Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance

Abstract

DNA-binding with one finger (Dof) transcription factors play a crucial role in plant abiotic stress regulatory networks, although massive Dofs have been systematically characterized in plants, they have not been identified in the hexaploid crop sweetpotato. Herein, 43 IbDof genes were detected to be disproportionally dispersed across 14 of the 15 chromosomes of sweetpotato, and segmental duplications were discovered to be the major driving force for the expansion of IbDofs. The collinearity analysis of IbDofs with their related orthologs from eight plants revealed the potential evolutionary history of Dof gene family. Phylogenetic analysis displayed that IbDof proteins were assigned into nine subfamilies, and the regularity of gene structures and conserved motifs was consistent with the subgroup classification. Additionally, five chosen IbDof genes were shown to be substantially and variably induced under various abiotic conditions (salt, drought, heat, and cold), as well as hormone treatments (ABA and SA), according to their transcriptome data and qRT-PCR experiments. Consistently, the promoters of IbDofs contained a number of cis-acting elements associated with hormone and stress responses. Besides, it was noted that IbDof2 had transactivation activity in yeasts, while IbDof-11/-16/-36 did not, and protein interaction network analysis and yeast two-hybrid experiments revealed a complicated interaction connection amongst IbDofs. Collectively, these data lay a foundation for further functional explorations of IbDof genes, especially with regards to the possible application of multiple IbDof members in breeding the tolerant plants.

Comparative Analysis of the PYL Gene Family in Three Ipomoea Species and the Expression Profiling of IbPYL Genes during Abiotic Stress Response in Sweetpotato

“…Similar situations were also reported in the PYLs from apple, cucumber, Medicago sativa, and Prunus avium [14,36,39,41]. Moreover, there is the largest number of collinear gene pairs between I. batatas and I. trifida, I. triloba, indicating that their two diploid wild relatives play key roles in the evolution of sweetpotato PYL genes, which is consistent with that of our previous reports of multiple transcription factor families [28,38,42].…”

Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

“…In addition to the E group, the D1 subgroup, also known as the CDF subfamily, contains the most Dof genes, including DhDof2 , DhDof20 , DhDof12 , and DhDof16 . AtDof1.4 was classified into Group IV or B2 subgroups in previous studies ( Yanagisawa, 2002 ; Lijavetzky et al, 2003 ; Zhang et al, 2023 ). However, the phylogenetic trees in our study indicated that AtDof1.4 did not group with AtDof1.7, AtDof3.1, AtDof3.4, and AtDof5.8 in the D2 subgroup but as an independent subgroup.…”

“…D. Huoshanense materials were collected at the Plant Cell Engineering Center of West Anhui University (Luan, China). The culture conditions were 25°C ± 2°C, with a 12 h day and 12 h dark cycle ( Zhang et al, 2023 ). MS medium (without hormone addition) was used for the tissue culture of seedlings.…”

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

“…The comparative genome-wide study was performed between four Ipomoea species to evaluate valine glutamine motif-containing genes and found 40 differentially expressed genes (DEGs) referring to various abiotic stresses [ 26 ]. The other genome-wide studies in different Ipomoea species were conducted for important TF families such as NAC ( NAM , ATAF , and CUC ) TFs family [ 27 ], hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase gene family [ 28 ], DNA-binding with one finger (Dof) TF family [ 29 ], myeloblastosis (MYB) gene family [ 30 ], phytochrome-interacting factors [ 25 ], domain of unknown function gene family [ 31 ], two-component system genes [ 32 ], xyloglucan endotransglucosylase/hydrolase gene family [ 33 ], expansin gene family [ 34 ], glycine-rich RNA-binding proteins [ 35 ], WRKY TFs family [ 36 ], zinc-finger domain-containing stress-associated proteins [ 37 ], plant-specific GRAS TFs [ 38 ], APETALA2/ethylene responsive factor (AP2/ERF) TFs family [ 38 ], jasmonate-ZIM (JAZ) TF family [ 39 ], and bZIP TF family [ 10 ]. These studies provide new insights for understanding the different TFs families-mediated stress responses and lays the foundation for future functional investigation of sweet potato TFs families.…”