Genome-wide Identification of Tomato (Solanum lycopersicum) β-BAM Gene Family and Its Expression Analysis Under Salt Stress and Exogenous Plant Growth Regulators
LI Xian-Guo1,2, CHEN Zhao-Long1,2, WANG Ze-Peng1,2, DAI Qi1, YU Qing-Hui1, LI Ning1,*
1 Institute of Horticultural Crops/Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; 2 College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
Abstract:β-amylase (BAM) is widely involved in the regulation of various biological processes in plants and responds to various external stimuli such as hormone and abiotic stress. In this study, 8 SlBAM members in tomato (Solanum lycopersicum) were identified through bioinformatics analysis, and their physical and chemical properties, gene structure, phylogenetic evolution and collinearity were analyzed. The expression pattern of SlBAM gene under salt stress and fruit development was analyzed by qPCR. The results showed that SlBAM possessed typical Glyco_hydro_14 domain, and most of them were acidic and hydrophilic proteins. Phylogenetic analysis showed that SlBAM could be divided into 6 groups, and the same groups had similar gene structure and motif distribution. The composition of cis-acting elements indicated that the expression of most SlBAM may be related to plant hormones, abiotic stress and light response. The results of collinearity analysis showed that tomato had certain homology with Arabidopsis thaliana BAM gene family, and was more closely related to potato (Solanum tuberosum). qRT-PCR analysis showed that SlBAM were mainly expressed in leaves, but almost not expressed in roots and stems. Under salt stress, the expressions of SlBAM2, SlBAM4 and SlBAM6 were up-regulated (P<0.05), while the expressions of SlBAM1 and SlBAM3 were down-regulated (P<0.05). When the concentration of 2,4-epibrassinolide (EBR) solution was 0.1 mol/L, the expression of all genes in green ripening stage was significantly up-regulated (P<0.05). Under the influence of 1-naphthaleneacetic acid (NAA), all the genes except SlBAM6 were up-regulated and only SlBAM6 was down-regulated. These results provide a reference for further elucidations of the functions of the BAM gene family in tomato in response to abiotic stress and fruit development.
李贤国, 陈兆龙, 王泽鹏, 戴麒, 余庆辉, 李宁. 番茄β-BAM基因家族全基因组鉴定及其盐胁迫和外源植物生长调节剂下的表达分析[J]. 农业生物技术学报, 2024, 32(5): 1008-1019.
LI Xian-Guo, CHEN Zhao-Long, WANG Ze-Peng, DAI Qi, YU Qing-Hui, LI Ning. Genome-wide Identification of Tomato (Solanum lycopersicum) β-BAM Gene Family and Its Expression Analysis Under Salt Stress and Exogenous Plant Growth Regulators. 农业生物技术学报, 2024, 32(5): 1008-1019.
[1] 郝心愿, 岳川, 唐湖, 等. 2017. 茶树β-淀粉酶基因CsBAM3的克隆及其响应低温的表达模式[J]. 作物学报, 43(10): 1417-1425. (Hao X, Yue C, Tang H, et al.2017. Cloning of β-amylase gene (CsBAM3) and its expression model response to cold stress in tea plant[J]. Journal of Crop, 43(10): 1417-1425.) [2] 江淑珍, 连辉, 熊远芳, 等. 2021. 锥栗β-淀粉酶基因家族的全基因组鉴定与分析[J]. 森林与环境学报, 41(05): 545-553. (Jiang S, Lian H, Xiong Y, et al.2021. Genome-wide identification and expression analysis of the β-amylase gene family in Castanea henryi[J]. Journal of Forest and Environment, 41(05): 545-553.) [3] 刘腾飞. 2019. 马铃薯StGRIK1的功能研究及低温诱导StBAM1与StBAM9表达的机制解析[D]. 博士学位论文, 华中农业大学, 导师: 宋波涛, pp. 81-98. (Liu T.2019. Functional study of StGRIK1 and deciphering mechanism for cold induced expression of StBAM1 and StBAM9 in potato[D]. Thesis for Ph.D., Huazhong Agricultural University, Supervisor: Song B T, pp. 81-98.) [4] 吴昱, 彭婷. 2022. 不同处理下枳β-淀粉酶基因家族PtrBAM2~PtrBAM8的表达分析[J]. 分子植物育种, 20(13): 4282-4288. (Wu Y, Peng T.2022. Expression analysis of seven β-amylase encoding gene PtrBAM2~PtrBAM8 in Poncirus trifoliata under various treatments[J]. Molecular Plant Breeding, 20(13): 4282-4288.) [5] Ahmed I, Cao F, Wu F, et al., 2013. Differential changes in grain ultrastructure, amylase, protein and amino acid profiles between Tibetan wild and cultivated barleys under drought and salinity alone and combined stress[J]. Food Chemistry, 141: 2743-2750. [6] Chen Y, Wang Y, Liang X, et al.2022. Mass spectrometric exploration of phytohormone profiles and signaling networks[J]. Trends in Plant Science, 28(4): 399-414. [7] Francisco P, Li J, Smith S.2010. The gene encoding the catalytically inactive β-amylase BAM4 involved in starch breakdown in Arabidopsis leaves is expressed preferentially in vascular tissues in source and sink organs[J]. Journal of Plant Physiology, 167(11): 890-895. [8] Kaplan F,Guy C.2005. RNA interference of Arabidopsis beta-amylase 8 prevents maltose accumulation upon cold shock and increases sensitivity of PSII photochemical efficiency to freezing stress[J]. Plant Journal for Cell & Molecular Biology, 2010, 44(5): 730-743. [9] Kulakova A, Efremov G, Shchennikova A, et al.2022. Dependence of the content of starch and reducing sugars on the level of expression of the genes of β-amylases StBAM1 and StBAM9 and the amylase inhibitor StAI during long-term low-temperature storage of potato tubers[J]. Vavilov Journal of Genetics and Breeding, 26(6): 507. [10] Li A, Chen J, Lin Q, et al.2021. Transcription factor MdWRKY32 participates in starch-sugar metabolism by binding to the MdBam5 promoter in apples during postharvest storage[J]. Journal of Agricultural and Food Chemistry, 69(49): 14906-14914. [11] Liang G, He H, Nai G, et al.2021. Genome-wide identification of BAM genes in grapevine (Vitis vinifera L.) and ectopic expression of VvBAM1 modulating soluble sugar levels to improve low-temperature tolerance in tomato[J]. BMC Plant Biology, 21: 1-15. [12] Luo D, Jia Z, Cheng Y, et al.2020. Genome-wide analysis of the β-amylase gene family in Brassica L. crops and expression profiles of BnaBAM genes in response to abiotic stresses[J]. Agronomy, 10(12): 1855. [13] Ma Y, Han Y, Feng X, et al.2022. Genome-wide identification of BAM (β-amylase) gene family in jujube (Ziziphus jujuba Mill.) and expression in response to abiotic stress[J]. BMC Genomics, 23(1): 1-21. [14] Mason.2005. The β-amylase genes of grasses and aphylogenetic analysis of the triticeae (Poaceae)[J]. American Journal of Botany, 92(6): 1045-1058. [15] Miao H, Sun P, Miao Y, et al., 2016. Genome-wide identification and expression analysis of the β-amylase genes strongly associated with fruit development, ripening, and abiotic stress response in two banana cultivars[J]. Frontiers of Agricultural Science and Engineering, 3: 346-356. [16] Monroe J, Storm A.2018. Review: The Arabidopsis β-amylase (BAM) gene family: Diversity of form and function[J]. Plant Science, 276: 163-170. [17] Monroe J, Storm A, Badley E, et al.2014. β-amylase1 and β-amylase 3 are plastidic starch hydrolases in Arabidopsis that seem to be adapted for different thermal, pH, and stress conditions[J]. Plant Physiology, 166(4): 1748-1763. [18] Peng T, Zhu X, Duan N, et al., 2014. PtrBAM1, a beta-amylase coding gene of Poncirus trifoliata, is a CBF regulon member with function in cold tolerance by modulating soluble sugar levels[J]. Plant Cell Environment, 37: 2754-2767. [19] Samojedny D, Orzechowski S.2007. New look at starch degradation in Arabidopsis thaliana L. chloroplasts[J]. Postepy Biochemii, 53: 74-83. [20] Sun C, Liu L, Wang L, et al.2021. Melatonin: A master regulator of plant development and stress responses[J]. Journal of Integrative Plant Biology, 63(1): 126-145. [21] Sun F, Palayam M, Shabek N.2022. Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation[J]. Journal of Structural Biology, 214(3): 107885. [22] Waadt R, Seller C, Hsu P, et al.2022. Plant hormone regulation of abiotic stress responses[J]. Nature Reviews: Molecular Cell Biology, 7: 23. [23] Wang Z, Wang Z, Li X, et al.2023. Identification and analysis of the expression of the PIP5K gene family in tomatoes[J]. International Journal of Molecular Sciences, 25(1): 159. [24] Wu F, Wang H, Xu G, et al., 2015. Research progress on the physiological and molecular mechanisms of woody plants under low temperature stress[J]. Scientia Silvae Sinicae, 51(7): 116-128. [25] Yue C, Cao H, Lin H, et al., 2019. Expression patterns of alpha-amylase and beta-amylase genes provide insights into the molecular mechanisms underlying the responses of tea plants (Camellia sinensis) to stress and postharvest processing treatments[J]. Planta, 250(1): 281-298. [26] Zhang D, Wang Y, Jia B, et al.2021. Genome-wide identification and expression analysis of the β-amylase gene family in Chenopodium quinoa[J]. DNA and Cell Biology, 40(7): 936-948. [27] Zhao L, Gong X, Gao J, et al.2019. Transcriptomic and evolutionary analyses of white pear (Pyrus bretschneideri) β-amylase genes reveals their importance for cold and drought stress responses[J]. Gene, 689: 102-113.