Identification and Expression Analysis of the TPP Gene Family Under Stress Response in Pepper（Capsicum annuum L.）

doi:10.16420/j.issn.0513-353x.2025-0351

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (8): 2289-2305.doi: 10.16420/j.issn.0513-353x.2025-0351

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Identification and Expression Analysis of the TPP Gene Family Under Stress Response in Pepper（Capsicum annuum L.）

WANG Meng, ZHENG Xiaomei, LIU Lu, ZANG Qiaolu^*()

College of Horticulture， Shanxi Agricultural University，Taigu， Shanxi 030801， China

Received:2025-12-25 Revised:2026-03-12 Online:2026-08-25 Published:2026-08-25
Contact: ZANG Qiaolu

Abstract

Abstract:

Trehalose-6-phosphate phosphatase（TPP）is a key enzyme that catalyzes the biosynthesis of trehalose and plays an important role in plant growth and development as well as stress response. To clarify the function of the CaTPP genes in the stress response of pepper，in this study，bioinformatics methods were used to identify the members of the CaTPP gene family in pepper，and their chromosomal localization，physicochemical properties，etc. were analyzed. Furthermore，transcriptome data and quantitative real-time PCR（qRT-PCR）were utilized to investigate the expression patterns of CaTPP genes across different tissues and under various hormone treatments and abiotic stresses. A total of eight CaTPP gene family members were identified in pepper. The physicochemical properties revealed that the CaTPP proteins were hydrophilic，with molecular weights ranging from 26.33 to 43.12 kD. Notably，about half of these proteins were classified as basic proteins. Subcellular localization prediction indicated that the majority of CaTPP proteins were localized in the chloroplast or vacuole. Phylogenetic analysis classified the pepper CaTPP family members into three groups，all of which contained a complete TPP（Trehalose_PPase）domain. Moreover，family members within the same group possessed similar conserved motifs and gene structures. The promoter region of the CaTPP gene contains a variety of cis-acting elements related to light response，hormone response and abiotic stress response. Collinearity analysis revealed one pair of CaTPP genes with fragment duplication in pepper. Besides，the pepper CaTPP family shared one and six pairs of homologous genes with Arabidopsis thaliana and Solanum lycopersicum，respectively. Transcriptome and qRT-PCR analyses indicated that the expression pattern of the CaTPP genes were tissue-specific and could play an important role in response to different hormones and stresses. The expression levels of CaTPP1 and CaTPP6 changed significantly under multiple stress conditions，implying their potential key roles in pepper resistance to stress.

Key words: pepper, TPP gene family, bioinformatics, stress response, promoter

WANG Meng, ZHENG Xiaomei, LIU Lu, ZANG Qiaolu. Identification and Expression Analysis of the TPP Gene Family Under Stress Response in Pepper（Capsicum annuum L.）[J]. Acta Horticulturae Sinica, 2026, 53(8): 2289-2305.

Figures/Tables 16

Table 1 qRT-PCR primers for CaTPP gene family

基因名称 Gene name	上游引物（5'-3'） Forward primer	下游引物（5'-3'） Reverse primer
CaUBI3	TTGGCAAGCAACAATCAT	GCAGATGGACAGCAGGAC
CaTPP1	GAGATGAGGGAAGCAGTG	CTTTAGCAGGTTGGCAGA
CaTPP2	TTGAAATGACTGGTGGTC	ACAATGGGAGAAAGGGTG
CaTPP4	GGCTGGCTAAGACTCAAA	GCTAAGTGCTGAAGGGTG
CaTPP5	GGGAGAAGTCGTGATAAG	CGATAGTGAACGGAAACA
CaTPP6	TTGGATTATGATGGCACTT	CTCTTTCGCAGGTTGGTA

Fig. 1 Chromosomal position of CaTPP family genes in pepper

Table 2 Physicochemical properties of CaTPP family genes

基因名称 Gene name	基因ID Gene ID	氨基酸数量 No. amino acids	分子量/ kD Molecular weight	等电点 Isoelectric point	平均疏水指数 Average hydropathicity value	亚细胞定位 Subcellular location
CaTPP1	Capana00g001331	366	41.49	9.47	-0.44	液泡Vacuole
CaTPP2	Capana00g004258	375	42.40	9.14	-0.35	叶绿体/液泡Chloroplast/vacuole
CaTPP3	Capana01g000524	382	43.12	8.03	-0.37	液泡Vacuole
CaTPP4	Capana03g002047	347	38.74	6.12	-0.31	过氧化物酶体/液泡Peroxisome/vacuole
CaTPP5	Capana03g002554	384	42.92	6.56	-0.31	叶绿体/液泡Chloroplast/vacuole
CaTPP6	Capana04g000072	232	26.33	6.24	-0.28	液泡Vacuole
CaTPP7	Capana06g001686	352	39.84	5.60	-0.38	叶绿体/液泡Chloroplast/vacuole
CaTPP8	Capana12g001588	358	40.21	9.19	-0.25	叶绿体/液泡Chloroplast/vacuole

Fig. 2 Phylogenetic analysis of the CaTPP gene family in Arabidopsis thaliana，Solanum lycopersicum and Capsicum annuum

Fig. 3 Phylogenetic tree（A），conserved motif（B），domain（C）and gene structure（D）analysis of CaTPP family

Fig. 4 Analysis of the types（A）and numbers（B）of cis-acting elements in the promoter of CaTPP genes

Fig. 5 Collinear analysis of CaTPP genes in pepper genome The red lines represent the collinear relationships of the TPP family genes，and the gray lines represent the collinear relationships between the genomes

Fig. 6 The collinearity relationship among the TPP family genes of Capsicum annuum，Arabidopsis thaliana，and Solanum lycopersicum The red lines represnt the collinear relationships of the TPP family genes，and the gray lines represent the collinear relationships between the genomes

Fig. 7 Expression analysis of the CaTPP gene in peppers under different tissues（A），plant growth regulator treatments（B），and abiotic stresses（C） L1-L9：Leaf samples at 2，5，10，15，20，25，30，40，and 50 days after the appearance of new leaves；F1-F9：Sampled flower buds of different size of 0.25，0.35，0.50，0.70，0.80，1.00，1.20，1.45 and 1.70 cm

Fig. 8 Expression of CaTPP genes of pepper in different tissues The error line represents the standard deviation，and different lowercase letters indicate significant differences （P < 0.05）. The same below

Fig. 9 Expression of CaTPP genes of pepper under IAA treatment

Fig. 10 Expression of CaTPP genes of pepper under ABA treatment

Fig. 11 Expression of CaTPP genes of pepper under MeJA treatment

Fig. 12 Expression of CaTPP genes of pepper under salt stress

Fig. 13 Expression of CaTPP genes of pepper under drought stress

Fig. 14 Expression of CaTPP genes of pepper under low temperature stress

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Identification and Expression Analysis of the TPP Gene Family Under Stress Response in Pepper（Capsicum annuum L.）

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