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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (6): 1480-1495.doi: 10.3724/SP.J.1006.2023.24113

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide identification and characterization of MAPK genes and their response to biotic stresses in foxtail millet

LIU Jia1,**(), ZOU Xiao-Yue1,2,**(), MA Ji-Fang1, WANG Yong-Fang1, DONG Zhi-Ping1, LI Zhi-Yong1,*(), BAI Hui1,*()   

  1. 1Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/Key Laboratory of Minor Cereal Crops of Hebei Province, Shijiazhuang 050035, Hebei, China
    2College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, China
  • Received:2022-05-05 Accepted:2022-07-21 Online:2023-06-12 Published:2022-08-09
  • Contact: *E-mail: lizhiyongds@126.com;E-mail: baihui_mbb@126.com
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Key Research & Development Program of China(2018YFD1000703);National Key Research & Development Program of China(2018YFD1000700);Natural Science Foundation of China(31872880);HAAFS Basic Science and Technology Contract Project(HBNKY-BGZ-02);China Agriculture Research System of MOF and MARA(CARS-06-14.5-A25);Hebei Key Research & Development Program(21326338D)

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Abstract:

MAPK plays an important role in plant growth and development regulation, biotic and abiotic stress responses, and hormone signal transduction. In order to elucidate the biological function of the SiMPK genes in foxtail millet, we identified the SiMPK family members in the genome and analyzed the distribution, structure, evolution, and its expression characteristics in response to different stresses. In this study, the SiMPK gene family members were identified in the genome-wide level using the amino acid sequences of conserved domains and specific TXY motifs of MAPK proteins between foxtail millet and rice. The protein physicochemical property, phylogenetic evolution, chromosome distribution, gene structure, protein conserved motif, promoter cis-acting regulatory elements, and collinearity were analyzed. The relative expression patterns of SiMPK genes in the different tissue, under the biotic stresses of Uromyces setariae-italicae Yoshino and Ostrinia furnacalis and with different hormone treatments were analyzed by qRT-PCR. The results showed that a total of 15 SiMPK genes were identified, and the encoded proteins contained 220-611 amino acids, the relative molecular weight ranged from 25.77 kD to 69.63 kD, and the isoelectric point ranged from 5.46 to 9.34. Phylogenetic analysis showed that SiMPK genes were divided into four groups. Group A, B, and C contained TEY motifs, and group D contained TDY motifs. SiMPK genes were distributed on chromosomes 1, 3, 4, 5, 8, and 9, and contained 3-11 exons. All SiMPK proteins contained motif 1 and motif 2. A number of cis-acting elements related to stress, hormones and plant growth and development were predicted in the promoter regions of the SiMPK genes. Most genes had obvious tissue expression specificity. Except for SiMPK21-2 and SiMPK6, the other members had obvious responses to 1 to 3 kinds of stresses, such as Uromyces setariae-italicae Yoshino infection, Ostrinia furnacalis feeding, and SA and MeJA treatments. The results laid a theoretical foundation for further research on the function of SiMPK genes in the biotic stresses of disease and pest in foxtail millet.

Key words: foxtail millet (Setaria italica), MAPK gene family, Uromyces setariae-italicae Yoshino, Ostrinia furnacalis, relative expression analysis

Table 1

List of qRT-PCR primers"

引物
Primer		 正向序列
Forward sequence (5'-3')		 反向序列
Reverse sequence (5'-3')
SiActin_F CGCATATGTGGCTCTTGACT GGGCACCTAAATCTCTCTGC
SiMPK3 AGCGACATGATGACGGAGTA TAGTCGGTGGAGTTGAGCAG
SiMPK4-1 GTGCAGTCGATTTGTTGGAG ATGCAGAGCCTCATCAACTG
SiMPK4-2 CAGCACGACCAGAAGAAGAA TATGGGTGTCCAGAGCAGAG
SiMPK4-3 AATCAGAGATGATGCACGGA TAACGCTCTGCAGAACCAAC
SiMPK6 ATGAGCCTGTCTGCTCAATG TTGTTCTTCGGACAGTGCAT
SiMPK7 TGTACCCACAAGCACATCCT CAGAGCCTCGGTGACACTAA
SiMPK14 TGTGCCTATCAAGCCCATAG CTTAGTGCATCCACACGGTT
SiMPK17-1 ACGGATTATGTGGCAACAAG TCAGCAAATATGCACCCAAT
SiMPK17-2 CTTCCAGATGCGCTATCAAA CACCCTGGGTACCTTGTCTAA
SiMPK20-1 TTGCAGGCTGAAAGGTACAC TCATGTCCAGAGCAACATCA
SiMPK20-2 TTCGGTGGGAGATCTGGTG TCTGTCGAGTGTGCAGATCA
SiMPK20-4 CCAAGTCATCAAGGCAAATG TTCTTTGGCTTCAAATCACG
SiMPK20-5 GTCGCCGATCAACACATTAC CCGGTCTTTCTCAAGCTCTC
SiMPK21-1 GAAAGCATCAGTGCTTCCAA AGCGATCTTCTTCGACACCT
SiMPK21-2 GACCCAATGGCTCTTCATTT GTGTTATAGGCTCGCGTTCA

Table 2

Characteristics of the 15 SiMPKs in foxtail millet"

基因名称
Gene name		 基因编号
Gene ID		 氨基酸数目
Number of amino acids (aa)		 分子量
Molecular weight (kD)		 等电点
Isoelectric point (pI)		 亚细胞定位
Subcellular
location		 信号肽
Signal
peptide
SiMPK3 Seita.9G444100 375 42.43 5.46 C 无 No
SiMPK4-1 Seita.9G344000 372 42.29 5.96 C 无 No
SiMPK4-2 Seita.3G058000 557 63.46 8.83 N 无 No
SiMPK4-3 Seita.8G104500 535 61.17 8.79 C 无 No
SiMPK6 Seita.4G069900 347 39.13 5.71 C 无 No
SiMPK7 Seita.4G243400 369 42.34 6.63 N 无 No
SiMPK14 Seita.1G089400 370 42.41 6.53 N 无 No
SiMPK17-1 Seita.4G273900 574 65.25 6.64 N 无 No
SiMPK17-2 Seita.1G095300 506 57.85 7.67 N 无 No
SiMPK20-1 Seita.5G235700 611 69.63 9.14 N 无 No
SiMPK20-2 Seita.3G131800 220 25.77 9.17 C 无 No
SiMPK20-4 Seita.5G261300 589 67.37 9.34 N 无 No
SiMPK20-5 Seita.3G145200 591 67.26 9.20 N 无 No
SiMPK21-1 Seita.3G136100 590 66.86 6.74 C 无 No
SiMPK21-2 Seita.5G241700 508 57.77 7.64 C 无 No

Fig. 1

Phylogenic tree of MAPK gene families in Setaria italica, Oryza sativa, and Arobidopsis thaliana Si: Setaria italica: Os: Oryza sativa: At: Arobidopsis thaliana."

Fig. 2

Distributions of SiMPKs on nine chromosomes in foxtail millet"

Fig. 3

Structure and conserved motif of SiMPKs genes in foxtail millet Motif: conserved base sequence; UTR: untranslated region; CDS: coding region sequence."

Fig. 4

Sequence Logo of the SiMPKs protein motifs in foxtail millet"

Fig. 5

Cis-acting elements in the promoter regions of 15 SiMPKs in foxtail millet"

Fig. 6

Collinearity analysis of the MAPK gene family in foxtail millet"

Fig. 7

Collinearity analysis of the MAPK genes between Setaria italica and Oryza sativa"

Fig. 8

Relative expression level of SiMPK genes in the different parts of foxtail millet SD: seedling stage; BT: booting stage; shoot: the aboveground part at seedling stage; root: the underground part at seedling stage or root at booting stage. The different letters mean significant difference at the 0.05 probability level."

Fig. 9

Expression analysis of SiMPK genes in Setaria italica leaves inoculated with Uromyces setariae-italicae * represents that the relative expression levels of genes in disease-resistant and disease-sensitive reactions at the same time point are significantly different at the probability level of 0.05."

Fig. 10

Expression analysis of SiMPK genes in Setaria italica leaves fed by Ostrinia furnacalis * represents that the relative expression levels of genes in the leaves at different time points after being fed by Ostrinia furnacalis are significantly different at the probability level of 0.05 compared with 0 h. **: P < 0.01; ***: P < 0.001."

Fig. 11

Expression analysis of SiMPK genes in Setaria italica leaves treated with SA and MeJA * represents that the relative expression levels of genes in the leaves at different time points after SA/JA treatment are significantly different at the probability level of 0.05 compared with 0 h; **: P < 0.01; ***: P < 0.001."

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