An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat

Flower development is a vital developmental process in the life cycle of woody perennials, especially fruit trees. Herein, we used transcriptomic, proteomic, and hormone analyses to investigate the key candidate genes/proteins in loquat (Eriobotrya japonica) at the stages of flower bud differentiation (FBD), floral bud elongation (FBE), and floral anthesis (FA). Comparative transcriptome analysis showed that differentially expressed genes (DEGs) were mainly enriched in metabolic pathways of hormone signal transduction and starch and sucrose metabolism. Importantly, the DEGs of hormone signal transduction were significantly involved in the signaling pathways of auxin, gibberellins (GAs), cytokinin, ethylene, abscisic acid (ABA), jasmonic acid, and salicylic acid. Meanwhile, key floral integrator genesFLOWERING LOCUS T(FT) andSUPPRESSOR OF OVEREXPRESSION OF CONSTANS1(SOC1) and floral meristem identity genesSQUAMOSA PROMOTER BINDING LIKE(SPL),LEAFY(LFY),APETALA1(AP1), andAP2were significantly upregulated at the FBD stage. However, key floral organ identity genesAGAMOUS(AG),AP3, andPISTILLATA(PI) were significantly upregulated at the stages of FBE and FA. Furthermore, transcription factors (TFs) such asbHLH(basic helix-loop-helix),NAC(no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF1/2) and cup-shaped cotyledon (CUC2)),MYB_related(myeloblastosis_related),ERF(ethylene response factor), andC2H2(cysteine-2/histidine-2) were also significantly differentially expressed. Accordingly, comparative proteomic analysis of differentially accumulated proteins (DAPs) and combined enrichment of DEGs and DAPs showed that starch and sucrose metabolism was also significantly enriched. Concentrations of GA(3)and zeatin were high before the FA stage, but ABA concentration remained high at the FA stage. Our results provide abundant sequence resources for clarifying the underlying mechanisms of the flower development in loquat.