Minor Effects of 11 Dof Family Genes Contribute to the Missing Heritability of Heading Date in Rice (Oryza sativa L.)

Abstract

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with important and diverse functions in seed germination, flowering time, and biotic and abiotic stresses. In this study, haplotype-based association analysis was conducted between heading date and 30 Dof family genes in a worldwide germplasm collection. Of these, 22 Dof genes were associated with heading date. Multiple comparisons among haplotypes revealed their diverse functions in promoting and suppressing heading date under shortday (SD) and long-day (LD) conditions. They cumulatively made a considerable contribution to the missing heritability of heading date. A set of knockout mutants of 30 Dof genes generated by CRISPR/Cas9-mediated genome editing technology showed that 11 and 9 Dof genes regulated heading date under LD and SD, respectively. Phenotype measurement of mutants showed that these 11 and 9 Dof genes slightly regulated heading with effects of 2-5 days under LD and SD, respectively. Both mutant and natural variation assays indicated functional redundancy in regulating heading date among Dof family genes. Nucleotide diversity analysis suggested that most Dof genes have been subjected to selection during domestication and improvement. Beyond heading date, this set of mutants is also a good resource for evaluating the function of Dof genes in regulating stress tolerance and seed germination.

DOF transcription factors: Specific regulators of plant biological processes

“…In particular, the issue of functional differences or redundancy is highly controversial. Some scientists believe that the functions of DOF proteins are highly redundant (Noguero et al, 2013;Huang et al, 2020), while others argue that large differences exist (Yanagisawa, 2016;Renau-Morata et al, 2020). Huang et al (2020) suggested that the functional redundancy of DOF genes in rice strain ZH11 might mask the phenotypes of individual mutants.…”

“…Some scientists believe that the functions of DOF proteins are highly redundant (Noguero et al, 2013;Huang et al, 2020), while others argue that large differences exist (Yanagisawa, 2016;Renau-Morata et al, 2020). Huang et al (2020) suggested that the functional redundancy of DOF genes in rice strain ZH11 might mask the phenotypes of individual mutants. In contrast, Yu et al (2021b) confirm that knockout lines of all OsDOF family members have significant phenotypic defects in the japonica rice strain TP309, indicating that the OsDOF family has low redundancy.…”

Emerging Roles of Plant DNA-Binding With One Finger Transcription Factors in Various Hormone and Stress Signaling Pathways

“…Yet, large numbers of Dofs remain uncharacterized in plants. Nonetheless, as exemplified with the success in small studies targeting individual Dofs ( Ramirez et al, 2021 ; Wang Z. et al, 2021 ) but also large-scale attempts to generate knockout lines for all Dof members within a single plant species such as all 30 OsDofs in rice ( Huang et al, 2019 ; Yu L. et al, 2021 ), CRISPR/Cas system is poised to be an effective and flexible way to study the function of Dofs through the generation of functional (e.g., loss- and/or gain-of-function) mutants. Long non-coding RNAs (lncRNAs) are a heterogeneous class of regulatory transcripts that represent a diverse class of regulatory loci with roles in development and stress responses in plants.…”

DNA-Binding with One Finger (Dof) Transcription Factor Gene Family Study Reveals Differential Stress-Responsive Transcription Factors in Contrasting Drought Tolerance Potato Species

“…DNA-binding with one finger (Dof) proteins are a group of plant-specific TFs [ 3 ]. Following the isolation of the first Dof gene ( Zmdof1 ) from maize, additional Dof genes have been identified in other plants and are the subject of extensive research [ 4 , 5 , 6 , 7 , 8 ]. In N-terminal regions, the Dof proteins contain a highly conserved Dof domain (about 52 amino acids with a Cys2/Cys2 zinc finger structure).…”