Welcome to Acta Agronomica Sinica，

Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (4): 780-786.doi: 10.3724/SP.J.1006.2021.04122

• RESEARCH NOTES • Previous Articles    

Identification of StIgt gene family and expression profile analysis of response to drought stress in potato

QIN Tian-Yuan1,2(), LIU Yu-Hui1,2, SUN Chao1,2, BI Zhen-Zhen1,2, LI An-Yi3, XU De-Rong1,2, WANG Yi-Hao1,2, ZHANG Jun-Lian1, BAI Jiang-Ping1,2,*()   

  1. 1Gansu Provincial Key Lab of Aridland Crop Science / Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, Gansu, China
    2College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China
    3College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu, China
  • Received:2020-06-04 Accepted:2020-10-14 Online:2021-04-12 Published:2020-11-06
  • Contact: BAI Jiang-Ping E-mail:1637835362@qq.com;baijp@gsau.edu.cn
  • Supported by:
    National Natural Science Foundation of China(31660432);China Agriculture Research System(CARS-09-P14);Gansu Province Potato Industry System(GARS-03-P1);Gansu Provincial Education Department(2019B-073);Gansu Provincial Science and Technology Department(19ZD2WA002-02);Gansu Provincial Science and Technology Department(18JR3RA174);Key Laboratory of Arid Land Crop Science of Gansu Agricultural University(GSCS-2017-9);Innovation Fund of Gansu Agricultural University(GAU-XKJS-2018-085)

RichHTML381

26

PDF

662

Abstract:

Drought stress is one of the main abiotic stress factors affecting potato yield and quality. The root growth, development and architecture play an important role in potato drought resistance. The Igt gene family is a functional gene family that are ubiquitous in plants, and has significant effects in regulating root architecture and improving plant stress resistance. In this study, the potato double haploid ‘DM-v4.03’ high-quality genome was used as a reference, and members of the StIgt gene family were identified and analyzed on a genome-wide scale. Phylogenetic trees, chromosomal location, conservative protein domains, gene structure and cis element prediction were carried out by bioinformatics software. Meanwhile, the expression profiles of StIgts in response to drought stress were analyzed based on the transcriptome sequencing results of potato tetraploid lines under different drought conditions. The results showed that a total of 10 StIgt family members were identified in potato, of which StIgt1 was obtained and cloned by our research group. Except for the unknown position information of StIgt1, the remaining genes are unevenly distributed on chromosome 1, 2, 5, 7, 10, and 11. StIgts proteins range in length from 110 to 283 amino acids and have molecular weights ranging from 13.136 kD to 32.542 kD. The predicted isoelectric point is 3.82 to 9.86. Phylogenetic tree analysis revealed that the gene family can be divided into three subfamilies. The gene structure, protein conserved domains and cis-acting elements differ significantly among three subfamilies. The expression profile analysis under drought stress showed that StIgt6, StIgt7, StIgt9 and StIgt10 responded to the early drought stress which rapidly up-regulated at two hours of drought treatment. These results provide a theoretical basis for elucidating the evolutionary relationship of the StIgt gene family and further studying the functional characteristics of its members.

Key words: genome-wide, potato, StIgt gene family, drought stress, gene expression analyses

Table 1

Registration number of Igt genes in Arabidopsis, peach, corn, and rice"

基因名称
Gene name		 基因登录号
GenBank No.		 基因名称
Gene name		 基因登录号
GenBank No.
AtDro1 AT1G72490 AtLazy6 AT3G27025
AtDro2 AT1G19115 PpeLazy1 LOC18782538
AtDro3 AT1G17400 PpeLazy2 LOC18790006
OsDro1 BAN59748.1 ZmLazy LOC100193776
PpeDro1 LOC103327608 OsLazy1 LOC4350543
PpeDro2 LOC18770522 PpeTac1 LOC18773917
AtLazy1 AT5G14090 Ostac1 LOC4347655
AtLazy5 AT3G24750 AtTac1 AT2G46640

Table 2

Information of StIgt gene family in potato"

基因名称
Gene name		 基因ID
Gene ID		 亚组
Group		 染色体位置
Chromosome location		 大小
Size		 分子量
MW (kD)		 等电点
pI
StIgt10 PGSC0003DMG400042006 I chr11: 19822270-19822602 110 13,136.1 9.86
StIgt9 PGSC0003DMG400035280 I chr01: 12153224-12154281 139 15,371.1 4.61
StIgt8 PGSC0003DMG400020205 I chr02: 48071799-48076548 256 29,350.3 6.41
StIgt7 PGSC0003DMG401019811 I chr05: 15169941-15172623 255 27,797.7 5.41
StIgt6 PGSC0003DMG400041371 II chr07: 26993146-27002422 275 31,382.8 4.38
StIgt5 PGSC0003DMG400005529 II chr10: 5159202-5164672 281 32,338.2 5.15
StIgt4 PGSC0003DMG400022847 II chr01: 59885567-59885980 137 15,989.9 3.82
StIgt3 PGSC0003DMG400000126 II chr01: 73826302-73827911 221 24,499.6 5.38
StIgt2 PGSC0003DMG400016036 III chr07: 39417955-39420740 228 26,123 6.17
StIgt1 StDro1 III 未知Unknown 283 32,542.3 6.68

Fig. 1

Phylogenetic tree of Igt gene family in potato and other species"

Fig. 2

Protein conserved domains and structural characteristics of StIgt gene family members in potato A: protein structure; B: gene structure."

Fig. 3

Chromosome location and cis-elements analysis of the StIgt genes in potato ABRE: cis-acting element involved in the abscisic acid responsiveness; ERE: elements involved in defense and stress response; MBS: MYB binding site involved in drought-inducibility; TCA-element: cis-acting element involved in salicylic acid responsiveness; TGA-element: cis-acting element involved in auxin responsiveness; W-box: cis-acting element involved in the stress responsiveness."

Fig. 4

Expression pattern of StIgt genes in different drought stress conditions in potato"

Fig. 5

Gene expression of StIgt1, StIgt3 and StIgt10 under drought stress in potato * and ** mean significant difference at the 0.05 and 0.01 probability levels, respectively."

[1] Boguszewskamańkowska D, Zarzyńska K, Nosalewicz A. Drought differentially affects root system size and architecture of potato cultivars with differing drought tolerance. Am J Potato Res, 2019,97:54-62.
doi: 10.1007/s12230-019-09755-2
[2] Guoju Q, Zhengji Z, Fengju M, Runyuan W. Influence of increased temperature on the potato yield and quality in a semiarid district of northwest china. Acta Ecol Sin, 2015,35:830-836.
[3] Devaux A, Haverkort A J. The effects of shifting planting dates and mulching on late blight ( Phytophthora infestans) and drought stress of potato crops grown under tropical highland conditions. Exp Agric, 2008,23:325-333.
doi: 10.1017/S001447970001721X
[4] Shuangyuan C. Growth and yield response of different crops sowing after potato ( Solanum tuberosum L.) harvest in Kunming area. J Anhui Agric Sci, 2013,41:3794-3796.
[5] Farooq M, Wahid A, Kobayashi N, Fujita D S M A. Plant drought stress: effects, mechanisms and management to cite this version: review article. Agron Sustain Dev, 2009,29:185-212.
doi: 10.1051/agro:2008021
[6] Raza M A S, Shahid A M, Saleem M F. Effects and management strategies to mitigate drought stress in oilseed rape ( Brassica napus L.): a review. Zemdirbyste, 2017,104:85-94.
[7] Siddiqui M H, Al-Khaishany M Y, Al-Qutami M A, Al-Whaibi M H, Grover A, Ali H M, Al-Wahibi M S, Bukhari N A. Response of different genotypes of faba bean plant to drought stress. Int J Mol Sci, 2015,16:10214-10227.
doi: 10.3390/ijms160510214 pmid: 25950766
[8] Hollender C A, Dardick C. Molecular basis of angiosperm tree architecture. New Phytol, 2015,206:541-556.
doi: 10.1111/nph.13204 pmid: 25483362
[9] Uga Y, Sugimoto K, Ogawa S. Control of root system architecture by deeper rooting 1 increases rice yield under drought conditions. Nat Genet, 2013,45:1097-1102.
doi: 10.1038/ng.2725 pmid: 23913002
[10] Arai-Sanoh Y, Takai T, Yoshinaga S, Nakano H, Kojima M, Sakakibara H, Kondo M, Uga Y. Deep rooting conferred by deeper rooting 1 enhances rice yield in paddy fields. Sci Rep, 2014,4:5544-5563.
[11] Guseman J M, Webb K, Srinivasan C. DRO1 influences root system architecture in Arabidopsis and Prunus species. Plant J, 2017,89:1093-1105.
pmid: 28029738
[12] Dardick C, Callahan A, Horn R. Ppetac1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. Plant J, 2013,75:618-630.
doi: 10.1111/tpj.12234 pmid: 23663106
[13] Coste A T, Karababa M, Ischer F, Bille J, Sanglard D. TAC1 transcriptional activator of CDR genes is a new transcription factor involved in the regulation of Candida albicans ABC transporters CDR1 and CDR2. Eukaryot Cell, 2004,6:1639-1652.
[14] Yu B, Lin Z, Li H. TAC1: a major quantitative trait locus controlling tiller angle in rice. Plant J, 2008,52:891-898.
pmid: 17908158
[15] Li P, Wang Y, Qian Q. LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res, 2007,17:327-327.
[16] Dong Z, Jiang C, Chen X, Zhang T. Maize lazy1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling and light response. Plant Physiol, 2013,163:1306-1322.
pmid: 24089437
[17] Altschul S F, Madden T L, Schäffer A A. Gapped blast and psi-blast: a new generation of protein databases search programs. Nucleic Acids Res, 1997,25:3389-3402.
pmid: 9254694
[18] Aron M B, Derbyshire M K, Gonzales N R. CDD: NCBI’s conserved domain database. Nucleic Acids Res, 2014,43:222-226.
[19] Finn R D, Alex B, Jody C. Pfam: the protein families database. Nucleic Acids Res, 2014,42:222-230.
[20] Thompson J D, Gibson T J, Higgins D G. Multiple sequence alignment using clustalw and clustalx. Curr Protoc Bioinf, 2003,23:1-22.
[21] Kumar S, Stecher G, Tamura K. Mega 7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol, 2016,33:1870-1874.
[22] Bailey T L, Nadya W, Chris M. Meme: discovering and analyzing dna and protein sequence motifs. Nucleic Acids Res, 2006,34:369-373.
[23] Madke S S, Cherian K J, Badere R S. A modified Murashige and Skoog media for efficient multipleshoot induction in G. arborea Roxb. J For Res, 2014,3:557-564.
[24] Eiasu B K, Soundy P, Hammes P S. Response of potato ( Solanum tuberosum L.) tuber yield components to gelpolymer soil amendments and irrigation regimes. Crop Hortic, 2007,35:25-31.
[25] Walworth J L, Carling D E. Tuber initiation and development in irrigated and nonirrigated potatoes. Am J Potato Res, 2002,79:387-395.
[26] Lopes M S, Reynolds M P. Partitioning of assimilates to deeper roots is associated with cooler canopies and increased yield under drought in wheat. Funct Plant Biol, 2010,37:147-156.
[27] Lynch J P. Steep cheap and deep: an ideotype to optimize water and nacquisition by maize root systems. Ann Bot, 2013,112:347-357.
[28] Villordon A Q, Ginzberg I, Firon N. Root architecture and root and tuber crop productivity. Trends Plant Sci, 2014,19:419-425.
pmid: 24630073
[29] Roychoudhry S, Kepinski S. Shoot and root branch growth angle control the wonderfulness of lateralness. Curr Opin Plant Biol, 2015,23:124-131.
[30] Yoshihara T, Spalding E P. LAZY genes mediate the effects of gravity on auxin gradients and plant architecture. Plant Physiol, 2017,175:959-969.
doi: 10.1104/pp.17.00942 pmid: 28821594
[31] Zhang S L, Li D F. The prediction of rice gene by Fgenesh. Agric Sci China, 2008,7:387-394.
[32] Scott M, Madden T L. Blast: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res, 2004,32:20-25.
[1] WANG Hai-Bo, YING Jing-Wen, HE Li, YE Wen-Xuan, TU Wei, CAI Xing-Kui, SONG Bo-Tao, LIU Jun. Identification of chromosome loss and rearrangement in potato and eggplant somatic hybrids by rDNA and telomere repeats [J]. Acta Agronomica Sinica, 2022, 48(5): 1273-1278.
[2] SHI Yan-Yan, MA Zhi-Hua, WU Chun-Hua, ZHOU Yong-Jin, LI Rong. Effects of ridge tillage with film mulching in furrow on photosynthetic characteristics of potato and yield formation in dryland farming [J]. Acta Agronomica Sinica, 2022, 48(5): 1288-1297.
[3] WANG Xia, YIN Xiao-Yu, Yu Xiao-Ming, LIU Xiao-Dan. Effects of drought hardening on contemporary expression of drought stress memory genes and DNA methylation in promoter of B73 inbred progeny [J]. Acta Agronomica Sinica, 2022, 48(5): 1191-1198.
[4] FENG Ya, ZHU Xi, LUO Hong-Yu, LI Shi-Gui, ZHANG Ning, SI Huai-Jun. Functional analysis of StMAPK4 in response to low temperature stress in potato [J]. Acta Agronomica Sinica, 2022, 48(4): 896-907.
[5] ZHANG Xia, YU Zhuo, JIN Xing-Hong, YU Xiao-Xia, LI Jing-Wei, LI Jia-Qi. Development and characterization analysis of potato SSR primers and the amplification research in colored potato materials [J]. Acta Agronomica Sinica, 2022, 48(4): 920-929.
[6] JIN Rong, JIANG Wei, LIU Ming, ZHAO Peng, ZHANG Qiang-Qiang, LI Tie-Xin, WANG Dan-Feng, FAN Wen-Jing, ZHANG Ai-Jun, TANG Zhong-Hou. Genome-wide characterization and expression analysis of Dof family genes in sweetpotato [J]. Acta Agronomica Sinica, 2022, 48(3): 608-623.
[7] TAN Xue-Lian, GUO Tian-Wen, HU Xin-Yuan, ZHANG Ping-Liang, ZENG Jun, LIU Xiao-Wei. Characteristics of microbial community in the rhizosphere soil of continuous potato cropping in arid regions of the Loess Plateau [J]. Acta Agronomica Sinica, 2022, 48(3): 682-694.
[8] DING Hong, XU Yang, ZHANG Guan-Chu, QIN Fei-Fei, DAI Liang-Xiang, ZHANG Zhi-Meng. Effects of drought at different growth stages and nitrogen application on nitrogen absorption and utilization in peanut [J]. Acta Agronomica Sinica, 2022, 48(3): 695-703.
[9] QU Jian-Zhou, FENG Wen-Hao, ZHANG Xing-Hua, XU Shu-Tu, XUE Ji-Quan. Dissecting the genetic architecture of maize kernel size based on genome-wide association study [J]. Acta Agronomica Sinica, 2022, 48(2): 304-319.
[10] ZHANG Hai-Yan, XIE Bei-Tao, JIANG Chang-Song, FENG Xiang-Yang, ZHANG Qiao, DONG Shun-Xu, WANG Bao-Qing, ZHANG Li-Ming, QIN Zhen, DUAN Wen-Xue. Screening of leaf physiological characteristics and drought-tolerant indexes of sweetpotato cultivars with drought resistance [J]. Acta Agronomica Sinica, 2022, 48(2): 518-528.
[11] JIAN Hong-Ju, SHANG Li-Na, JIN Zhong-Hui, DING Yi, LI Yan, WANG Ji-Chun, HU Bai-Geng, Vadim Khassanov, LYU Dian-Qiu. Genome-wide identification and characterization of PIF genes and their response to high temperature stress in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 86-98.
[12] XU De-Rong, SUN Chao, BI Zhen-Zhen, QIN Tian-Yuan, WANG Yi-Hao, LI Cheng-Ju, FAN You-Fang, LIU Yin-Du, ZHANG Jun-Lian, BAI Jiang-Ping. Identification of StDRO1 gene polymorphism and association analysis with root traits in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 76-85.
[13] ZHANG Ming-Cong, HE Song-Yu, QIN Bin, WANG Meng-Xue, JIN Xi-Jun, REN Chun-Yuan, WU Yao-Kun, ZHANG Yu-Xian. Effects of exogenous melatonin on morphology, photosynthetic physiology, and yield of spring soybean variety Suinong 26 under drought stress [J]. Acta Agronomica Sinica, 2021, 47(9): 1791-1805.
[14] WANG Yan-Peng, LING Lei, ZHANG Wen-Rui, WANG Dan, GUO Chang-Hong. Genome-wide identification and expression analysis of B-box gene family in wheat [J]. Acta Agronomica Sinica, 2021, 47(8): 1437-1449.
[15] ZHANG Si-Meng, NI Wen-Rong, LYU Zun-Fu, LIN Yan, LIN Li-Zhuo, ZHONG Zi-Yu, CUI Peng, LU Guo-Quan. Identification and index screening of soft rot resistance at harvest stage in sweetpotato [J]. Acta Agronomica Sinica, 2021, 47(8): 1450-1459.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd