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Liu C.-H.,Guangdong Academy of Agricultural Sciences | Liu C.-H.,Key Laboratory of South Subtropical Fruit Biology | Fan C.,Guangdong Academy of Agricultural Sciences | Fan C.,Key Laboratory of South Subtropical Fruit Biology
Frontiers in Plant Science

A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL•L−1 (T1) or 2.40 mL•L−1 ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including threeERF-like genes, one ETR-like gene, one LTI-like gene, oneFT-like gene, one VRN1-like gene, three FRI-like genes, oneAP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple. © 2016, Liu and Fan. Source

Li C.-Y.,Guangdong Academy of Agricultural Sciences | Li C.-Y.,Key Laboratory of South Subtropical Fruit Biology | Deng G.-M.,South China Agricultural University | Yang J.,South China Agricultural University | And 19 more authors.
BMC Genomics

Background: Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is considered the most lethal disease of Cavendish bananas in the world. The disease can be managed in the field by planting resistant Cavendish plants generated by somaclonal variation. However, little information is available on the genetic basis of plant resistance to Foc TR4. To a better understand the defense response of resistant banana plants to the Fusarium wilt pathogen, the transcriptome profiles in roots of resistant and susceptible Cavendish banana challenged with Foc TR4 were compared.Results: RNA-seq analysis generated more than 103 million 90-bp clean pair end (PE) reads, which were assembled into 88,161 unigenes (mean size = 554 bp). Based on sequence similarity searches, 61,706 (69.99%) genes were identified, among which 21,273 and 50,410 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 33,243 (37.71%) unigenes to 119 KEGG pathways. A total of 5,008 genes were assigned to plant-pathogen interactions, including disease defense and signal transduction. Digital gene expression (DGE) analysis revealed large differences in the transcriptome profiles of the Foc TR4-resistant somaclonal variant and its susceptible wild-type. Expression patterns of genes involved in pathogen-associated molecular pattern (PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, cell wall modification genes and genes with other functions were analyzed and compared. The results indicated that basal defense mechanisms are involved in the recognition of PAMPs, and that high levels of defense-related transcripts may contribute to Foc TR4 resistance in banana.Conclusions: This study generated a substantial amount of banana transcript sequences and compared the defense responses against Foc TR4 between resistant and susceptible Cavendish bananas. The results contribute to the identification of candidate genes related to plant resistance in a non-model organism, banana, and help to improve the current understanding of host-pathogen interactions. © 2012 Li et al.; licensee BioMed Central Ltd. Source

Ma Y.,Southwest University | Ma Y.,Key Laboratory of South Subtropical Fruit Biology | Ma Y.,Guangdong Academy of Agricultural Sciences | Zhang L.,Guizhou Normal University | And 10 more authors.
Scientia Horticulturae

The ERF1 gene was well characterized in Arabidopsis to be responsive to salt, drought, heat and necrotrophic fungi. In this paper, an ortholog of ERF1, designated as CsERF that was isolated originally as an ethylene induced gene from Citrus sinensis (L.) Osbeck, was characterized. Sequence analysis revealed that CsERF and ERF1 belonged to the same AP2/ERF superfamily, or more specifically, the same IXc subgroup of the ERF subfamily. Transient expression experiment revealed that CsERF protein was localized in nuclei. Quantitative real-time PCR results showed that the expression of CsERF was induced not only by various stresses including salt, dehydration and cold, but also by stress-related hormones, such as ethylene, jasmonic acid and abscissic acid, with ethylene and cold as the two most potent inducers. Its ethylene induction could be blocked by 1-MCP, indicating ethylene signaling pathway was required for its activation. Overexpressing CsERF conferred tobacco plants with much stronger tolerance to chilling stress, and activated constitutively four indicator genes: two cold responsive transcription factor genes, NtCBF1 and NtCBF3, and two cold-induced genes, NtERD10B and NtERD10C. Under cold treatment, proline content and superoxide dismutase activity increased more rapidly and were much higher in overexpression lines than in wild type. These data suggest that CsERF plays a role in cold response in addition to the roles shared with its ortholog ERF1. © 2014. Source

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