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An Integrative Analysis of Transcriptome, Proteome And International Journal of Molecular Sciences Article An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat 1,2, 1,2, 2 2 1,2 Danlong Jing y , Weiwei Chen y, Ruoqian Hu , Yuchen Zhang , Yan Xia , Shuming Wang 1,2, Qiao He 1,2, Qigao Guo 1,2,* and Guolu Liang 1,2,* 1 Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400715, China; [email protected] (D.J.); [email protected] (W.C.); [email protected] (Y.X.); [email protected] (S.W.); [email protected] (Q.H.) 2 Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China; [email protected] (R.H.); [email protected] (Y.Z.) * Correspondence: [email protected] (Q.G.); [email protected] (G.L.) These authors contributed equally to this work. y Received: 11 June 2020; Accepted: 16 July 2020; Published: 20 July 2020 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. Keywords: Eriobotrya japonica; transcriptome; flower development; transcription factor; regulatory pathways 1. 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, Int. J. Mol. Sci. 2020, 21, 5107; doi:10.3390/ijms21145107 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2020, 21, 5107 2 of 22 the United States, and Australia [1]. Reproductive development of loquat is a continuous process that is not interrupted by winter dormancy [2,3]. Moreover, almost all shoots that develop on the loquat tree are flowering shoots, whereas the number of panicles remains practically constant every year [2]. Thus, it is used as an important material of floral development for evergreen perennials in the Rosaceae family. Therefore, the regulatory mechanisms of floral development in loquat contributes to a better understanding of the flowering process in the Rosaceae family. Flowering time is critical for reproductive success and is therefore strictly regulated by endogenous and environmental signal pathways [4–7]. In Arabidopsis, six major pathways, which include photoperiod, vernalization, thermosensory, gibberellin, autonomous, and aging pathways, contribute to the regulation of flower development [8–11]. For example, 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]. Functional analysis of the floral integrators such as FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and floral meristem identity genes SQUAMOSA PROMOTER BINDING LIKE (SPL), LEAFY (LFY), and APETALA1 (AP1), have revealed complex regulatory networks of flower development [13–18]. Considerable progress in elucidating the flowering mechanism in model plants has greatly improved our understanding of the molecular networks of flower development [9,19,20]. At present, the regulatory mechanisms underlying the flower development of loquat are sorely lacking. 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. At present, transcriptomic analyses have been mainly reported in fruit development in loquat, providing sequence resources that are involved in fruit setting, development, and ripening processes [23,24]. Meanwhile, transcriptomic analysis of flower development has also been used to select the DEGs in some eudicots, such as Camellia azalea, Rosa chinensis, and Annona squamosal. In C. azalea, transcriptomic analysis revealed that some floral integrators and MADS-box (MCM1, AGAMOUS, DEFICIENS and SRF) transcription factors (TFs) are involved in floral development [25]. Comparative transcriptome analysis of flower development in R. chinensis reported that DEGs are involved in the pathways of circadian clock, sugar metabolism, and hormones [26]. Transcriptomic analysis of A. squamosal indicated that various transcription factors are associated with floral transition and flower development [27]. However, an integrative analysis of transcriptome and proteome in the flower development of non-vernalization requiring loquat remains largely unknown and requires further research. In this study, we investigated the changes of gene expression dynamics and protein fluctuations during flower development in loquat at three stages, i.e., flower bud differentiation (FBD), flower bud elongation (FBE) and floral anthesis (FA), using transcriptome and proteome sequencing. Analyses of some key DEGs, metabolic pathways, and endogenous hormones highlighted the effect of key flowering genes and metabolic pathways on flower development. Our data provide abundant sequence resources for further clarification of the underlying mechanisms of flower development in loquat and other Rosaceae species. 2. Results 2.1. Morphological Characterization of Flower Development To characterize flower development, we assessed morphological changes during the flower development process. Nine morphologically distinct stages were defined. Vegetativeapex development was stage 1, which was embraced by rudimentary leaves (Figure1S1). Floral meristem initiation and Int. J. Mol. Sci. 2020, 21, 5107 3 of 22 Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 3 of 21 flowerinitiation bud and di ffflowererentiation bud weredifferentiation stage 2 (Figure were 1stageS2). Rapid2 (Figure di ff erentiation1S2). Rapid ofdifferentiation floral buds was of stagefloral 3,buds when was the stage top leaves 3, when were darkthe top green, leaves and thewere flower dark buds green, elongated and the longitudinally flower buds (Figure elongated1S3). Stagelongitudinally 4 was rapid (Figure panicle 1S3). elongation Stage 4 (Figurewas rapid1S4). panicle Then, floral elongation bud elongation (Figure and1S4). visible Then,floral floral buds bud wereelongation stage 5and (Figure visible1S5). floral Stage buds 6 waswere the stage elongation 5 (Figure of 1S5). branches Stage in 6 awas panicle the elongation (Figure1S6). of branches Stage 7 wasin a whitepanicle corollas (Figure of 1S6). floral Stage buds 7 (Figure was white1S7). corollas Stage 8was of floral floral buds anthesis (Figure and full1S7). bloom Stage (Figure8 was 1floralS8). Stageanthesis 9 was and petal full bloom fall (Figure (Figure1S9). 1S8). Stage 9 was petal fall (Figure 1S9). Figure 1. Morphological changes of flower flower development in loquat (excellent triploid line ‘CB-1 ‘CB-1 Q11’). Q11’). ((S1)) VegetativeVegetative apex.apex. ( S2) FloralFloral meristemmeristem initiationinitiation andand flowerflower budbud didifferentiation.fferentiation. (S3) RapidRapid didifferentiationfferentiation of floralfloral buds.buds. (S4) PaniclePanicle elongation.elongation. ( S5) Floral bud elongationelongation with visiblevisible floralfloral buds. ( S6) Elongation of branches inin aa panicle.panicle. (S7) White corollas ofof floralfloral
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