Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.)

• Published in: BMC genomics Vol. 21; no. 1; pp. 685 - 17
• Main Authors: Li, Peiting, Chai, Zhe, Lin, Pingping, Huang, Chaohua, Huang, Guoqiang, Xu, Liangnian, Deng, Zuhu, Zhang, Muqing, Zhang, Yu, Zhao, Xinwang
• Format: Journal Article
• Language: English
• Published: England BioMed Central 02.10.2020; BMC
• Subjects: Abiotic stress; AP2/ERF gene; Cellular stress response; Chromosomes; Dehydration; Developmental stages; Energy crops; Environmental changes; Ethanol; Gene expression; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Genes; Genetic structure; Genomes; Genomics; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Hormones; Introns; Phylogenetics; Phylogeny; Plant breeding; Plant growth; Plant Proteins - genetics; Plant Proteins - metabolism; Plant resistance; Promoter Regions, Genetic; Proteins; Regulatory sequences; Rice; Saccharum - genetics; Saccharum - growth & development; Saccharum - metabolism; Saccharum spontaneum; Salt Stress; Signal transduction; Sorghum; Stresses; Structural analysis; Sugarcane; Transcription factor; Transcription factors; AP2/ERF gene; Transcription factor; Abiotic stress; Sugarcane
• DOI: 10.1186/s12864-020-07076-x
• ISSN: 1471-2164

APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide. A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum. In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.