Abstract:
BACKGROUND:During 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). RESULTS:In 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. CONCLUSIONS:This 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.
journal_name
BMC Plant Bioljournal_title
BMC plant biologyauthors
Chu Z,Chen J,Sun J,Dong Z,Yang X,Wang Y,Xu H,Zhang X,Chen F,Cui Ddoi
10.1186/s12870-017-1204-2subject
Has Abstractpub_date
2017-12-19 00:00:00pages
244issue
1issn
1471-2229pii
10.1186/s12870-017-1204-2journal_volume
17pub_type
杂志文章abstract:BACKGROUND:Homeostasis of the proteome is critical to the development of chloroplasts and also affects the expression of certain nuclear genes. CLPC1 facilitates the translocation of chloroplast pre-proteins and mediates protein degradation. RESULTS:We found that proteins involved in photosynthesis are dramatically de...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1396-0
更新日期:2018-09-12 00:00:00
abstract:BACKGROUND:Alfalfa is a high-quality forage cultivated widely in northern China. Recently, the failure of alfalfa plants to survive the winter has caused substantial economic losses. Water management has attracted considerable attention as a method for the potential improvement of winter survival. The aim of this study...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-2233-9
更新日期:2020-01-08 00:00:00
abstract:BACKGROUND:Suaeda salsa L. (S. salsa) is an annual euhalophyte with high salt tolerance and high value as an oil crop, traditional Chinese medicine and vegetable. However, there are few comprehensive studies on the metabolomics of S. salsa under saline conditions. RESULTS:Seedlings of S. salsa were cultured with 0, 20...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-2006-5
更新日期:2019-09-06 00:00:00
abstract:BACKGROUND:Flavonoids are secondary metabolites that play important roles in the entire tea plant life cycle and have potential health-promoting properties. MYB transcription factors (TFs) are considered potentially important regulators of flavonoid biosynthesis in plants. However, the molecular mechanisms by which MYB...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1502-3
更新日期:2018-11-20 00:00:00
abstract:BACKGROUND:Rice is highly sensitive to temperature fluctuations. Recently, the frequent occurrence of high temperature stress has heavily influenced rice production. Proper heading date in specific environmental conditions could ensure high grain yield. Rice heading greatly depends on the accurate measurement of enviro...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1330-5
更新日期:2018-06-07 00:00:00
abstract:BACKGROUND:The plant nuclear pore complex has strongly attracted the attention of the scientific community during the past few years, in particular because of its involvement in hormonal and pathogen/symbiotic signalling. In Arabidopsis thaliana, more than 30 nucleoporins have been identified, but only a few of them ha...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-015-0695-y
更新日期:2016-01-05 00:00:00
abstract:BACKGROUND:Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research. RESULTS:We developed a novel Cross-...
journal_title:BMC plant biology
pub_type: 杂志文章,meta分析
doi:10.1186/s12870-015-0493-6
更新日期:2015-05-03 00:00:00
abstract:BACKGROUND:ANGUSTIFOLIA (AN), one of the CtBP family proteins, plays a major role in microtubule-dependent cell morphogenesis. Microarray analysis of mammalian AN homologs suggests that AN might function as a transcriptional activator and regulator of a wide range of genes. Genetic characterization of AN mutants sugges...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-13-79
更新日期:2013-05-14 00:00:00
abstract:BACKGROUND:TIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in d...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-13-26
更新日期:2013-02-13 00:00:00
abstract:BACKGROUND:Among various pests, the brown planthopper (BPH) that damages rice is the major destructive pests. Understanding resistance mechanisms is a critical step toward effective control of BPH. This study investigates the proteomics of BPH interactions with three rice cultivars: the first resistant (PR) to BPH, the...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1622-9
更新日期:2019-01-18 00:00:00
abstract:BACKGROUND:miR399 and miR827 are both involved in conserved phosphorus (P) deficiency signalling pathways. miR399 targets the PHO2 gene encoding E2 enzyme that negatively regulates phosphate uptake and root-to-shoot allocation, while miR827 targets SPX-domain-containing genes that negatively regulate other P-responsive...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-13-214
更新日期:2013-12-13 00:00:00
abstract:BACKGROUND:Dehydrins play positive roles in regulating plant abiotic stress responses. The objective of this study was to characterize two dehydrin genes, CdDHN4-L and CdDHN4-S, generated by alternative splicing of CdDHN4 in bermudagrass. RESULTS:Overexpression of CdDHN4-L with φ-segment and CdDHN4-S lacking of φ-segm...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1511-2
更新日期:2018-11-26 00:00:00
abstract:BACKGROUND:During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-016-0945-7
更新日期:2016-12-01 00:00:00
abstract:BACKGROUND:We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied ...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-017-1028-0
更新日期:2017-04-21 00:00:00
abstract:BACKGROUND:High-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. How...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02645-4
更新日期:2020-09-16 00:00:00
abstract:BACKGROUND:Drought is a major abiotic stress factors that reduces agricultural productivity. GRAS transcription factors are plant-specific proteins that play diverse roles in plant development. However, the functions of a number of GRAS genes identified in rice are unknown, especially the GRAS genes related to rice dro...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-015-0532-3
更新日期:2015-06-13 00:00:00
abstract:BACKGROUND:The dispensable maize (Zea mays L.) B chromosome is highly heterochromatic and widely believed to be devoid of functional genes. Although low-copy B chromosome causes no obvious phenotype variation, its existence might influence A genome gene expression. Previous studies suggested that B chromosomes are evol...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-016-0775-7
更新日期:2016-04-16 00:00:00
abstract:BACKGROUND:Cytochrome P450 monooxygenases form a large superfamily of enzymes that catalyze diverse reactions. The P450 SU1 gene from the soil bacteria Streptomyces griseolus encodes CYP105A1 which acts on various substrates including sulfonylurea herbicides, vitamin D, coumarins, and based on the work presented here, ...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-11-67
更新日期:2011-04-15 00:00:00
abstract:BACKGROUND:Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysa...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-2138-7
更新日期:2019-11-27 00:00:00
abstract:BACKGROUND:Alternative splicing (AS) involving tandem acceptors that are separated by three nucleotides (NAGNAG) is an evolutionarily widespread class of AS, which is well studied in Homo sapiens (human) and Mus musculus (mouse). It has also been shown to be common in the model seed plants Arabidopsis thaliana and Oryz...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-10-76
更新日期:2010-04-28 00:00:00
abstract:BACKGROUND:With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological di...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-10-116
更新日期:2010-06-18 00:00:00
abstract:BACKGROUND:Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, culti...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-8-55
更新日期:2008-05-15 00:00:00
abstract:BACKGROUND:Plant defensins are small (45-54 amino acids), basic, cysteine-rich proteins that have a major role in innate immunity in plants. Many defensins are potent antifungal molecules and are being evaluated for their potential to create crop plants with sustainable disease resistance. Defensins are produced as pre...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-14-41
更新日期:2014-02-05 00:00:00
abstract:BACKGROUND:Tomato gray leaf spot caused by Stemphylium lycopersici (S. lycopersici) is a serious disease that can severely hinder tomato production. To date, only Sm has been reported to provide resistance against this disease, and the molecular mechanism underlying resistance to this disease in tomato remains unclear....
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02588-w
更新日期:2020-08-15 00:00:00
abstract:BACKGROUND:Apple is a widely cultivated fruit crop for its quality properties and extended storability. Among the several quality factors, texture is the most important and appreciated, and within the apple variety panorama the cortex texture shows a broad range of variability. Anatomically these variations depend on d...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-13-37
更新日期:2013-03-04 00:00:00
abstract:BACKGROUND:Nicotiana tabacum is an important economic crop. Topping, a common agricultural practice employed with flue-cured tobacco, is designed to increase leaf nicotine contents by increasing nicotine biosynthesis in roots. Many genes are found to be differentially expressed in response to topping, particularly gene...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-2241-9
更新日期:2020-01-20 00:00:00
abstract:BACKGROUND:Plant breeding has been proposed as one of the most effective and environmentally safe methods to control fungal infection and to reduce fumonisin accumulation. However, conventional breeding can be hampered by the complex genetic architecture of resistance to fumonisin accumulation and marker-assisted selec...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-1759-1
更新日期:2019-04-27 00:00:00
abstract:BACKGROUND:The function of 4-coumarate-CoA ligases (4CL) under abiotic stresses has been studied in plants, however, limited is known about the 4CL genes in cotton (G. hirsutum L.) and their roles in response to drought stress. RESULTS:We performed genome-wide identification of the 4CL genes in G. hirsutum and investi...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-2329-2
更新日期:2020-03-23 00:00:00
abstract:BACKGROUND:Because flavonoids and trichomes play crucial roles in plant defence, their formation requires fine transcriptional control by multiple transcription factor families. However, little is known regarding the mechanism of the R2R3-MYB transcription factors that regulate both flavonoid metabolism and trichome de...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-1876-x
更新日期:2019-06-18 00:00:00
abstract:BACKGROUND:Trees belonging to the Casuarinaceae and Betulaceae families play an important ecological role and are useful tools in forestry for degraded land rehabilitation and reforestation. These functions are linked to their capacity to establish symbiotic relationships with a nitrogen-fixing soil bacterium of the ge...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-014-0342-z
更新日期:2014-12-10 00:00:00