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Summary Plants activate induced defenses through the recognition of molecular patterns. Like pathogen-associated molecular patterns (PAMPs), herbivore-associated molecular patterns (HAMPs) can be recognized by cell surface pattern recognition receptors leading to defensive transcriptional changes in host plants. Herbivore-induced defensive outputs are regulated by the circadian clock, but the underlying molecular mechanisms remain unknown. To investigate how the plant circadian clock regulates transcriptional reprogramming of a specific HAMP-induced pathway, we characterized the daytime and nighttime transcriptional response to caterpillar-derived In11 peptide, in the legume crop cowpea (Vigna unguiculata). Using diurnal and free-running conditions, we found that daytime In11 elicitation resulted in stronger late-induced gene expression than nighttime. Plants with a conditional arrhythmic phenotype in constant light (LL) conditions lost time-of-day dependent responses to In11 treatment, and this was associated with arrhythmic expression of circadian clock core transcription factorLate Elongated Hypocotyl VuLHY1andVuLHY2. Reporter assays with VuLHY homologs indicated that they interact with the promoter of daytime In11-inducedKunitz Trypsin Inhibitor(VuKTI) via a canonical and a polymorphic CCA1/LHY Binding Site (CBS), consistent with a mechanism of direct regulation by circadian clock transcription factors. This study improves our understanding of the time-dependent mechanisms that regulate herbivore-induced gene expression. 

Summary Day neutrality, or insensitivity to photoperiod (day length), is an important domestication trait in many crop species. Although the oilseed cropCamelina sativahas been cultivated since the Neolithic era, day-neutral accessions have yet to be described. We sought to leverage genetic diversity in existing germplasms to identifyC. sativaaccessions with low photoperiod sensitivity for future engineering of this trait. We quantified variation in the photoperiod response across 161 accessions ofC. sativaby measuring hypocotyl length of four-day-old seedlings grown in long-day and short-day conditions, finding wide variation in photoperiod response. Similarly, soil-grown adult plants from selected accessions showed variation in photoperiod response in several traits; however, photoperiod responses in seedling and adult traits were not correlated, suggesting complex mechanistic underpinnings. Although RNA-seq experiments of the reference accession Licalla identified several differentially regulatedArabidopsissyntelogs involved in photoperiod response, includingCOL2, FT, LHYandWOX4, expression of these genes in the accessions did not correlate with differences in their photoperiod sensitivity. Taken together, we show that all tested accessions show some degree of photoperiod response, and that this trait is likely complex, involving several and separable seedling and adult traits. Significance StatementDay neutrality (photoperiod insensitivity) is a common trait in domesticated crops; however, the ancient oilseed cropCamelina sativahas remained photoperiod-sensitive, which likely limits seed yields. Here, we show that photoperiod sensitivity is conserved across manyC. sativacultivars, albeit to different degrees, and we establish that photoperiod sensitivity is a complex trait, which will require genetic engineering to achieve day neutrality. 

Abstract The precise onset of flowering is crucial to ensure successful plant reproduction. The geneFLOWERING LOCUS T(FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes,FTis induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of theFT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression inFT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated thatFT-expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with highFTexpression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters ofFTand the genes co-expressed withFTin the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogousNIGT1.2andNIGT1.4repressedFTexpression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependentFTrepressors. Taken together, our results demonstrate that majorFT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development. 

Summary Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), inArabidopsis.FTis expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed withFTand whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, theFT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The masterFTregulator, CONSTANS (CO), controlsFLP1expression, suggestingFLP1’s involvement in the photoperiod pathway. FLP1 promotes early flowering independently ofFT,is active in the shoot apical meristem, and induces the expression ofSEPALLATA 3(SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions. 

The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana . We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T ( FT ), CONSTANS ( CO ), and BROTHER OF FT (BFT) . Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental-associated genes. These results provide insights into how the clock-controlled CDF6 modulates plant development during moderate cold stress. 

Many living organisms track the 24-hour cycle of day and night via collections of proteins and other molecules that together act like an internal clock. These clocks, also known as circadian clocks, help these organisms to predict regular changes in their environment, like light and temperature, and adjust their activities according to the time of day. Plants use circadian clocks to predict, for example, when dawn will occur and get ready to harness sunlight to fuel their growth. A plant called Arabidopsis thaliana has a light-sensitive protein called ZEITLUPE (or ZTL for short) that helps it keep its circadian clock in sync with the cycle of night and day. Previous studies have shown that light activates this protein causing part of it to change shape and then revert back after a period of about an hour and a half. However, it was unclear if this timing was important for ZEITLUPE to allow plants to keep track of time. To help answer this question, Pudasaini et al. set out to identify a specific chemical event behind ZEITLUPE’s changes in shape. A chemical bond forms when light activates ZEITLUPE, and it turns out that how long this bond lasts before it breaks plays an important role in allowing plants to maintain a 24-hour circadian clock. This chemical bond controls the shape changes that guide the protein’s activities and, when Pudasaini et al. modified ZEITLUPE so that it took much longer for this bond to break, they could tune how fast the plant’s internal clocks run. In essence, the time between the bond forming and breaking breaks acts like a countdown on a stopwatch, and it must be precisely timed to keep the clock in pace with the environment. These findings improve our understanding of how light can regulate an internal biological clock. This improved understanding could, in the future, allow researchers to manipulate how plants and other organisms respond to their environment. This in turn could change how these organisms develop, and how much they grow. As such, extending these findings into agricultural crops may one day lead to new ways to increase crop yields.