Bioinformatic and Expression Analysis of the SiGeBP Gene Family in Setaria italica

doi:10.13560/j.cnki.biotech.bull.1985.2025-1439

Abstract

Abstract:

Objective Glabrous-enhancer binding proteins (GeBPs) are a class of plant-specific transcriptional regulators that participate in the regulation of growth and development and the responses to abiotic stress. This study aimed to clarify the member composition, molecular characteristics, and expression response patterns of the SiGeBP gene family in Setaria italica, thereby laying a foundation for elucidating the functions of this gene family. Method S. italica was used as the experimental material. Bioinformatics tools, including TBtools, MEGA 11.0, and PlantCARE, together with relevant databases such as NCBI and Pfam, were employed to identify the members of the SiGeBP gene family, followed by systematic analyses of their chromosomal localization, physicochemical properties, phylogenetic relationships, protein conserved motifs, functional domains, gene^{structures, and cis-acting elements. Additionally, quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the expression characteristics of the SiGeBP gene family under four types of abiotic stress and four types of hormone treatment conditions. Result A total of 16 SiGeBP genes were identified and they unevenly distributed across 8 chromosomes. Physicochemical property analysis revealed that all SiGeBP proteins were unstable hydrophilic proteins with high thermal stability, and 9 members were alkaline proteins. Gene structure analysis indicated that SiGeBP genes contained 0-2 introns, exhibiting a typical intron-poor feature. Phylogenetic analysis clustered the 16 SiGeBP proteins into 5 subfamilies. Members within the same subfamily shared highly similar conserved motifs and functional domains, and all members possessed the DUF573 domain. The prediction of cis-acting elements showed that the promoter regions of SiGeBP genes were enriched with various abiotic stress-responsive elements and hormone-responsive elements. RT-qPCR results demonstrated that members of the SiGeBP gene family exhibited significant differential expression patterns, compared with the control group under abiotic stresses and exogenous hormone treatments; the relative expressions of SiGeBP-1 and SiGeBP-2 were significantly upregulated under all four hormone treatments; the expressions of SiGeBP-6 and SiGeBP-13 were significantly downregulated under all four abiotic stresses. Conclusion The SiGeBP gene family in S. italica exhibits conserved structural characteristics and diverse expression response patterns, implying that it may synergistically regulate the stress resistance and growth and development processes of S. italica by participating in hormone regulatory networks and stress response pathways.}

Key words: Setaria italica, SiGeBP gene family, bioinformation analysis, abiotic stresses, hormones

CAO Hai-yan, ZHANG Zi-tong, MENG Zi-yu, SONG Ji-ce, HAO Xue-feng, JIN Zhu-ping. Bioinformatic and Expression Analysis of the SiGeBP Gene Family in Setaria italica[J]. Biotechnology Bulletin, 2026, 42(10): 67-76.

Figures/Tables 7

Fig. 1 Chromosomal localization of SiGeBP gene family

Fig. 2 Phylogenetic tree of GeBP proteins from Setaria italica, Arabidopsis thaliana and Oryza sativa

Fig. 3 Prediction of conserved motifs (A) and functional domain (B) of SiGeBP proteins

Fig. 4 Prediction of gene structure of SiGeBP gene family in S. italica

Fig. 5 Analysis of cis-acting elements of the SiGeBP gene family in S. italica

Fig. 6 Expression pattern analysis of the SiGeBP gene family under abiotic stresses*: Significant difference at the P<0.05 level. **: Highly significant difference at the P<0.01 level. ns: No significant difference. The same below

Fig. 7 Expression pattern analysis of the SiGeBP gene family under exogenous hormone treatments

References 34

[1]	钟姗辰, 武舒, 王黎, 等. 植物毛状体研究进展 [J]. 分子植物育种, 2023, 21(21): 7215-7224.
	Zhong SC, Wu S, Wang L, et al. Advances in molecular mechanisms of plant trichomonas [J]. Mol Plant Breed, 2023, 21(21): 7215-7224.
[2]	韩金凤, 夏天, 刘一华, 等. 基因调控植物表皮毛发育的研究进展 [J]. 植物生理学报, 2023, 59(8): 1517-1523.
	Han JF, Xia T, Liu YH, et al. Research progress on gene regulation of plant trichome development [J]. Plant Physiol J, 2023, 59(8): 1517-1523.
[3]	Yang SL, Xue SD, Shan L, et al. The CsTM alters multicellular trichome morphology and enhances resistance against aphid by interacting with CsTIP1;1 in cucumber [J]. J Adv Res, 2025, 69: 17-30.
[4]	Heng SP, Li XL, Li M, et al. Two novel alleles of the MYB transcription factor BjA06.GL1 and BjB02.GL1 control leaf trichomes and enhance resistance to aphids in Brassica juncea [J]. Hortic Res, 2025, 12(2): uhae314.
[5]	Lan JQ, Zhang JZ, Yuan RR, et al. TCP transcription factors suppress Cotyledon trichomes by impeding a cell differentiation-regulating complex [J]. Plant Physiol, 2021, 186(1): 434-451.
[6]	Wu ML, Chang J, Han XQ, et al. A HD-ZIP transcription factor specifies fates of multicellular trichomes via dosage-dependent mechanisms in tomato [J]. Dev Cell, 2023, 58(4): 278-288.
[7]	Vanhoutte B, Schenkels L, Ceusters J, et al. Water and nutrient uptake in Vriesea cultivars: trichomes vs. roots [J]. Environ Exp Bot, 2017, 136: 21-30.
[8]	阿拉依·哈那提, 刘艳霞, 兰海燕. 荒漠植物表皮毛的凝结水形成及吸收机制研究进展 [J]. 干旱区研究, 2024, 41(1): 114-123.
	Hanati A, Liu YX, Lan HY. Research progress on the mechanism of formation, absorption and utilization of condensed water on leaf trichomes of desert plants [J]. Arid Zone Res, 2024, 41(1): 114-123.
[9]	刘晓梦, 唐宁, 陈泽雄, 等. 植物表皮毛发育研究进展 [J]. 园艺学报, 2021, 48(4): 705-718.
	Liu XM, Tang N, Chen ZX, et al. Progress in plant trichome development research [J]. Acta Hortic Sin, 2021, 48(4): 705-718.
[10]	崔占虎, 黄显章, 李超, 等. 多组学策略在药用植物表皮毛次生代谢调控中的应用与展望 [J]. 中国现代中药, 2021, 23(3): 548-554.
	Cui ZH, Huang XZ, Li C, et al. Application and prospect of multi-omics in regulation of secondary metabolism of trichome from medicinal plant [J]. Mod Chin Med, 2021, 23(3): 548-554.
[11]	Saadat NP, van Aalst M, Brand A, et al. Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes [J]. Plant J, 2023, 115(6): 1716-1728.
[12]	Zekri MA, Lang I. Lack of trichomes and variation in stomata properties influence the quantum efficiency of photosynthesis in Arabidopsis [J]. Environ Exp Bot, 2024, 227: 105948.
[13]	Curaba J, Herzog M, Vachon G. GeBP, the first member of a new gene family in Arabidopsis, encodes a nuclear protein with DNA-binding activity and is regulated by KNAT1 [J]. Plant J, 2003, 33(2): 305-317.
[14]	Chevalier F, Perazza D, Laporte F, et al. GeBP and GeBP-like proteins are noncanonical leucine-zipper transcription factors that regulate cytokinin response in Arabidopsis [J]. Plant Physiol, 2008, 146(3): 1142-1154.
[15]	张瑞杰, 李明, 李迎超, 等. 红树莓GeBP基因家族鉴定及表达分析 [J]. 植物生理学报, 2024, 60(6): 1007-1015.
	Zhang RJ, Li M, Li YC, et al. Identification and expression analysis of GeBP gene family in red raspberry [J]. Plant Physiol J, 2024, 60(6): 1007-1015.
[16]	朱贵爽, 李艳肖, 张安宁, 等. 蓖麻GeBP转录因子的全基因组鉴定与GeBP2基因的克隆、表达分析 [J]. 浙江农业学报, 2024, 36(8): 1731-1740.
	Zhu GS, Li YX, Zhang AN, et al. Identification of RcGeBP transcription factor and cloning and expression analysis of RcGeBP2 gene in castor [J]. Acta Agric Zhejiangensis, 2024, 36(8): 1731-1740.
[17]	巩元勇, 赵丽华, 闫飞, 等. 大豆GeBP转录因子基因家族的生物信息学分析 [J]. 广西植物, 2022, 42(2): 294-303.
	Gong YY, Zhao LH, Yan F, et al. Bioinformatics analysis of GeBP transcription factor gene family in Glycin max [J]. Guihaia, 2022, 42(2): 294-303.
[18]	李鸿燕, 唐泽成, 李嘉欣, 等. 拟南芥GeBP转录因子基因家族生物信息学分析[J]. 分子植物育种, 2024: 1-21.
	Li HY, Tang ZC, Li JX, et al. Bioinformatics analysis of the GeBP transcription factor gene family in Arabidopsis thaliana [J]. Mol Plant Breed, 2024: 1-21.
[19]	Khare D, Mitsuda N, Lee S, et al. Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana [J]. New Phytol, 2017, 213(3): 1257-1273.
[20]	孙瑞青, 杨楠, 刘志鑫, 等. 杧果GeBP转录因子家族基因的鉴定及表达分析 [J]. 经济林研究, 2021, 39(4): 137-147.
	Sun RQ, Yang N, Liu ZX, et al. Identification and expression analysis of mango GeBP transcription factor family genes [J]. Nonwood For Res, 2021, 39(4): 137-147.
[21]	贾冠清, 刁现民. 中国谷子种业创新现状与未来展望 [J]. 中国农业科学, 2022, 55(4): 653-665.
	Jia GQ, Diao XM. Current status and perspectives of innovation studies related to foxtail millet seed industry in China [J]. Sci Agric Sin, 2022, 55(4): 653-665.
[22]	李顺国, 刘斐, 刘猛, 等. 中国谷子产业和种业发展现状与未来展望 [J]. 中国农业科学, 2021, 54(3): 459-470.
	Li SG, Liu F, Liu M, et al. Current status and future prospective of foxtail millet production and seed industry in China [J]. Sci Agric Sin, 2021, 54(3): 459-470.
[23]	Rathinapriya P, Pandian S, Rakkammal K, et al. The protective effects of polyamines on salinity stress tolerance in foxtail millet (Setaria italica L.), an important C₄ model crop [J]. Physiol Mol Biol Plants, 2020, 26(9): 1815-1829.
[24]	Zhao XT, Ma K, Li Z, et al. Transcriptome analysis reveals brassinolide signaling pathway control of foxtail millet seedling starch and sucrose metabolism under freezing stress, with implications for growth and development [J]. Int J Mol Sci, 2023, 24(14): 11590.
[25]	王心悦, 陈畅, 李康平, 等. 谷子HMA基因家族的全基因组表征及其功能预测 [J]. 山西农业大学学报: 自然科学版, 2025, 45(4): 3-15.
	Wang XY, Chen C, Li KP, et al. Genome-wide characterization and functional prediction of the heavy metal ATPase (HMA) gene family in foxtail millet [J]. J Shanxi Agric Univ Nat Sci Ed, 2025, 45(4): 3-15.
[26]	Jing XQ, Deng N, Cai YD. Genome-wide identification and characterization of RopGEF gene family in C₄ crops [J]. Genes, 2024, 15(9): 1112.
[27]	贺日升, 肖硕定, 游亮, 等. 甘蓝型油菜BnGeBP基因家族的生物信息学分析及表达分析[J]. 分子植物育种, 2025: 1-14.
	He RS, Xiao SD, You L, et al. Bioinformatics and expression analysis of the BnGeBP gene family in Brassica napus [J]. Molecular Plant Breeding, 2025: 1-14.
[28]	邵禹萌, 姚卓尔, 王鑫翌, 等. 毛果杨GeBP转录因子家族鉴定及表达分析 [J]. 林业与生态科学, 2025, 40(4): 389-398.
	Shao YM, Yao ZE, Wang XY, et al. Identification and expression analysis of GeBP transcription factor family in Populus trichocarpa [J]. For Ecol Sci, 2025, 40(4): 389-398.
[29]	Jeffares DC, Penkett CJ, Bähler J. Rapidly regulated genes are intron poor [J]. Trends Genet, 2008, 24(8): 375-378.
[30]	Chen Y, Ma T, Zhang TT, et al. Trends in the evolution of intronless genes in Poaceae [J]. Front Plant Sci, 2023, 14: 1065631.
[31]	Wang RL, Wu XY, Wang ZW, et al. Genome-wide identification and expression analysis of BrGeBP genes reveal their potential roles in cold and drought stress tolerance in Brassica rapa [J]. Int J Mol Sci, 2023, 24(17): 13597.
[32]	Cao HH, Wang DF, Li XL, et al. Genome-wide identification and expression profiling of SlGeBP gene family in response to hormone and abiotic stresses in Solanum lycopersicum L. [J]. Int J Mol Sci, 2025, 26(13): 6008.
[33]	Sun WN, Xia LJ, Deng JW, et al. Evolution and subfunctionalization of CIPK6 homologous genes in regulating cotton drought resistance [J]. Nat Commun, 2024, 15: 5733.
[34]	Sun SL, Liu DF, Luo W, et al. Domestication-selected COG4-OsbZIP23 module regulates chilling tolerance in rice [J]. Cell Rep, 2024, 43(11): 114965.