Identification and Analysis of GASA Gene Family in Pepper （Capsicum annuum L.）

doi:10.13560/j.cnki.biotech.bull.1985.2024-0878

Abstract

Abstract:

Objective The gene structure and expression analysis of GASA in pepper (Capsicum annuum L.) were studied to provide reference for elucidating the biological function of CaGASA gene and further cultivating pepper varieties with strong stress resistance. Method Bioinformatics method was applied to identify eight GASA family members in pepper, and systematically analyze their physical and chemical properties, phylogenetic relationships, gene structures, conserved motifs, chromosomal locations, gene synteny analyses, and promoter regions. Real-time fluorescence quantitative PCR (RT-qPCR) was used to verify the expression patterns of GASA gene family members in the pepper under different tissues, abiotic stresses and hormone treatments. Result Eight CaGASA proteins were distributed unevenly on the five chromosomes of pepper, and all CaGASA proteins had a common domain. The prediction of subcellular localization indicated that CaGASA protein existed in the extracellular region. The results of co-linear analysis of GASA gene in pepper, Arabidopsis, tomato (Solanum lycopersicum L.) and rice (Oryza sativa L.) showed that there were 14 co-linear events between pepper and other three species. CaCAGA5 was found to be co-linear with that of the three species. According to the cis-elements analyses, CaGASA genes may be induced by a variety of phytohormones and stresses. Transcriptome data analysis showed that the expression of CaGASA in the flower and fruit was higher than that in the leaf. RT-qPCR analysis showed that CaGASA gene was induced by low and high temperature stress and abscisic acid, gibberellin, indole acetic acid and jasmonic acid hormones. Conclusion The GASA gene family may be involved in pepper flower development, response to hormones and response to high and low temperature stress.

Key words: pepper, GASA gene family, identification of gene family, bioinformatic analysis, expression analysis

WANG Tian-tian, CHANG Xue-rui, HUANG Wan-yang, HUANG Jia-xin, MIAO Ru-yi, LIANG Yan-ping, WANG Jing. Identification and Analysis of GASA Gene Family in Pepper （Capsicum annuum L.）[J]. Biotechnology Bulletin, 2025, 41(4): 166-175.

Figures/Tables 11

Table 1 RT-qPCR primers for expression analysis of CaGASA family genes

基因 Gene	正向引物 Forward primer （5′‒3′）	反向引物 Reverse primer （5′‒3′）
CaGASA1	CATTCCAAAAGGCATTTGCT	GCAAGGGCATGCTTCATAAT
CaGASA2	TGCAGCTTTGCTTATTGCAT	GTACGCAGTGGCATCTGTTG
CaGASA3	GCAGCAGCAACAACAAAGAA	TAGCAAGGGCAAGTTTGCTT
CaGASA4	TGATGCCCAGTACCACATTG	GGTCCTCCTTCCTTGGTCTT
CaGASA5	ACTTGAACAACGGGGATTTG	AAGGGCACTTGGTCTTGTTG
CaGASA6	CCACTGCACCGACATACATT	TGGTGGAACACATTGACACC
CaGASA7	TCTCTCCTTGCTCCTTCTCG	GCAAGGGCAAGTCTGAGTGT
CaGASA8	TGAGCTTGTGGAAGCTGATG	CACCATGGGTAAGCATGTCA
β-Actin	CAACATCTTCACTCTCTGCTCT	ACTAGGAAAAACAGCACTTGGT

Table 2 Information of GASA gene family members in pepper

基因号 Gene ID	基因 Gene	氨基酸数 Number of amino acids/aa	分子量 Molecular weight/kD	等电点 Theoretical pI	不稳定指数 Instability index	脂肪指数 Aliphatic index	总平均亲水系数 Grand average of hydropathicity	亚细胞定位 Subcellular localization	跨膜结构域 Transmembrane domain
Capana02g002587	CaGASA1	102	11.15	9.01	46.06	49.90	-0.288	细胞外	0
Capana02g002588	CaGASA2	101	10.97	9.12	72.87	56.14	-0.166	细胞外	1
Capana02g003203	CaGASA3	112	12.67	9.42	42.06	53.04	-0.478	细胞外	0
Capana03g000783	CaGASA4	104	11.46	9.35	45.52	62.88	-0.026	细胞外	1
Capana03g001010	CaGASA5	145	15.74	9.27	39.20	81.38	-0.043	细胞外	0
Capana06g002956	CaGASA6	113	12.55	9.46	48.91	73.27	0.103	细胞外	1
Capana08g002677	CaGASA7	104	11.18	9.24	37.42	71.44	-0.138	细胞外	0
Capana12g000591	CaGASA8	113	12.27	7.97	36.80	79.38	0.040	细胞外	0

Fig. 1 Predicted three-dimensional structures of GASA proteins in pepper

Fig. 2 Chromosome location of CaGASA family genes

Fig. 3 Interaction network analysis of CaGASA proteinsT459_27842:Inhibitor I9 domain-containing protein. T459_18858: Putative purine permease 5. T459_18848: Putative purine permease 5. T459_03219: Fe2OG dioxygenase domain-containing protein. T459_17925, T459_24899, T459_28071, T459_18373, T459_16468, T459_05110: Uncharacterized protein. Purple line indicates experimental determination; the blue line indicates co-occurrence; the yellow line indicates text mining evidence; and the black line indicates co-expression

Fig. 4 Phylogenetic tree of GASA family members of Arabidopsis thaliana (At), Solanum lycopersicum (Sl), Oryza sativa (Os), and Capsicum annuum (Ca)

Fig. 5 Prediction of GASA family protein structure in pepper

Fig. 6 Synteny analysis of GASA genes among C. annuum (Ca), A. thaliana (At), S. lycopersicum (Sl), and O. sativa (Os)

Fig. 7 Cis-acting element prediction in the CaGASA promoters

Fig. 8 Expression analysis of GASA in different tissues in pepperL1‒L9 refers to 2, 5, 10, 15, 20, 30, 40, 50, and 60 d after new leaf emergence; F1‒F9 refers to 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60 d after flower bud emergence; G1‒G11 refers to 10, 15, 20, 25 30, 35, 40, 45, 50, 55, and 60 d after pollination; St1 and St2 refers to 10, 15 d after pollination; S3‒S11 refer to 20, 25, 30, 35, 40, 45, 50, 55, and 60 d after pollination; T3‒T11 refers to 20, 25, 30, 35, 40, 45, 50, 55, and 60 d after pollination

Fig. 9 Relative expressions of eight CaGASA genes under abiotic stress treatment*, **, and *** indicate significant differences at the level of 0.05, 0.01 and 0.001 respectively

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