甘蔗属割手密与热带种PEBP基因家族的鉴定及其开花调控功能分析

doi:10.3864/j.issn.0578-1752.2026.04.003

Abstract

Abstract:

【Objective】The phosphatidylethanolamine-binding protein (PEBP) family serves as pivotal regulators of plant flowering, orchestrating floral transition through the coordination of photoperiodic and hormonal signaling pathways. This study systematically characterized PEBP gene family members in the ancestral Saccharum species S. spontaneum and S. officinarum, elucidating their structural architecture, evolutionary trajectories, and expression profiles to unravel the molecular mechanisms governing flowering regulation and facilitate molecular breeding strategies.【Method】The PEBP gene family was identified by performing sequence alignment of Arabidopsis and rice PEBP protein sequences against the genomes of S. spontaneum and S. officinarum, supplemented with screening using the hidden Markov model profile PF01161. Phylogenetic reconstruction, gene structure analysis, conserved motif identification, and synteny evaluation were performed using MEGA-X and TBtools. Putative cis-regulatory elements within promoter regions were predicted via the PlantCARE database. Transcriptomic profiling coupled with qRT-PCR validation delineated expression dynamics, while functional characterization of FT3 and TFL1 genes was achieved through Arabidopsis transformation.【Result】Our analysis identified 23 and 20 PEBP genes in S. spontaneum and S. officinarum, respectively, classified into three subfamilies: FT-like, TFL1-like, and MFT-like. Protein characterization revealed greater variability in S. spontaneum PEBPs (151-364 aa; 17.1-40.4 kDa) compared to S. officinarum (170-191 aa; 19.2-20.8 kDa), though both predominantly encoded hydrophilic alkaline proteins. Conserved motif analysis demonstrated stringent conservation in TFL1-like subfamily members, while MFT-like proteins exhibited remarkable structural plasticity, exemplified by elongated PEBP domains in SspMFT1.1/1.2/1.3. Gene architecture analysis showed FT-like members possessed the highest exon variability (2-5), contrasting with TFL1-like (3-4) and MFT-like (fixed 4-exon) subfamilies. Evolutionary analysis revealed whole-genome and segmental duplications as primary expansion mechanisms, with tandem duplication frequency substantially higher in S. officinarum (8%) than S. spontaneum (1%). Syntenic analysis uncovered species-specific duplication events (e.g., SspFT5.1/SspFT5.2 and SoFT12.1/SoFT12.2) and stronger conservation between S. spontaneum and sorghum. Promoter analysis identified abundant light- and hormone-responsive elements, particularly jasmonic acid and abscisic acid response motifs. Expression profiling identified two key genes, FT3 and TFL1, with contrasting expression dynamics. FT3 displayed a sustained, photoperiod-sensitive upregulation, whereas TFL1 showed an initial decrease followed by an increase and was independent of photoperiod regulation. Transgenic validation confirmed FT3 orthologs consistently accelerated flowering (~19 days early), whereas TFL1 genes functioned as floral repressors.【Conclusion】Genomic analysis revealed 23 and 20 PEBP genes in S. spontaneum and S. officinarum, respectively, phylogenetically clustered into three well-defined subfamilies (FT-like, TFL1-like, and MFT-like) that exhibited substantial structural and functional divergence. FT3 and TFL1 demonstrated opposite expression patterns during floral induction, with FT3 showing marked photoperiod responsiveness and significantly elevated transcript abundance in S. spontaneum relative to S. officinarum. Transgenic functional analysis confirmed that FT3 typically promotes flowering, whereas the TFL1 gene suppresses it.

Key words: Saccharum spontaneum, Saccharum officinarum, PEBP gene family, flowering regulation, expression profiling, photoperiod

LUO ZhengYing, HU SiZhen, LIN XiuQin, HU Xin, ZHANG Min, XU ChaoHua, LIU XinLong, ZENG QianChun. Identification and Functional Characterization of the PEBP Gene Family in Regulating Flowering Time in Saccharum spontaneum and Saccharum officinarum[J].Scientia Agricultura Sinica, 2026, 59(4): 734-749.

Figures/Tables 8

Fig. 1

Table 1

The physiochemical characteristics of PEBP family in S. spontaneum and S. officinarum"

物种 Species	蛋白 Protein	染色体 Chromosome	亚族分类 Subfamily classification	氨基酸数 No. of amino acids (aa)	分子量Molecular weight (kDa)	等电点 pI	不稳定系数Instability index	脂肪族指数Aliphatic index	平均亲水指数Grand average of hydropathicity
割手密 S. spontaneum	SspFT1.1	Chr.6C	FT-Like	173	19.365	7.94	34.57	76.01	-0.236
	SspFT1.2	Chr.10A	FT-Like	191	21.227	5.57	40.07	78.48	-0.206
	SspFT2	Chr.3D	FT-Like	191	21.040	8.47	49.68	75.45	-0.285
	SspFT3	Chr.3D	FT-Like	173	19.299	6.73	42.61	85.55	-0.131
	SspFT4	Chr.10A	FT-Like	179	19.978	7.73	30.58	75.53	-0.244
	SspFT5.2	Chr.5B	FT-Like	364	40.368	10.08	51.96	78.52	-0.163
	SspFT5.1	Chr.9B	FT-Like	180	20.355	8.76	41.91	64.39	-0.451
	SspFT6	Chr.6C	FT-Like	151	17.101	9.33	31.35	81.26	-0.307
	SspFT7	Chr.4C	FT-Like	185	20.517	6.90	40.35	69.51	-0.301
	SspFT8	Chr.3D	FT-Like	177	20.089	9.09	40.34	88.02	-0.132
	SspFT9	Chr.4C	FT-Like	174	19.676	8.56	42.54	77.18	-0.389
	SspFT10	Chr.9B	FT-Like	175	19.880	7.89	40.52	79.09	-0.264
	SspFT11	Chr.8B	FT-Like	176	19.249	6.89	40.75	74.83	-0.228
	SspFT12	Chr.2D	FT-Like	178	19.987	7.85	43.09	84.89	-0.303
	SspFT13	Chr.6C	FT-Like	185	20.625	6.41	42.94	68.54	-0.305
	SspTFL1	Chr.5B	TFL-Like	173	19.595	7.96	48.39	86.65	-0.150
	SspTFL2	Chr.1D	TFL-Like	197	22.540	9.77	52.12	73.15	-0.467
	SspTFL3	Chr.4C	TFL-Like	173	19.517	8.76	37.76	78.21	-0.294
	SspTFL4	Chr.8B	TFL-Like	173	19.532	8.82	44.44	83.24	-0.258
	SspMFT1.1	Chr.10A	MFT-Like	302	33.077	10.01	55.20	84.04	-0.064
	SspMFT1.2	Chr.10B	MFT-Like	268	29.412	10.35	48.32	88.84	-0.025
	SspMFT1.3	Chr.10C	MFT-Like	273	30.119	10.54	43.96	87.25	-0.094
	SspMFT2	Chr.3D	MFT-Like	171	18.718	8.62	35.35	85.50	-0.139
热带种 S. officinarum	SoFT1	Chr.10A	FT-Like	175	19.651	6.91	38.87	74.00	-0.305
	SoFT2	Chr.02H	FT-Like	191	20.848	8.59	53.76	79.53	-0.242
	SoFT3	Chr.03B	FT-Like	173	19.341	6.73	42.61	87.23	-0.116
	SoFT4	Chr.10A	FT-Like	179	19.978	7.73	30.58	75.53	-0.244
	SoFT5.1	Chr.05D	FT-Like	177	20.061	8.64	44.88	69.32	-0.407
	SoFT5.2	Chr.09G	FT-Like	176	19.869	9.00	46.31	69.72	-0.404
	SoFT6	Chr.06H	FT-Like	174	19.627	7.72	33.87	77.76	-0.386
	SoFT7	Chr.04C	FT-Like	185	20.517	6.90	40.35	69.51	-0.301
	SoFT8	Chr.03B	FT-Like	177	20.005	9.38	39.33	85.25	-0.156
	SoFT9	Chr.04C	FT-Like	174	19.676	8.56	42.54	77.18	-0.389
	SoFT10	Chr.09B	FT-Like	175	19.876	7.89	40.52	79.09	-0.269
	SoFT11	Chr.08E	FT-Like	176	19.176	7.71	46.44	75.97	-0.186
	SoFT12.2	Chr.02H	FT-Like	178	19.979	7.87	42.45	82.70	-0.325
	SoFT12.1	Chr.02C	FT-Like	170	19.029	8.82	43.18	84.29	-0.279
	SoFT13	Chr.06H	FT-Like	185	20534	6.50	38.75	68.54	-0.282
	SoTFL1	Chr.05D	TFL-Like	173	19.556	7.94	50.38	86.07	-0.146
	SoTFL2	Chr.06H	TFL-Like	173	19.669	9.25	44.16	75.95	-0.299
	SoTFL3	Chr.04C	TFL-Like	173	19.517	8.76	37.76	78.21	-0.294
	SoTFL4	Chr.08E	TFL-Like	173	19.533	7.93	45.21	83.24	-0.258
	SoMFT1	Chr.10A	MFT-Like	181	19.630	6.96	42.23	87.29	0.024

Table 1

Fig. 2

Fig. 3

Fig. 4

Table 2

Fig. 5

Fig. 6

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粤糖93-159基因编号 Yuetang 93-159 gene ID	热带种比对 Homology to S. officinarum		割手密比对 Homology to S. spontaneum		早期花穗vs 茎尖分生组织 Early panicle_vs_SAM		中期花穗vs 茎尖分生组织 Mid panicle_vs_SAM		晚期花穗vs 茎尖分生组织 Late panicle_vs_SAM
粤糖93-159基因编号 Yuetang 93-159 gene ID	同源基因Ortholog	一致性 Identity (%)	同源基因Ortholog	一致性 Identity (%)	Log₂FC	P值 P value	Log₂FC	P值 P value	Log₂FC	P值 P value
TRINITY_DN783_c1_g1	SoFT3	99.62	SspFT3	99.62	4.4855	0.0205	6.1656	0.0004	6.2672	0.0004
TRINITY_DN65785_c0_g1_orf1	SoTFL1	99.09	SspTFL1	98.63	-0.9004	0.0562	-0.6374	0.0688	1.0995	0.0233

Identification and Functional Characterization of the PEBP Gene Family in Regulating Flowering Time in Saccharum spontaneum and Saccharum officinarum

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