Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (20): 4021-4034.doi: 10.3864/j.issn.0578-1752.2023.20.008

• PLANT PROTECTION • Previous Articles     Next Articles

Genome-Wide Identification of AP2/ERF Gene Family in Alternanthera philoxeroides and Its Expression Patterns Under Herbicide Stresses

HAN XiaoWen1(), HAN Shuo1, HU YiFeng2, WANG MengRu1, CHEN ZhongYi1, ZHU YongXing1, YIN JunLiang1()   

  1. 1 Engineering Research Center of Wetland Ecology and Agricultural Use, Ministry of Education/College of Agriculture/College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei
    2 College of Life Science, South-Central University for Nationalities, Wuhan 430074
  • Received:2023-06-26 Accepted:2023-08-14 Online:2023-10-16 Published:2023-10-31
  • Contact: YIN JunLiang

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Abstract:

【Background】Alternanthera philoxeroides is a malignant invasive weed that is extremely difficult to control, causing serious harm to ecology and environment in China. The AP2/ERF (APETALA2/ethylene responsive factor) family is one of the largest transcription factor families in plants, which not only participates in the regulation of various signal networks in plants, but also plays an important role in plant response to herbicides. 【Objective】The objective of this study is to systematically analyze the basic characteristics of ApAP2/ERF, reveal its expression patterns under herbicide stress, decipher the biological functions of ApAP2/ERF in response to herbicide stress, identify potential target genes for herbicide resistance, and to provide a theoretical basis for accurate and reasonable selection of herbicides. 【Method】The AP2/ERF family members were identified from A. philoxeroides genome database using local BLASTp. MEME, ExPASyServer10, Plant-mPLoc, SWISS-MODEL, NCBI SRA database, and psRNA Target online website were used to obtain conserved motif, protein physicochemical property, subcellular localization, tertiary structure, transcriptome, and targeted miRNA information. Gene structure information was obtained from the GFF3 genome annotation file. Phylogenetic tree, expression pattern heatmap, and miRNA target relationship network were constructed using MEGA 11, TBtools, and R software. The expression patterns of AP2/ERF family members in response to five herbicides and at different time points (0-7 d) were analyzed using RT-qPCR. 【Result】A total of 96 ApERF, 9 ApAP2, and 4 ApRAV genes were identified from A. philoxeroides, and they were named ApERF1 to ApERF96, ApAP2-1 to ApAP2-9, and ApRAV1 to ApRAV4, respectively. The identified ApAP2/ERF proteins are hydrophilic. Subcellular localization prediction revealed that the ApAP2/ERFs are located in the nucleus and cytoplasm. The expression patterns of ApAP2/ERFs were regulated by geographical condition, water condition, and low potassium stress. Under 41% glyphosate treatment, ApERF7/74/94 were highly induced within 3-7 days; under 50% isoproturon treatment, all six ApERFs were highly induced at a specific time; under 10% fluoroglycofen treatment, the expression levels of ApERF7/13/49/94 showed a trend of first increasing, then decreasing, and then increasing; under 20% fluroxypyr treatment, ApERF7/13/49/54/94 were highly induced at 0.5 d; under 13% oxadiazon treatment, ApERF13/49/54/74 were significantly downregulated in expression in a short period of time. 【Conclusion】109 ApAP2/ERF family members were identified, and members located in the same group have similar motifs. The expression of ApAP2/ERFs is regulated by geographical condition, water condition, and low potassium stress, and is also induced by herbicides, suggesting that it responds to herbicide stress by influencing the ethylene signaling pathway.

Key words: Alternanthera philoxeroides, bioinformatics, transcription factor, herbicide, expression pattern, AP2/ERF gene family

Table 1

The test herbicides and concentrations"

除草剂
<BOLD>H</BOLD>erbicide		 施液量
Application amount (g·m-2)		 生产商
Manufacturer		 剂型
Dosage form
41%草甘膦Glyphosate 0.08 江苏快达农化股份有限公司 Jiangsu Kuaida Agrochemical Co., Ltd 水剂 Aqueous agent
50%异丙隆 Isoproturon 0.05 美丰农业科技（上海）有限公司
Meifeng Agricultural Technology (Shanghai) Co., Ltd		 可湿性粉剂 Wettable powder
13%噁草酮 Oxadiazon 0.04 大连越达农药化工有限公司 Dalian Yueda Pesticide Chemical Co., Ltd 乳油 Emulsifiable concentrate
10%乙羧氟草醚 Fluoroglycofen 0.008 潍坊鸿汇化工有限公司 Weifang Honghui Chemical Co., Ltd 乳油 Emulsifiable concentrate
20%氯氟吡氧乙酸 Fluroxypyr 0.01 山东绿霸化工股份有限公司 Shandong Lvba Chemical Co., Ltd 乳油 Emulsifiable concentrate

Table 2

The RT-qPCR primers for ApERF family members"

基因<BOLD>G</BOLD>ene 正向引物Forward primer (5′-3′) 反向引物Reverse primer (5′-3′)
Tubby CGGTCTAGCCGAAGATTCCA CGCTTGGTGAAGGCAGACATT
ApERF7 ACCCCAAGCCCAACAACC TCCTCACCGAACACGTCTCC
ApERF13 TCCTCACCGAACACGTCTCC CAAACGACATTCACCCAAGAGT
ApERF49 CTCTCCTGCTTCTGTGCTCG GCCCGATTTCACTACATTGG
ApERF54 CCAAAGTGTTCCCACCCAA CCCCACCTTCACCTCCAC
ApERF74 GCAACATTAACTGCCAAGCTTC GGCCCAATTTCATTAGTAGAGCT
ApERF94 TTCAGAGTACCCAAAGAAACGTG AAATGTCCCGAGCCAAATTC

Fig. 1

Phylogenetic tree of A. philoxeroides AP2/ERF members"

Fig. 2

Gene structure and motif analysis of ApAP2/ERFs"

Fig. 3

Predicted 3D models of ApAP2/ERFs"

Fig. 4

Heat map of growth and development and abiotic stress treatment of ApAP2/ERFs"

Fig. 5

Sankey diagram for the relationship of miRNAs targeting to ApAP2/ERF transcripts"

Fig. 6

Effect of different herbicides on plant control of A. philoxeroides"

Fig. 7

Expression pattern of ApERFs under different herbicide treatments"

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