Analysis of data of select genes suggests that the induction phase of somatic embryogenesis is accompanied by the expression of genes that may also be involved in zygotic embryogenesis. The developmental reprogramming process may in fact involve multiple cellular pathways and unfolding of as yet unknown molecular events. Thus, an interaction network draft using bioinformatics and system biology strategy was constructed. The outcome of a systematic and comprehensive analysis of somatic embryogenesis associated interactome in a monocot leaf base system is presented.

Altered levels of primary metabolites in response to exogenous indole-3-acetic acid in wild type and auxin signaling mutants of <i>Arabidopsis thaliana</i>: A capillary electrophoresis-mass spectrometry analysis

“…Armstrong et al (2004) showed that 10% of the auxin-responsive genes were involved in metabolism of Arabidopsis in treated with 5 µM IAA for 1 h. Similar changes in genes related to cellular metabolism have been reported in plants treated with IAA (Goda et al 2004;Okushima et al 2005;Singla et al 2007). The IAA-induced changes in the levels of metabolites could be ascribed to altered changes in expression of appropriate genes induced by the auxin treatment.…”

Transcription Factors in the Regulation of Somatic Embryogenesis

“…In support of the expected similarities in SE-and ZE-related transcriptomes, an analysis of an embryogenic culture in rice revealed that out of 242 rice homologues of the genes that are essential for ZE in Arabidopsis, 87 % were expressed during SE (Su et al 2007). Further support for some type of convergence of the genetic determinants that control SE and ZE was provided by the observation that most of the genes that are differentially regulated during SE in various plants were revealed to represent the major TF families that are engaged in ZE (Singla et al 2007;Imin et al 2008;Chakrabarty et al 2010;Wisniewska et al 2012;Gliwicka et al 2013;Wickramasuriya and Dunwell 2015).…”

“…Besides microarrays, EST sequencing in wheat (Singla et al 2007) and RNA-seq in Arabidopsis (Wickramasuriya and Dunwell 2015) and cotton (Yang et al 2012) have been applied in order to reveal SE-related transcriptomes. The microarray-based data showed that 1-12 % of all of the genes that were significantly modulated during embryogenic induction in different plants were found to encode TFs.…”

LEAFY COTYLEDON1, FUSCA3 expression and auxin treatment in relation to somatic embryogenesis induction in Arabidopsis

“…In addition, the implementation of genomic expression methods in the recent decade has greatly speed up the identification of numerous genes with potential involvement in the determination of SE. With the use of transcriptome analysis, candidate SE-specific genes were identified in a number of plant species, including gymnosperms (Stasolla et al 2004;Aquea and Arce-Johnson 2008), Glycine max (ThibaudNissen et al 2003), Triticum aestivum (Singla et al 2007), cotton (Zeng et al 2006), maize (Che et al 2006), potato (Sharma et al 2008), oil palm (Low et al 2008) and Cyclamen persicum (Hoenemann et al 2010). The available data confirmed a substantial complexity of gene networks involved in the onset and progress of SE (Zeng et al 2007), in which genes with regulatory functions, such as transcription factors (TFs), are predominantly represented and predicted to have an essential role (Singla et al 2007).…”