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

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.

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.

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.

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.

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.