Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication

Abstract

Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.

Identification and characterization of Dof genes in Cerasus humilis

“…Only seven subfamilies of Dof genes have been identified in lotus. In rice and sorghum, at least 11% of Dof genes disappeared between 70 and 50 million years ago (MYA), because of changes in amino acid substitution rates in the critical Dof domain ( Yu et al., 2021 ). This confirms that the deletion of Dof gene family members is common among plant species.…”

DOF transcription factors: Specific regulators of plant biological processes

“…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. The structural diversity of DOF TFs may be closely related to complex physiological regulatory networks established during plant evolution.…”

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.…”