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1. Expression of Concern: PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon

   https://doi.org/10.1371/journal.pgen.1010955  

   Woods D P ; Li, W ; Sibout, R ; Shao, M ; Laudencia-Chingcuanco, D ; Vogel, J P ; Dubcovsky, J ; Amasino, R M ( September 2023 , PLOS Genetics)

   Köhler, C (Ed.)

   Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon. 

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2. The H3K4 demethylase JMJ1 is required for proper timing of flowering in Brachypodium distachyon

   https://doi.org/10.1093/plcell/koae124  

   Liu, Bing ; Li, Chengzhang ; Li, Xiang ; Wang, Jiachen ; Xie, Wenhao ; Woods, Daniel_P ; Li, Weiya ; Zhu, Xiaoyu ; Yang, Shuoming ; Dong, Aiwu ; et al ( April 2024 , The Plant Cell)

   Flowering is a key developmental transition in the plant life cycle. In temperate climates, flowering often occurs in response to the perception of seasonal cues such as changes in day-length and temperature. However, the mechanisms that have evolved to control the timing of flowering in temperate grasses are not fully understood. We identified a Brachypodium distachyon mutant whose flowering is delayed under inductive long-day conditions due to a mutation in the JMJ1 gene, which encodes a Jumonji domain-containing protein. JMJ1 is a histone demethylase that mainly demethylates H3K4me2 and H3K4me3 in vitro and in vivo. Analysis of the genome-wide distribution of H3K4me1, H3K4me2, and H3K4me3 in wild-type plants by chromatin immunoprecipitation and sequencing combined with RNA sequencing revealed that H3K4m1 and H3K4me3 are positively associated with gene transcript levels, whereas H3K4me2 is negatively correlated with transcript levels. Furthermore, JMJ1 directly binds to the chromatin of the flowering regulator genes VRN1 and ID1 and affects their transcription by modifying their H3K4me2 and H3K4me3 levels. Genetic analyses indicated that JMJ1 promotes flowering by activating VRN1 expression. Our study reveals a role for JMJ1-mediated chromatin modification in the proper timing of flowering in B. distachyon.

    

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3. Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass

   https://doi.org/10.1111/pce.13546  

   Weng, Xiaoyu ; Lovell, John T. ; Schwartz, Scott L. ; Cheng, Changde ; Haque, Taslima ; Zhang, Li ; Razzaque, Samsad ; Juenger, Thomas E. ( April 2019 , Plant, Cell & Environment)

   Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost‐effective 3′‐Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C₄perennial grass,Panicum hallii. We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine‐scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming ofcis‐regulatory elements and biological processes under short‐ and long‐day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod‐dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis ofGIGANTEAhomolog predicted 1,668 potential coincidence partners, including five well‐known GI‐interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.

    

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4. Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

   https://doi.org/10.1111/nph.16507  

   MacKinnon, Kirk J‐M. ; Cole, Benjamin J. ; Yu, Chang ; Coomey, Joshua H. ; Hartwick, Nolan T. ; Remigereau, Marie‐Stanislas ; Duffy, Tomás ; Michael, Todd P. ; Kay, Steve A. ; Hazen, Samuel P. ( April 2020 , New Phytologist)

   Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events.

   We used RNA sequencing to characterize theBrachypodium distachyontranscriptome under light and temperature cycles, as well as under constant conditions.

   Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome inB. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors.

   When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmicB. distachyontranscriptome represents a foundational resource with implications in other grass species.

    

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5. Quantitative Trait Loci and Candidate Genes Associated with Photoperiod Sensitivity in Lettuce (Lactuca spp.)

   https://doi.org/10.1007/s00122-021-03908-w  

   Han, Rongkui ; Lavelle, Dean ; Truco, Maria José ; Michelmore, Richard ( July 2021 , Theoretical and Applied Genetics)

   A population of lettuce that segregated for photoperiod sensitivity was planted under long-day and short-day conditions. Genetic mapping revealed two distinct sets of QTLs controlling daylength-independent and photoperiod-sensitive flowering time.

   The molecular mechanism of flowering time regulation in lettuce is of interest to both geneticists and breeders because of the extensive impact of this trait on agricultural production. Lettuce is a facultative long-day plant which changes in flowering time in response to photoperiod. Variations exist in both flowering time and the degree of photoperiod sensitivity among accessions of wild (Lactuca serriola) and cultivated (L. sativa) lettuce. An F₆population of 236 recombinant inbred lines (RILs) was previously developed from a cross between a late-flowering, photoperiod-sensitiveL. serriolaaccession and an early-flowering, photoperiod-insensitiveL. sativaaccession. This population was planted under long-day (LD) and short-day (SD) conditions in a total of four field and screenhouse trials; the developmental phenotype was scored weekly in each trial. Using genotyping-by-sequencing (GBS) data of the RILs, quantitative trait loci (QTL) mapping revealed five flowering time QTLs that together explained more than 20% of the variation in flowering time under LD conditions. Using two independent statistical models to extract the photoperiod sensitivity phenotype from the LD and SD flowering time data, we identified an additional five QTLs that together explained more than 30% of the variation in photoperiod sensitivity in the population. Orthology and sequence analysis of genes within the nine QTLs revealed potential functional equivalents in the lettuce genome to the key regulators of flowering time and photoperiodism,FDandCONSTANS, respectively, in Arabidopsis.

    

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