Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

Abstract

AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.

BnAP2-12 overexpression delays ramie flowering: evidence from AP2/ERF gene expression

“…Abscisic acid response elements (253) existed in the promoters of 73 BnAP2/ERF genes. These results support the cis-element types found in other plant species (Wong et al, 2017;Jiang et al, 2022;Qiu et al, 2022;Wan et al, 2022).…”

“…Ka/Ks represents the ratio between non-synonymous (Ka) and synonymous (Ks) substitutions, which can determine whether the gene encoding the protein is under selection pressure. Ka/Ks > 1 denotes positive selection, Ka/Ks ≈ 1 denotes neutral selection, and Ka/Ks < 1 denotes purifying selection ( Qiu et al., 2022 ). All Ka/Ks values of BnAP2/ERF were < 1.…”

“…Additionally, based on multiple reports, AP2/ERF transcription factors play an important role in flowering regulation and development in model plants, such as rice and Arabidopsis ( Jofuku et al., 1994 ; Nakano et al., 2006 ; Tanaka et al., 2014 ). Although these AP2/ERF TF members were reported in studies on waterlogging and the ramet development of ramie ( Qiu et al., 2022 ), no AP2/ERFs were found to be involved in the regulation of flowering and development. Our data provide novel insights into the roles of AP2/ERF TF in flower development.…”

“…(Jofuku et al, 1994;Nakano et al, 2006;Tanaka et al, 2014). Although these AP2/ERF TF members were reported in studies on waterlogging and the ramet development of ramie (Qiu et al, 2022), no AP2/ERFs were found to be involved in the regulation of flowering and development. Our data provide novel insights into the roles of AP2/ERF TF in flower development.…”

Differentially Expressed Genes Identification of Kohlrabi Seedlings (Brassica oleracea var. caulorapa L.) under Polyethylene Glycol Osmotic Stress and AP2/ERF Transcription Factor Family Analysis

“…The AP2 subfamily members contain two AP2 domains, while the ERF subfamily members contain an AP2 domain, and the RAV subfamily members contain one AP2 domain and one B3 domain [ 21 , 22 , 23 ]. Research on the AP2/ERF family has been conducted in a variety of plants, including rhododendron [ 24 ], oily persimmon [ 25 ], maize [ 26 ], sand pear [ 27 ], tomato [ 28 ], Juglans mandshurica [ 29 ], ramie [ 30 ], and so on. The identification and analysis of AP2 / ERF family members lays the foundation for clarifying the function of the AP2 / ERF gene.…”