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作物学报 ›› 2024, Vol. 50 ›› Issue (9): 2297-2309.doi: 10.3724/SP.J.1006.2024.34193

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

马铃薯TIFY基因家族的全基因组鉴定及表达分析

祁稼民1,*(), 许春苗2, 肖斌2   

  1. 1定西市农业综合行政执法队安定分队, 甘肃定西 743000
    2定西市安定区园艺工作站, 甘肃定西 743000
  • 收稿日期:2023-11-16 接受日期:2024-04-01 出版日期:2024-09-12 网络出版日期:2024-04-24
  • 通讯作者: *祁稼民, E-mail: 149289262@qq.com
  • 基金资助:
    定西市科技计划项目(DX2023BZ81)

Genome-wide identification and expression analysis of TIFY gene family in potato (Solanum tuberosum L.)

QI Jia-Min1,*(), XU Chun-Miao2, XIAO Bin2   

  1. 1Anding Unit, Administrative Enforcement of Law in Agriculture, Dingxi 743000, Gansu, China
    2Horticulture Workstation of Anding District, Dingxi 743000, Gansu, China
  • Received:2023-11-16 Accepted:2024-04-01 Published:2024-09-12 Published online:2024-04-24
  • Contact: *E-mail: 149289262@qq.com
  • Supported by:
    Science and Technology Program of Dingxi City(DX2023BZ81)

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摘要：

TIFY家族是植物所特有的包含保守TIFY结构域(TIF [F/Y]XG)的转录因子基因家族, 在调节植物发育、响应非生物胁迫和植物激素方面具有重要作用。本研究在马铃薯(Solanum tuberosum L.)全基因组水平共鉴定出了26个StTIFY家族成员, 根据系统发育特征和蛋白结构将StTIFY分为4大亚家族, 其中JAZ亚家族分为了5个亚组。串联重复和片段重复事件在马铃薯TIFY基因家族的扩张中起主要作用。通过共线性分析发现, StTIFY与双子叶植物番茄(Solanum lycopersicum)、拟南芥(Arabidopsis)、甘蓝(Brassica oleracea)分别有21对、5对和6对直系同源基因, 而和单子叶植物水稻(Oryza sativa)、玉米(Zea mays)则分别只有1对和3对直系同源基因, 这些基因均在纯化选择下进化。RNA-seq数据分析发现, TIFY基因和ZML亚家族的2个基因在13个组织部位均有较高的表达量, 而其余成员则呈现组织表达特异性。同时我们进一步分析了StTIFY基因对非生物胁迫以及激素处理的响应, 发现有19个基因响应非生物胁迫(干旱/盐/热), 其中分别有3个和2个基因同时响应3种和2种非生物胁迫; 有5个基因在BAP、ABA、IAA和GA3处理下差异表达。利用qPCR进一步检测了在干旱胁迫条件下抗旱品种和水分敏感品种中4个候选基因的表达量, 结果发现这4个基因在2个品种的落花期显著差异表达。本研究为了解StTIFY基因家族的特征, 深入分析StTIFY家族成员在马铃薯响应激素信号和抵御非生物胁迫的功能提供了理论依据。

关键词: 马铃薯, TIFY基因家族, 激素处理, 非生物胁迫, 表达分析

Abstract:

The TIFY family is a gene family of transcription factor unique to plants. It contains conserved TIFY domains (TIF [F/Y]XG), which plays an important role in regulating plant development, responding to abiotic stress, and plant hormones. In this study, a total of 26 members of the StTIFY family at the genome-wide level in potatoes (Solanum tuberosum L.) were identified. Based on phylogenetic characteristics and protein structure, StTIFY was divided into 4 subfamilies, and the JAZ subfamily was divided into 5 subgroups. Tandem duplication and segmental duplication events played a major role in the expansion of the StTIFY gene family. Collinearity analysis showed that there were 21, 5, and 6 orthologous gene pairs between StTIFYs and TIFYs of dicotyledonous plants, which were tomato (Solanum lycopersicum), Arabidopsis, and cabbage (Brassica oleracea). There were only 1 and 2 orthologous gene pairs between StTIFYs and TIFYs of monocotyledonous rice (Oryza sativa) and maize (Zea mays), respectively, which had evolved under purification selection. RNA-seq data analysis showed that TIFY gene and two genes in ZML subfamily were highly expressed in 13 tissues, while the other members exhibited tissue-specificity. Furthermore, we analyzed the response of the StTIFY gene to abiotic stresses and hormone treatments, and found that 19 genes responded to abiotic stress (drought/salt/heat), among which 3 genes and 2 genes simultaneously responded to 3 and 2 abiotic stresses, respectively. Five genes were differentially expressed under BAP, ABA, IAA, and GA3 treatments. The relative expression levels of four candidate genes in drought-tolerant and water-sensitive cultivars under drought stress were further detected using qPCR. The results showed that these four genes were significantly differentially expressed in the two cultivars during flower-falling period. This study provides a theoretical basis for understanding the characteristics of the StTIFY gene family, as well as in-depth analysis of the functions of StTIFY family members response to hormone signals and resistance to abiotic stress.

Key words: potato, TIFY gene family, abiotic stress, hormone treatments, expression analysis

图1

拟南芥AtTIFY和马铃薯StTIFY家族成员的系统进化树分析"

表1

StTIFY基因家族的理化性质分析"

基因ID
Gene ID		 染色体定位
Chromosome
localization		 亚族分类
Subgroup		 氨基酸长度
Amino acid
length		 相对分子量
Molecular weight
(Da)		 等电点
Point isoelectric (pI)		 总平均亲水性
GRAVY
Soltu.DM.12G026270 Chr.12 JAZ I 254 28,431.98 9.24 -0.794
Soltu.DM.07G012950 Chr.07 JAZ I 215 23,905.17 8.84 -0.591
Soltu.DM.12G008980 Chr.12 JAZ I 200 22,397.20 9.30 -0.711
Soltu.DM.03G036980 Chr.03 JAZ I 309 33,698.76 8.51 -0.660
Soltu.DM.11G002570 Chr.11 JAZ II 228 26,127.31 6.40 -0.763
Soltu.DM.03G032770 Chr.03 JAZ II 390 41,118.75 9.43 -0.190
Soltu.DM.06G024860 Chr.06 JAZ II 228 24,889.77 10.00 -0.614
Soltu.DM.01G000760 Chr.01 JAZ II 306 32,163.62 8.81 -0.236
Soltu.DM.01G042530 Chr.01 JAZ III 153 17,798.16 8.97 -0.746
Soltu.DM.01G007210 Chr.01 JAZ IV 815 90,598.20 9.41 -0.280
Soltu.DM.05G012690 Chr.05 JAZ IV 176 19,800.60 8.99 -0.489
Soltu.DM.01G007200 Chr.01 JAZ IV 729 80,676.58 9.36 -0.342
Soltu.DM.08G007160 Chr.08 JAZ V 106 12,530.24 9.81 -0.940
Soltu.DM.08G007190 Chr.08 JAZ V 116 13,350.27 9.30 -0.810
Soltu.DM.08G007150 Chr.08 JAZ V 108 12,628.42 10.00 -0.851
Soltu.DM.08G007130 Chr.08 JAZ V 110 12,999.89 9.26 -0.739
Soltu.DM.08G007100 Chr.08 JAZ V 124 14,341.22 9.17 -0.885
Soltu.DM.08G007110 Chr.08 JAZ V 115 13,198.17 9.74 -0.672
Soltu.DM.06G034530 Chr.06 PPD 255 28,312.02 9.03 -0.761
Soltu.DM.09G020260 Chr.09 PPD 339 37,486.27 8.23 -0.665
Soltu.DM.06G019740 Chr.06 TIFY 427 44,702.42 9.32 -0.544
Soltu.DM.04G031220 Chr.04 ZML 354 38,715.17 5.11 -0.604
Soltu.DM.10G013010 Chr.10 ZML 322 34,689.39 6.64 -0.690
Soltu.DM.04G031210 Chr.04 ZML 280 31,238.37 8.84 -0.608
Soltu.DM.01G045340 Chr.01 ZML 375 40,849.43 4.93 -0.557
Soltu.DM.01G045330 Chr.01 ZML 328 34,998.60 6.13 -0.779

图2

StTIFY的进化关系、基因结构和保守motif分析 A: StTIFY的系统发育进化树。B: StTIFY基因的外显子/内含子结构分析; 蓝色框表示外显子, 黑线表示内含子, 红色方框表示上游/下游区域。C: StTIFY中的motif分析; 10个不同颜色的框代表了10个不同的motif。"

图3

StTIFY基因在马铃薯12条染色体上的分布及串联重复分析 A: StTIFY在染色体上的分布; B: StTIFY在染色体上的数目。串联重复的基因对用紫色框表示。"

图4

StTIFY基因家族片段重复分析"

图5

StTIFY基因家族与AtTIFY、BoTIFY、OsTIFY和ZmTIFY基因家族的同源性分析 数字编号代表不同物种的染色体, 红线表示马铃薯与番茄(Solanum lycopersicum)、拟南芥(Arabidopsis thaliana)、甘蓝(Brassica oleracea)、水稻(Oryza sativa)和玉米(Zea mays)中的TIFY直系同源基因。小提琴图表示TIFY串联重复、片段重复和马铃薯与不同物种间TIFY直系同源基因的Ka、Ks和Ka/Ks比值。"

图6

StTIFYs在马铃薯不同组织部位中的表达量 对StTIFYs基因表达量进行log2FPKM标准化处理, 不同颜色的色块范围(0~8)表示基因在不同组织中的表达水平。"

图7

StTIFYs基因不同非生物胁迫和激素处理下的表达量分析 热图表示log2 (处理下的表达量与对照之间的比值)。"

图8

4个StTIFY基因在马铃薯品种“大西洋(A)”和“青薯9号(Q)”在3个时期(初花期S1、盛花期S2和落花期S3)的表达量分析 A和Q分别代表“大西洋”和“青薯9号”, D代表干旱胁迫。数据为3个独立生物重复的平均值(±SE)。条形图上方的不同字母表示P < 0.05时的显著差异(最小显著差异法, LSD)。"

[1] Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G. The tify family previously known as ZIM. Trends Plant Sci, 2007, 12: 239-244.
doi: 10.1016/j.tplants.2007.04.004 pmid: 17499004
[2] Bai Y, Meng Y, Huang D, Qi Y, Chen M. Origin and evolutionary analysis of the plant-specific TIFY transcription factor family. Genomics, 2011, 98: 128-136.
doi: 10.1016/j.ygeno.2011.05.002 pmid: 21616136
[3] Chung H S, Niu Y, Browse J, Howe G A. Top hits in contemporary JAZ: an update on jasmonate signaling. Phytochemistry, 2009, 70: 1547-1559.
doi: 10.1016/j.phytochem.2009.08.022 pmid: 19800644
[4] Staswick P E. JAZing up jasmonate signaling. Trends Plant Sci, 2008, 13: 66-71.
doi: 10.1016/j.tplants.2007.11.011 pmid: 18261950
[5] Gupta A, Bhardwaj M, Tran P L-S. JASMONATE ZIM-DOMAIN family proteins: important nodes in jasmonic acid-abscisic acid crosstalk for regulating plant response to drought. Curr Protein Pept Sci, 2021, 22: 759-766.
[6] Hu S, Yu K, Yan J, Shan X, Xie D. Jasmonate perception: ligand- receptor interaction, regulation and evolution. Mol Plant, 2023, 16: 23-42.
[7] Chini A, Boter M, Solano R. Plant oxylipins: COI1/JAZs/MYC2 as the core jasmonic acid-signalling module. FEBS J, 2009, 276: 4682-4692.
doi: 10.1111/j.1742-4658.2009.07194.x pmid: 19663905
[8] Pan J, Hu Y, Wang H, Guo Q, Chen Y, Howe G A, Yu D. Molecular mechanism underlying the synergetic effect of jasmonate on abscisic acid signaling during seed germination in Arabidopsis. Plant Cell, 2020, 32: 3846-3865.
[9] Liu S, Zhang P, Li C, Xia G. The moss jasmonate ZIM-domain protein PnJAZ1 confers salinity tolerance via crosstalk with the abscisic acid signalling pathway. Plant Sci, 2019, 280: 1-11.
doi: S0168-9452(18)31122-1 pmid: 30823987
[10] Shikata M, Matsuda Y, Ando K, Nishii A, Takemura M, Yokota A, Kohchi T. Characterization of Arabidopsis ZIM, a member of a novel plant-specific GATA factor gene family. J Exp Bot, 2004, 55: 631-639.
[11] White D W R. PEAPOD regulates lamina size and curvature in Arabidopsis. Proc Natl Acad Sci USA, 2006, 103: 13238-13243.
doi: 10.1073/pnas.0604349103 pmid: 16916932
[12] Alexandra B, Laurens P, Zhibiao W, Na L, Liesbeth D M, Annelore N, Mattias V, Yunhai L, Alain G, Dirk I. Arabidopsis leaf flatness is regulated by PPD2 and NINJA through repression of CYCLIN D3 genes. Plant Physiol, 2018, 178: 217-232.
[13] Zhu Y, Luo X, Liu X, Cui X, He Y, Huang J. Arabidopsis PEAPODs function with LIKE HETEROCHROMATIN PROTEIN1 to regulate lateral organ growth. J Integr Plant Biol, 2020, 62: 812-831.
[14] Hakata M, Kuroda M, Ohsumi A, Hirose T, Nakamura H, Muramatsu M, Ichikawa H, Yamakawa H. Overexpression of a rice TIFY gene increases grain size through enhanced accumulation of carbohydrates in the stem. Biosci Biotechnol Biochem, 2012, 76: 2129-2134.
[15] Ebel C, BenFeki A, Hanin M, Solano R, Chini A. Characterization of wheat (Triticum aestivum) TIFY family and role of Triticum durum TdTIFY11a in salt stress tolerance. PLoS One, 2018, 13: e0200566.
[16] Ye H, Du H, Tang N, Li X, Xiong L. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol, 2009, 71: 291-305.
doi: 10.1007/s11103-009-9524-8 pmid: 19618278
[17] Zhang C, Yang R J, Zhang T T, Zheng D Y, Li X L, Zhang Z B, Li L G, Wu Z Y. ZmTIFY16, a novel maize TIFY transcription factor gene, promotes root growth and development and enhances drought and salt tolerance in Arabidopsis and Zea mays. Plant Growth Regul, 2023, 100: 149-160.
[18] Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol, 2016, 33: 1870-1874.
doi: 10.1093/molbev/msw054 pmid: 27004904
[19] Hu B, Jin J P, Guo A Y, Zhang H, Luo J C, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 2015, 31: 1296-1297.
doi: 10.1093/bioinformatics/btu817 pmid: 25504850
[20] Wang Y, Tang H, Debarry J D, Tan X, Li J, Wang X, Lee T-H, Jin H, Marler B, Guo H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 2012, 40: e49.
[21] Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinf, 2010, 8: 77-80.
doi: 10.1016/S1672-0229(10)60008-3 pmid: 20451164
[22] Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature, 2011, 475: 189-195.
[23] Heidari P, Faraji S, Ahmadizadeh M, Ahmar S, Mora-Poblete F. New insights into structure and function of TIFY genes in Zea mays and Solanum lycopersicum: a genome-wide comprehensive analysis. Front Genet, 2021, 12: 657970.
[24] Zhang L, You J, Chan Z. Identification and characterization of TIFY family genes in Brachypodium distachyon. J Plant Res, 2015, 128: 995-1005.
[25] Ferguson N M, Galvani A P, Bush R M. Ecological and immunological determinants of influenza evolution. Nature, 2003, 422: 428-433.
[26] Zhang Z, Li X, Yu R, Han M, Wu Z. Isolation, structural analysis, and expression characteristics of the maize TIFY gene family. Mol Genet Genomics, 2015, 290: 1849-1858.
doi: 10.1007/s00438-015-1042-6 pmid: 25862669
[27] Zhu D, Bai X, Chen C, Chen Q, Cai H, Li Y, Ji W, Zhai H, Lyu D, Luo X, Zhu Y. GsTIFY10, a novel positive regulator of plant tolerance to bicarbonate stress and a repressor of jasmonate signaling. Plant Mol Biol, 2011, 77: 285-297.
doi: 10.1007/s11103-011-9810-0 pmid: 21805375
[28] Liu Y L, Zheng L, Jin L G, Liu Y X, Kong Y N, Wang Y X, Yu T F, Chen J, Zhou Y B, Chen M, Wang F Z, Ma Y Z, Xu Z S, Lan J H. Genome-wide analysis of the soybean TIFY family and identification of GmTIFY10e and GmTIFY10g response to salt stress. Front Plant Sci, 2022, 13: 845314.
[29] Wang X D, Li N, Zan T X, Xu K, Gao S H, Yin Y X, Yao M H, Wang F. Genome-wide analysis of the TIFY family and function of CaTIFY7 and CaTIFY10b under cold stress in pepper (Capsicum annuum L.). Front Plant Sci, 2023, 14: 1308721
[30] Liu F, Sun T T, Wang L, Su W H, Gao S W, Su Y C, Xu L P, Que Y X. Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane. BMC Genomics, 2017, 18: 771
doi: 10.1186/s12864-017-4142-3 pmid: 29020924
[31] Zheng L L, Wan Q, Wang H G, Guo C L, Niu X L, Zhang X F, Zhang R, Chen Y H, Luo K. Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz). Front Plant Sci, 2022, 13: 1017840.
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