Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane ( Saccharum spontaneum
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RESEARCH ARTICLE
Open Access
Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.) Peiting Li1†, Zhe Chai2†, Pingping Lin1, Chaohua Huang1, Guoqiang Huang1, Liangnian Xu1, Zuhu Deng1, Muqing Zhang2* , Yu Zhang3* and Xinwang Zhao1,2,4*
Abstract Background: 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. Results: 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 GAassociated 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. (Continued on next page)
* Correspondence: [email protected]; [email protected]; [email protected]; [email protected] † Peiting Li and Zhe Chai contributed equally to this work. 2 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530005, China 3 Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China 1 National Engineering Research Center for Sugarcane & Guangxi Key Laboratory for Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China Full list of author information is available at the end of the article © The Author(s)
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