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

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 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. Conclusions 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.

Genome-Wide Identification and Characterization of AP2/ERF Transcription Factor Family Genes in Oil Palm under Abiotic Stress Conditions

“…Our study demonstrated the occurrence of tandem duplications in oil palm for the expansion of all AP2/ERF family members during evolution. These results also agreed with previous findings of the tandem duplications of AP2/ERF members in Saccharum spontaneum L. [ 15 ].…”

“…AP2/ERF superfamily genes act as vital regulators for governing various physiological and stress responses in a wide range of plants [ 25 , 26 , 27 , 28 , 29 , 30 ]. Few genome-wide studies have been carried out to identify AP2/ERF family members in plant genomes [ 4 , 10 , 11 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. To date, no genome-wide studies have been conducted to explore the structure and role of AP2/ERF family genes in oil palm.…”

“…The identified number (172) of AP2/ERF s in the E. guineensis genome was greater than the identified number of AP2/ERF members in various plants, but less than the number of AP2/ERF genes in poplar (200) [ 12 ], sugarcane (218) [ 15 ], orchardgrass(193) [ 23 ], Ammopiptanthus nanus (174) [ 22 ], and sunflower (288) [ 24 ] genomes. The oil palm AP2/ERF gene structural analysis revealed that a higher number of AP2 family members contained more introns (6–10) compared to ERF, RAV or Soloist family members.…”

“…Based on whole-genome and EST sequence analyses, several researchers identified various numbers of AP2/ERF family members in the genomes of a wider range of plants, including: 147 in Arabidopsis [ 4 , 10 ]; 163 in rice [ 4 , 11 ]; 200 in poplar [ 12 ]; 132 in grapevine [ 13 ]; 131 in cucumber [ 14 ]; 218 in sugarcane [ 15 ]; 119 in Chinese jujube [ 16 ]; 98 in soybean [ 17 ]; 85 in tomato [ 18 ]; 117 in wheat [ 19 ]; 171 in cauliflower [ 20 ]; 134 in California poppy [ 21 ]; 193 in orchardgrass [ 22 ]; 174 in Ammopiptanthus nanus [ 23 ]; and 288 in sunflower [ 24 ]. Moreover, reports have described their prominent role in regulating abiotic stress responses (e.g., cold, salinity, drought, heat, and osmotic stress) in various plants [ 25 , 26 , 27 , 28 , 29 , 30 ].…”

Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions

“…It has been used to study smut infection response 19 , 20 , vital genes involved in cellulose and lignin biosynthesis 21 , plant growth-promoting rhizobacteria inoculation response 22 , and water, salt, and cold stress response 23 – 25 in cultivated sugarcane. Transcriptome sequencing has also been extensively applied to study gene expression changes in S. spontaneum in response to drought stress 26 , 27 , cold damage 28 – 31 , and identification of transcription factors 32 .…”