Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon

Abstract

Summary The timing of reproduction is a critical developmental decision in the life cycle of many plant species. Fine mapping of a rapid‐flowering mutant was done using whole‐genome sequence data from bulked DNA from a segregating F2 mapping populations. The causative mutation maps to a gene orthologous with the third subunit of DNA polymerase δ (POLD3), a previously uncharacterized gene in plants. Expression analyses of POLD3 were conducted via real time qPCR to determine when and in what tissues the gene is expressed. To better understand the molecular basis of the rapid‐flowering phenotype, transcriptomic analyses were conducted in the mutant vs wild‐type. Consistent with the rapid‐flowering mutant phenotype, a range of genes involved in floral induction and flower development are upregulated in the mutant. Our results provide the first characterization of the developmental and gene expression phenotypes that result from a lesion in POLD3 in plants.

The wild grass Brachypodium distachyon as a developmental model system

“…These mutants are, in a sense, constitutively vernalized, and the role of the functional alleles is to repress VRN1 prior to cold exposure (Woods et al, 2017b). Indeed, the transcriptomes (via RNAseq) of several of our mutants overlap substantially with vernalized plants (Woods et al, 2020(Woods et al, , 2017bWoods unpubl.). We found that one of the mutations was in a gene with a Bromo-Adjacent Homology and a TFIIS domain; we refer to the gene as REPRESSOR OF VERNALIZATION1 (RVR1; Woods et al, 2017b).…”

“…Another route to gene discovery is the use of B. distachyon to conduct forward genetic screens to identify novel genes which is not possible in polyploid crops such as wheat (Ream et al, 2012). We have streamlined mapping B. distachyon mutants and have identified the causative lesion of many EMS-induced flowering time mutants using a mapping by sequencing pipeline (Minevich et al, 2012;Woods et al, 2014b;Woods and Amasino, 2015;Woods et al, 2020). Interestingly, most of the genes we have mapped are in novel flowering-time genes -i.e, these genes have not been described before in other plants (Figure 4) or are in genes which, in other plants have a minor role impacting flowering time but play a major role in B. distachyon (e.g.…”

“…We have isolated a number of mutants from forward genetic screens looking for mutants where VRN1 is expressed and flowering occurs without cold exposure in conditions in which the wild type requires cold for flowering and VRN1 induction (e.g. Lomax et al, 2018;Woods et al, 2020Woods et al, , 2017bWoods and Amasino, 2015)). Consistent with the key role of VRN1 expression in achieving competence to flower upon prolonged cold exposure, these mutants no longer have a vernalization requirement for rapid flowering.…”

A splice site mutation in theFvePHPgene is associated with leaf development and flowering time in woodland strawberry

“…Mutations in the splice sites exert a major influence on splicing events. For example, an alternative splice site mutation in the third subunit of a DNA polymerase accelerates flowering in Brachypodium distachyon by promoting the expression of flowering-related genes [ 22 ]. In Arabidopsis thaliana , two DNA polymerases, AtPOLH and AtREV1, play a key role in DNA replication and are regulated by alternative splicing [ 23 ].…”

Advances on genomics, biology, ecology and evolution of Brachypodium, a bridging model grass system for cereals and biofuel grasses

“…Woods et al (2020, in this issue) highlight work that advances our knowledge of the regulatory processes that control flowering time in B. distachyon . Through a combination of forward and reverse genetics, ChIP and histone immunoblotting, the authors demonstrate that a single mutation in the third subunit of DNA polymerase (POLD3), a previously uncharacterized gene in plants, is responsible for a vernalization‐independent rapid‐flowering phenotype.…”