[1]孙扬名,张明亮,葛敏,等.玉米ZmZIM家族基因鉴定及其对氮素的响应特征[J].江苏农业学报,2024,(04):577-590.[doi:doi:10.3969/j.issn.1000-4440.2024.04.001]
　SUN Yang-ming,ZHANG Ming-liang,GE Min,et al.Identification of ZmZIM family genes and their response to nitrogen in maize[J].,2024,(04):577-590.[doi:doi:10.3969/j.issn.1000-4440.2024.04.001]
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玉米ZmZIM家族基因鉴定及其对氮素的响应特征()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2024年04期
页码:
577-590
栏目:
遗传育种·生理生化
出版日期:
2024-04-30

文章信息/Info

Title:
Identification of ZmZIM family genes and their response to nitrogen in maize
作者:
孙扬名1; 2; 张明亮2; 葛敏2; 邬奇2; 赵涵2
(1.南京农业大学农学院,江苏南京210095；2.江苏省农业科学院种质资源与生物技术研究所,江苏南京210014)
Author(s):
SUN Yang-ming1; 2; ZHANG Ming-liang2; GE Min2; WU Qi2; ZHAO Han2
(1.College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China;2.Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China)
关键词:
玉米; ZIM转录因子; 基因家族分析; 氮响应
Keywords:
maize; ZIM transcription factors; gene family analysis; nitrogen response
分类号:
S513
DOI:
doi:10.3969/j.issn.1000-4440.2024.04.001
摘要:
为明确玉米ZmZIM家族基因结构、位置、编码蛋白质性质及其对氮素的响应特征,本研究利用TBtools、MEGA X等软件分析玉米ZmZIM家族基因的结构、染色体位置、顺式作用元件及系统发育关系及其编码蛋白质的理化性质、保守结构域及基序,结合玉米不同发育时期不同器官的转录组数据及充足氮与低氮水平下四叶一心期玉米地上部转录组数据解析玉米ZmZIM家族基因的表达模式及差异。结果表明：从玉米全基因组中共鉴定到32个玉米ZmZIM基因,主要分布于1号、2号、5号和7号染色体, 8号和10号染色体上无ZmZIM基因。32个ZmZIM基因可划分为4个亚类,其编码蛋白质由134～467个氨基酸残基构成,均为亲水性蛋白质且全部定位在细胞核中。32个ZmZIM基因启动子区域顺式作用元件主要有调控元件、光信号响应元件、激素信号响应元件、胁迫响应元件、生长发育元件及蛋白质结合位点等6大类。不同发育时期,ZmZIM基因在玉米不同器官中存在差异性表达；在充足氮与低氮处理下，随着处理时间的增加，玉米植株地上部12个ZmZIM基因无表达或相对表达量较低，6个ZmZIM基因相对表达量较高且稳定，其余的14个ZmZIM基因的相对表达量差异较大；ZmZIM5、ZmZIM16、和ZmZIM31 3个基因的相对表达量普遍高于其他基因。充足氮条件下，ZmZIM8、ZmZIM15、ZmZIM20、ZmZIM24、ZmZIM29和ZmZIM31基因的相对表达量普遍高于低氮条件。本研究结果为玉米氮高效吸收利用基因筛选和利用奠定基础。
Abstract:
In order to clarify the structure, location, encoded protein properties and response characteristics of maize ZmZIM family genes to nitrogen, this study used TBtools, MEGA X and other softwares to analyze the structure, chromosome location, cis-acting elements and phylogenetic relationships of maize ZmZIM family genes and the physical and chemical properties, conserved domain and motifs of their encoded proteins. The expression patterns and differences of maize ZmZIM family genes were analyzed by combining the transcriptome data of different organs at different development stages of maize and the transcriptome data of maize shoots at four-leaf and one-heart stage under sufficient nitrogen and low nitrogen levels. The results showed that a total of 32 ZmZIM genes were identified from the whole genome of maize, which were mainly distributed on chromosomes 1, 2, 5 and 7, and no ZmZIM genes were found on chromosomes 8 and 10. The 32 ZmZIM genes could be divided into four subclasses, and the encoded proteins were composed of 134-467 amino acid residues, all of which were hydrophilic proteins and located in the nucleus. The cis-acting elements in the promoter region of 32 ZmZIM genes were mainly divided into six categories: regulatory elements, light signal response elements, hormone signal response elements, stress response elements, growth and development elements and protein binding sites. At different developmental stages, ZmZIM gene was differentially expressed in different organs of maize. Under sufficient nitrogen and low nitrogen treatments, with the increase of treatment time, the 12 ZmZIM genes in the aboveground part of maize plants had no expression or low relative expression, the relative expression of six ZmZIM genes was high and stable, and the relative expression of the remaining 14 ZmZIM genes varied greatly. The relative expression levels of ZmZIM5, ZmZIM16, and ZmZIM31 were generally higher than other genes. Under sufficient nitrogen conditions, the relative expression levels of ZmZIM8, ZmZIM15, ZmZIM20, ZmZIM24, ZmZIM29 and ZmZIM31 were generally higher than those under low nitrogen conditions. The results of this study lay a foundation for the screening and utilization of nitrogen efficient absorption and utilization genes in maize.

参考文献/References:

[1]NISHII A, TAKEMURA M, FUJITA H, et al. Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana[J]. Biosci Biotechnol Biochem,2000,64(7):1402-1409.
[2]REYES J C, MURO-PASTOR M I, FLORENCIO F J. The GATA family of transcription factors in Arabidopsis and rice[J]. Plant Physiol,2004,134(4):1718-1732.
[3]SHIKATA M, MATSUDA Y, ANDO K, et al. Characterization of Arabidopsis ZIM, a member of a novel plant-specific GATA factor gene family[J]. Journal of Experimental Botany,2004,55(397):631-639.
[4]WHITE D W. PEAPOD regulates lamina size and curvature in Arabidopsis[J]. Proceedings of the National Academy of Sciences,2006,103(35):13238-13243.
[5]VANHOLME B, GRUNEWALD W, BATEMAN A, et al. The tify family previously known as ZIM[J]. Trends Plant Sci,2007,12(6):239-244.
[6]CHINI A, BEN-ROMDHANE W, HASSAIRI A, et al. Identification of TIFY/JAZ family genes in Solanum lycopersicum and their regulation in response to abiotic stresses[J]. PLoS One,2017,12(6):e177381.
[7]CAI Q, YUAN Z, CHEN M, et al. Jasmonic acid regulates spikelet development in rice[J]. Nat Commun,2014,5:3476.
[8]TIAN J, CAO L, CHEN X, et al. The OsJAZ1 degron modulates jasmonate signaling sensitivity during rice development[J]. Development,2019,146(4):dev173419.
[9]YAN Y, STOLZ S, CHETELAT A, et al. A downstream mediator in the growth repression limb of the jasmonate pathway[J]. Plant Cell,2007,19(8):2470-2483.
[10]CUI T T, HE K H, CHANG L G, et al. QTL mapping for leaf area in maize(Zea mays L.) under multi-environments[J]. Journal of Integrative Agriculture,2017，16(4):800-808．
[11]JU M, ZHOU Z, MU C, et al. Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis[J]. Sci Rep,2017,7:46446.
[12]AHMED M, RAUF M, MUKHTAR Z, et al. Excessive use of nitrogenous fertilizers: an unawareness causing serious threats to environment and human health[J]. Environ Sci Pollut Res,2017,24:26983-26987.
[13]ZHANG L, YOU J, CHAN Z. Identification and characterization of TIFY family genes in Brachypodium distachyon[J]. J Plant Res,2015,128(6):995-1005.
[14]刘俊,陈玉龙,刘燕,等. 杜仲TIFY转录因子鉴定与表达分析[J]. 中国实验方剂学杂志,2021,27(19):165-174.
[15]YE H, DU H, TANG N, et al. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice[J]. Plant Mol Biol,2009,71(3):291-305.
[16]ZHANG Y, GAO M, SINGER S D, et al. Genome-wide identification and analysis of the TIFY gene family in grape[J]. PLoS One,2012,7(9):e44465.
[17]ZHU D, BAI X, LUO X, et al. Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress[J]. Plant Cell Rep,2013,32(2):263-272.
[18]ZHAO G, SONG Y, WANG C, et al. Genome-wide identification and functional analysis of the TIFY gene family in response to drought in cotton[J]. Mol Genet Genomics,2016,291(6):2173-2187.
[19]SUN Q, WANG G, ZHANG X, et al. Genome-wide identification of the TIFY gene family in three cultivated Gossypium species and the expression of JAZ genes[J]. Sci Rep,2017,7:42418.
[20]XIE S, CUI L, LEI X, et al. The TIFY gene family in wheat and its progenitors:genome-wide identification, evolution and expression analysis[J]. Curr Genomics,2019,20(5):371-388.
[21]YANG Y, AHAMMED G J, WAN C, et al. Comprehensive analysis of TIFY transcription factors and their expression profiles under jasmonic acid and abiotic stresses in watermelon[J]. Int J Genomics,2019,2019:6813086.
[22]ZHENG L, WAN Q, WANG H, et al. Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz)[J]. Front Plant Sci,2022,13:1017840.
[23]张沪,肖翠,王贵元,等. 柑橘TIFY基因结构特征及响应低温表达分析[J]. 中国南方果树,2020,49(2):34-39.
[24]SONG S, QI T, HUANG H, et al. The Jasmonate-ZIM domain proteins interact with the R2R3-MYB transcription factors MYB21 and MYB24 to affect Jasmonate-regulated stamen development in Arabidopsis[J]. Plant Cell,2011,23(3):1000-1013.
[25]AN J P, XU R R, LIU X, et al. Abscisic acid insensitive 4 interacts with ICE1 and JAZ proteins to regulate ABA signaling-mediated cold tolerance in apple[J]. J Exp Bot,2022,73(3):980-997.
[26]TANG B, TAN T, CHEN Y, et al. SlJAZ10 and SlJAZ11 mediate dark-induced leaf senescence and regeneration[J]. PLoS Genet,2022,18(7):e1010285.
[27]罗冬兰,巴良杰,陈建业,等. 香蕉MaTIFY1转录因子特性及其在成熟过程中基因表达分析[J]. 园艺学报,2017,44(1):43-52.
[28]LIU H, LI T, WANG Y, et al. TaZIM-A1 negatively regulates flowering time in common wheat (Triticum aestivum L.)[J]. J Integr Plant Biol,2019,61(3):359-376.
[29]EBEL C, BENFEKI A, HANIN M, et al. Characterization of wheat (Triticum aestivum) TIFY family and role of Triticum Durum TdTIFY11a in salt stress tolerance[J]. PLoS One,2018,13(7):e200566.
[30]LIU S, ZHANG P, LI C, et al. The moss jasmonate ZIM-domain protein PnJAZ1 confers salinity tolerance via crosstalk with the abscisic acid signalling pathway[J]. Plant Sci,2019,280:1-11.
[31]WANG Y, PAN F, CHEN D, et al. Genome-wide identification and analysis of the Populus trichocarpa TIFY gene family[J]. Plant Physiol Biochem,2017,115:360-371.
[32]CHEN C, CHEN H, ZHANG Y, et al. TBtools:an integrative toolkit developed for interactive analyses of big biological data[J]. Mol Plant,2020,13(8):1194-1202.
[33]KUMAR S, STECHER G, LI M, et al. MEGA X:molecular evolutionary genetics analysis across computing platforms[J]. Mol Biol Evol,2018,35(6):1547-1549.
[34]BOLGER A M, LOHSE M, USADEL B. Trimmomatic: a flexible trimmer for Illumina sequence data[J]. Bioinformatics,2014,30(15):2114-2120.
[35]KIM D, LANGMEAD B, SALZBERG S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nat Methods,2015,12(4):357-360.
[36]LI H, HANDSAKER B, WYSOKER A, et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[37]RIECHMANN J L, HEARD J, MARTIN G, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes[J]. Science,2000,290(5499):2105-2110.
[38]QU L J, ZHU Y X. Transcription factor families in Arabidopsis: major progress and outstanding issues for future research[J]. Curr Opin Plant Biol,2006,9(5):544-549.
[39]LIU L, WHITE M J, MACRAE T H. Transcription factors and their genes in higher plants functional domains, evolution and regulation[J]. Eur J Biochem,1999,262(2):247-257.
[40]ZHANG Z, LI X, YU R, et al. Isolation, structural analysis, and expression characteristics of the maize TIFY gene family[J]. Mol Genet Genomics,2015,290(5):1849-1858.

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备注/Memo

备注/Memo:
收稿日期：2023-05-09基金项目：国家自然科学基金项目(32272133)；江苏省种业振兴“揭榜挂帅”项目[JBGS(2021)012]作者简介：孙扬名(1998-),男,吉林长春人,博士研究生,主要从事玉米氮素吸收及高效利用研究。(Tel)18151665609;(E-mail)Sunyangming9808@163.com通讯作者：赵涵,(E-mail)zhaohan@jaas.ac.cn
更新日期/Last Update: 2024-05-22