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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (4): 532-543.doi: 10.3724/SP.J.1006.2020.93040


Genome-wide identification and expression analysis of HD-ZIP I subfamily genes in maize

LIANG Si-Wei1,JIANG Hao-Liang1,ZHAI Li-Hong2,WAN Xiao-Rong1,LI Xiao-Qin1,JIANG Feng1,*(),SUN Wei1,*()   

  1. 1 College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China
    2 Medical College, Hubei University of Arts and Science, Xiangyang 441053, Hubei, China
  • Received:2019-07-13 Accepted:2019-12-26 Online:2020-04-12 Published:2020-01-15
  • Contact: Feng JIANG,Wei SUN E-mail:breakthrough@139.com;starking521@126.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31901565);the National Key Research and Development Program of Guangdong Province(2018B020202013);the Program of the Science and Technology Bureau of Guangdong Province(粤科产学研字[2016]176号)


Transcription factors (TFs) are indispensable regulators of plant response to abiotic stress and play an important role in the whole growth and development process. HD-ZIP proteins constitute a large family of transcription factors that are found only in plants and are divided into four subfamilies (HD-ZIP I-IV). HD-ZIP I subfamily genes mainly participate in response to extreme environments such as drought and osmotic stress and treatments of ABA and ethylene. Here, we identified 17 HD-ZIP I subfamily genes in the maize genome using the hidden Markov model (HMM), which distributed non-uniformly on six chromosomes of maize and were more closely related to rice than to Arabidopsis. Furthermore, these HD-ZIP I subfamily genes exhibited multiple expression patterns in seven tissues, showing strong tissues-specific expression. Moreover, maize HD-ZIP I subfamily genes showed different response patterns and degrees to different stresses, such as high salinity, waterlogging and cold stress. In addition, maize HD-ZIP I subfamily genes also showed a complex response pattern under treatment of five different hormones. These results provide valuable reference information for dissecting function and molecular mechanism of HD-ZIP I subfamily genes in maize.

Key words: HD-ZIP I subfamily, abiotic stress, expression analysis, maize

Supplementary table 1

List of primers used in the present study"

Gene accession number
Forward primer (5′-3′)
Reverse primer (5′-3′)
Gene accession number
Forward primer (5′-3′)
Reverse primer (5′-3′)

Table 1

Basic information of HD-ZIP I subfamily genes in maize"

Gene accession
Bin 基因组位置
Genome location
sequence (bp)
Protein (aa)
Exon number
ZmHB5 GRMZM2G132367 1.02 19250088:19252388 981 326 3
ZmHB7 GRMZM2G122076 4.05 77636576:77641035 819 272 3
ZmHB12 AC233899.1_FGP004 9.07 149912584:149914098 1134 377 3
ZmHB22 GRMZM2G178741 9.07 151525953:151528343 1035 344 3
ZmHB34 GRMZM2G002915 2.06 178781917:178784182 852 283 3
ZmHB41 GRMZM2G117164 5.05 190526953:190528628 708 235 2
ZmHB49 GRMZM2G097349 1.08 243185151:243187447 1092 363 2
ZmHB54 GRMZM2G041127 2.07 188712314:188714917 825 274 3
ZmHB66 GRMZM2G351330 2.03 22220873:22222180 786 261 2
ZmHB68 GRMZM2G005624 1.02 23240104:23243489 720 239 3
ZmHB102 GRMZM2G139963 1.02 14957965:14960921 1035 344 3
ZmHB112 GRMZM2G003304 1.07 218768608:218773418 813 270 3
ZmHB115 GRMZM2G021339 4.06 165861785:165863994 1020 339 4
ZmHB120 GRMZM2G056600 7.03 129296234:129298384 786 261 3
ZmHB126 GRMZM2G034113 2.07 195705583:195707271 735 244 2
ZmHB127 GRMZM2G119999 1.05 139960481:139962631 885 294 3
ZmHB128 GRMZM2G041462 7.03 142432248:142434060 720 239 2

Fig. 1

Chromosomal location of maize HD-ZIP I subfamily genes"

Fig. 2

Diagram of structure of HD-ZIP I subfamily genes and functional domains in maize The line indicates intron, wide black rectangle indicates exon, and narrow black rectangle indicates untranslated region (UTR) in left figure; the black round corner rectangle indicates HD domain and black hexagon indicates ZIP domain in right figure."

Fig. 3

Phylogenetic tree of HD-ZIP I proteins in maize, rice, and Arabidopsis The HD-ZIP I subfamily protein sequences of maize, rice, and Arabidopsis were obtained from the MaizeGDB (http://maizegdb.org/), TIGR (http://www.tigr.org/), and TAIR (http://www.arabidopsis.org/) databases, respectively. Multiple alignment of amino acid sequences was carried out by ClustalX 2.0 software and Neighbor-Joining evolutionary tree was constructed by MEGA 5.1 (1000 replications of bootstrap test). Arabidopsis genes are highlighted in yellow background, rice genes are highlighted in green background, and maize genes are highlighted in purple background."

Fig. 4

Expression profile of HD-ZIP I subfamily genes of maize Leaves: fully expended leaves; Tassels: immature tassels; Ears: immature ears; Seedling_shoots: the shoots of maize seedlings; Seedling_roots: the roots of maize seedlings; Seeds_5DAP: the seeds at 5 days after pollination; Seeds_10DAP: the seeds at 10 days after pollination. Colors in square represent the logarithm of the HD-Zip I subfamily gene expression level (ln (RPKM))."

Fig. 5

Expression pattern of maize HD-ZIP I genes under abiotic stresses NT: non-treatment; NaCl: NaCl treatment; WL: waterlogging stress; CT: chilling stress; RCT: recuperative treatment after chilling stress. The ordinate indicates the relative expression of genes, using the expression of the non-treatment group (NT) as 1. The significance of difference was evaluated using analysis of variance. *P < 0.05, **P < 0.01, and ***P < 0.001."

Fig. 6

Expression profiling of maize HD-ZIP I genes in response to hormones MOCK: control; ABA: Abscisic Acid; Eth: Ethylene; GA3: Gibberellin; KT: Kinetin; NAA: 1-naphthylacetic acid. The ordinate represents the relative expression of genes, using the expression of the non-treatment group (MOCK) as 1. The significance of difference was evaluated using analysis of variance. *P < 0.05, **P < 0.01, and ***P < 0.001."

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