Liu Chuan-He, Fan Chao
Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China; Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China.
Front Plant Sci. 2016 Feb 26;7:203. doi: 10.3389/fpls.2016.00203. eCollection 2016.
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 three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-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 VRN1 expression 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.
菠萝的一个显著特征是其能够响应外部乙烯刺激而进行成花诱导。然而，关于这一过程背后的分子机制的信息却很少。在本研究中，通过RNA测序和基因表达谱分析，鉴定了与Ct植株（对照，清水）相比，暴露于1.80 mL·L(-1)（T1）或2.40 mL·L(-1)乙烯利（T2）的植株中的差异表达基因（DEG）。Illumina测序产生了65,825,224条高质量读段，这些读段被组装成129,594个单基因，平均序列长度为1173 bp。在这些单基因中，24,775个被分配到特定的KEGG途径，其中代谢途径和次生代谢物的生物合成是最主要的。对注释的单基因进行基因本体（GO）分析表明，大多数基因参与代谢和细胞过程、细胞和细胞部分、催化活性和结合。基因表达谱分析显示，在T1与Ct、T2与Ct以及T2与T1的比较中，分别有3788、3062和758个DEG。GO分析表明，这些DEG主要被注释到代谢和细胞过程、细胞和细胞部分、催化活性以及结合。KEGG途径分析揭示了DEG中几个重要途径的富集，包括代谢途径、次生代谢物的生物合成和植物激素信号转导。13个DEG被鉴定为与乙烯利诱导成花过程相关的候选基因，包括3个类ERF基因、1个类ETR基因、1个类LTI基因、1个类FT基因、1个类VRN1基因、3个类FRI基因、1个类AP1基因、1个类CAL基因和1个类AG基因。qPCR分析表明，这13个候选基因表达的变化与相应的RPKM值的变化一致，证实了RNA测序和基因表达谱分析结果的准确性和可靠性。乙烯利介导的诱导可能通过增加LTI、FT和VRN1的表达以及促进参与花发育的花分生组织特征基因的上调，来模拟菠萝花转变过程中的春化作用。筛选出的候选基因可用于研究菠萝开花途径的分子机制以及其他各种生物学机制。
