Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

Xue Yong; Tangchun Zheng; Xiaokang Zhuo; Sagheer Ahmad; Lulu Li; Ping Li; Jiayao Yu; Jia Wang; Tangren Cheng; Qixiang Zhang

doi:10.7717/peerj.10785

Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

PeerJ. 2021 Feb 4:9:e10785. doi: 10.7717/peerj.10785. eCollection 2021.

Authors

Xue Yong^{1

2

3

4

5

6}, Tangchun Zheng^{1

2

3

4

5

6}, Xiaokang Zhuo^{1

2

3

4

5

6}, Sagheer Ahmad^{1

2

3

4

5

6}, Lulu Li^{1

2

3

4

5

6}, Ping Li^{1

2

3

4

5

6}, Jiayao Yu^{1

2

3

4

5

6}, Jia Wang^{2

3

4

5

6}, Tangren Cheng^{2

3

4

5

6}, Qixiang Zhang^{1

2

3

4

5

6}

Affiliations

¹ Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.
² Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China.
³ National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China.
⁴ Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China.
⁵ Engineering Research Center of Landscape Environment of Ministry of Education, Beijing Forestry University, Beijing, China.
⁶ Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China.

Abstract

Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely unknown in Rosaceae. Abscisic acid (ABA) is a stress hormone involving abiotic stress response pathways. The ABRE-binding factor/ABA-responsive element-binding protein (ABF/AREB) is a subfamily of the basic domain/leucine zipper (bZIP) transcription factor family. It plays an important role in the ABA-mediated signaling pathway. Here, we analyzed the ABF/AREB subfamily genes in nine Rosaceae species. A total of 64 ABF/AREB genes were identified, including 18, 28, and 18 genes in the Rosoideae, Amygdaloideae, and Maloideae traditional subfamilies, respectively. The evolutionary relationship of the ABF/AREB subfamily genes was studied through the phylogenetic analysis, the gene structure and conserved motif composition, Ka/Ks values, and interspecies colinearity. These gene sets were clustered into four groups. In the Prunus ABF/AREB (PmABF) promoters, several cis-elements related to light, hormone, and abiotic stress response were predicted. PmABFs expressed in five different tissues, except PmABF5, which expressed only in buds. In the dormancy stages, PmABF1, 2, 5 and 7 showed differential expression. The expression of PmABF3, 4 and 6 was positively correlated with the ABA concentration. Except for PmABF5, all the PmABFs were sensitive to ABA. Several ABRE elements were contained in the promoters of PmABF1, 3, 6, 7. Based on the findings of our study, we speculate that PmABFs may play a role in flower bud dormancy in P. mume.

Keywords: ABF/AREB; ABRE; Dormancy; Evolution; Expression; Prunus mume; Rosaceae.

Grants and funding

The research was supported by the National Natural Science Foundation of China (No. 31800595), the Beijing Municipal Science and Technology Project (No. Z181100002418006), and the Special Fund for Beijing Common Construction Project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.