The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play crucial roles in plant growth, development, and responses to biotic and abiotic stresses. This study was performed to comprehensively identify and characterize the
AP2/ERF
gene family in quinoa (
Chenopodium quinoa
Willd.), a highly resilient pseudocereal crop known for its salinity tolerance. A total of 150
CqAP2/ERF
genes were identified in the quinoa genome; these genes were unevenly distributed across the chromosomes. Phylogenetic analysis divided the CqAP2/ERFs into five subfamilies: 71 ERF, 49 DREB, 23 AP2, 3 RAV, and 4 Soloist. Additionally, the DREB and ERF subfamilies were subdivided into four and seven subgroups, respectively. The exon-intron structure of the putative
CqAP2/ERF
genes and the conserved motifs of their encoded proteins were also identified, showing general conservation within the phylogenetic subgroups. Promoter analysis revealed many
cis
-regulatory elements associated with light, hormones, and response mechanisms within the promoter regions of
CqAP2/ERF
genes. Synteny analysis revealed that segmental duplication under purifying selection pressure was the major evolutionary driver behind the expansion of the
CqAP2/ERF
gene family. The protein-protein interaction network predicted the pivotal CqAP2/ERF proteins and their interactions involved in the regulation of various biological processes including stress response mechanisms. The expression profiles obtained from RNA-seq and qRT-PCR data detected several salt-responsive
CqAP2/ERF
genes, particularly from the ERF, DREB, and RAV subfamilies, with varying up- and downregulation patterns, indicating their potential roles in salt stress responses in quinoa. Overall, this study provides insights into the structural and evolutionary features of the
AP2/ERF
gene family in quinoa, offering candidate genes for further analysis of their roles in salt tolerance and molecular breeding.
Supplementary Information
The online version contains supplementary material available at 10.1038/s41598-024-81046-1.
