De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

Abstract

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.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1204-2) contains supplementary material, which is available to authorized users.

Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

“…We have established an e cient rubber tree SE system using immature anthers. The transcriptome analysis of plant SE revealed a large number of potential key factors of embryogenesis [25,26,[44][45][46]. In this study, we obtained the transcriptome analysis of rubber tree SE derived from EC, PE, CE, AE, MCE and WAE.…”

“…The WRKY genes showed higher expression and be related to embryogenic callus formation [82]. The up-regulated WRKY genes were high ratio in embryogenic callus formation of bread wheat [44]. In addition, MYB family was also involved in plant development and growth [83][84][85][86], hormone signal transduction [87,88].…”

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…As a functional molecular marker, SSRs generated from expressed sequence tags (EST-SSRs) can investigate the effects of environmental heterogeneity and local adaptation due to its tight linkage with functional genes controlling phenotype [20][21][22]. Up till now numbers of EST-SSRs developed and checked for polymorphism in many species, such as sweet potato [23], Sesamum indicum [24], radish [25], Cymbidium sinense [26], Chinese bayberry [27], Silver r [28], Salix, Populus, Eucalyptus [29]; Rosa roxburghii [30], Neottopteris nidus [16], Lacquar tree [31], Bread wheat [32], Proso Millet [33], Almond [34] and Ginseng [35]. Limited genomic resources have been developed for Panax species so far, e.g., P. vietnamensis var.…”

Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

“…The molecular mechanisms that orchestrate somatic embryogenesis and endow biological totipotency are becoming better understood [28]. Previous studies have shown that genes expressed during the induction of SE can be divided into three primary categories; stress-related genes, plant growth regulator (PGR) related genes, and transcription factors [29][30][31]. A biological stress, such as senescence or an acute stress such as abiotic/biotic factors can trigger stem cell formation through altered chromatin conformation and promiscuous expression of transcription factors [32][33][34].…”