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

Shuming Wang,Yuchen Zhang,Yan Xia,Danlong Jing,Ruoqian Hu,Qiao He,Guolu Liang,Weiwei Chen,Qigao Guo

doi:10.3390/ijms21145107

Abstract

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 genes FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and floral meristem identity genes SQUAMOSA PROMOTER BINDING LIKE (SPL), LEAFY (LFY), APETALA1 (AP1), and AP2 were significantly upregulated at the FBD stage. However, key floral organ identity genes AGAMOUS (AG), AP3, and PISTILLATA (PI) were significantly upregulated at the stages of FBE and FA. Furthermore, transcription factors (TFs) such as bHLH (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), and C2H2 (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 GA3 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.

Highlights

Loquat (Eriobotrya japonica Lindl.), an important tropical and subtropical fruit tree species that belongs to the family Rosaceae and is broadly cultivated in many countries such as China, Japan, Spain, the United States, and Australia [1]
Differentially Expressed Genes (DEGs) involved in auxin, GA, cytokinin, ethylene, abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA)-signaling pathways were significantly enriched during flower development in loquat. Consistent with these results, concentrations of GA3 and ZT were high before the floral anthesis (FA) stage, but ABA concentration remained high at the FA stage
Different from previous transcriptome analysis of loquat fruit development [23,24], our results provide key DEGs that were found to be mainly involved in flowering-related genes and the pathways of plant hormone signal transduction and starch and sucrose metabolism during flower development in loquat

Summary

Introduction

Loquat (Eriobotrya japonica Lindl.), an important tropical and subtropical fruit tree species that belongs to the family Rosaceae and is broadly cultivated in many countries such as China, Japan, Spain, the United States, and Australia [1]. The photoperiod and vernalization pathways are involved in light and cold to regulate flowering, respectively, and the flowering response to temperature relies on the thermosensory pathway, which is crucial for mitigating the effects of temperature change [12] All of these pathways converge to activate a small number of floral integrator genes, which control floral development by merging signals from various pathways [8,13]. An integrative analysis of transcriptome and proteome is an extremely effective method for identifying differentially expressed genes (DEGs) from plant developmental phase at the whole genome level [21,22] This can provide further insight into the underlying mechanisms for flower development in perennial woody plants. Our data provide abundant sequence resources for further clarification of the underlying mechanisms of flower development in loquat and other Rosaceae species

Morphological Characterization of Flower Development

Key Gene Cross-Talk Between the Protein and Transcription Levels

Key Genes of TFs and Floral Integrators Associated with Flower Development

Key DEGs and DAPs Involved in Starch and Sucrose Metabolism Pathways

Plant Materials

RNA Extraction and Construction of cDNA Library

Protein Extraction and Digestion

Protein Digestion and TMT Labeling

Bioinformatics Analysis of Proteomic Data

4.10. Validation Analysis of Transcriptome Data by qRT-PCR

Conclusions