Loss-of-Function Mutations in Three Homoeologous PHYTOCLOCK 1 Genes in Common Wheat Are Associated with the Extra-Early Flowering Phenotype

Eukaryotic genomes give rise to thousands of long non-coding RNAs (lncRNAs), yet the purpose of lncRNAs remains largely enigmatic. Functional characterization of lncRNAs is challenging due to multiple orthogonal hypothesis for molecular activities of lncRNA loci. Here, we identified a flowering associated intergenic lncRNA (FLAIL) that represses flowering in Arabidopsis. An allelic series of flail loss-of-function mutants generated by CRISPR/Cas9 and T-DNA mutagenesis showed an early flowering phenotype. Gene expression analyses in flail mutants revealed differentially expressed genes linked to the regulation of flowering. A genomic rescue fragment of FLAIL introduced in flail mutants complemented gene expression defects and early flowering, consistent with trans-acting effects of the FLAIL RNA. Knock-down of FLAIL RNA levels using the artificial microRNA approach revealed an early flowering phenotype shared with genomic mutations, indicating a trans-acting role of FLAIL RNA in the repression of flowering time. Genome-wide detection of FLAIL-DNA interactions by ChIRP-seq suggested that FLAIL may directly bind genomic regions. FLAIL bound to genes involved in regulation of flowering that were differentially expressed in flail, consistent with the interpretation of FLAIL as a trans-acting lncRNA directly shaping gene expression. Our findings highlight FLAIL as a trans-acting lncRNA that affects flowering in Arabidopsis, likely through mediating transcriptional regulation of genes directly bound by FLAIL.

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Actin-Related Protein 4 Interacts with PIE1 and Regulates Gene Expression in Arabidopsis

Genes ◽

10.3390/genes12040520 ◽

2021 ◽

Vol 12 (4) ◽

pp. 520

Author(s):

Wenfeng Nie ◽

Jinyu Wang

Keyword(s):

Gene Expression ◽

Plant Growth ◽

Chromatin Remodeling ◽

Leaf Size ◽

Early Flowering ◽

Physical Interaction ◽

Loss Of Function ◽

Single Nucleotide Change ◽

Chromatin Remodeling Complex ◽

Related Proteins

As essential structural components of ATP-dependent chromatin-remodeling complex, the nucleolus-localized actin-related proteins (ARPs) play critical roles in many biological processes. Among them, ARP4 is identified as an integral subunit of chromatin remodeling complex SWR1, which is conserved in yeast, humans and plants. It was shown that RNAi mediated knock-down of Arabidopsis thaliana ARP4 (AtARP4) could affect plant development, specifically, leading to early flowering. However, so far, little is known about how ARP4 functions in the SWR1 complex in plant. Here, we identified a loss-of-function mutant of AtARP4 with a single nucleotide change from glycine to arginine, which had significantly smaller leaf size. The results from the split luciferase complementation imaging (LCI) and yeast two hybrid (Y2H) assays confirmed its physical interaction with the scaffold and catalytic subunit of SWR1 complex, photoperiod-independent early flowering 1 (PIE1). Furthermore, mutation of AtARP4 caused altered transcription response of hundreds of genes, in which the number of up-regulated differentially expressed genes (DEGs) was much larger than those down-regulated. Although most DEGs in atarp4 are related to plant defense and response to hormones such as salicylic acid, overall, it has less overlapping with other swr1 mutants and the hta9 hta11 double-mutant. In conclusion, our results reveal that AtARP4 is important for plant growth and such an effect is likely attributed to its repression on gene expression, typically at defense-related loci, thus providing some evidence for the coordination of plant growth and defense, while the regulatory patterns and mechanisms are distinctive from other SWR1 complex components.

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Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis

BMC Plant Biology ◽

10.1186/s12870-020-02775-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dongmei Ma ◽

Bei Liu ◽

Lingqiao Ge ◽

Yinyin Weng ◽

Xiaohui Cao ◽

...

Keyword(s):

Medicago Sativa ◽

Secondary Metabolism ◽

Flowering Time ◽

Degradation Pathway ◽

Early Flowering ◽

Receptor Kinase ◽

Leucine Rich Repeat ◽

Kinase Family ◽

Pathogenesis Related ◽

Early Flowering Phenotype

Abstract Background Alfalfa (Medicago sativa L.) is a perennial legume extensively planted throughout the world as a high nutritive value livestock forage. Flowering time is an important agronomic trait that contributes to the production of alfalfa hay and seeds. However, the underlying molecular mechanisms of flowering time regulation in alfalfa are not well understood. Results In this study, an early-flowering alfalfa genotype 80 and a late-flowering alfalfa genotype 195 were characterized for the flowering phenotype. Our analysis revealed that the lower jasmonate (JA) content in new leaves and the downregulation of JA biosynthetic genes (i.e. lipoxygenase, the 12-oxophytodienoate reductase-like protein, and salicylic acid carboxyl methyltransferase) may play essential roles in the early-flowering phenotype of genotype 80. Further research indicated that genes encode pathogenesis-related proteins [e.g. leucine rich repeat (LRR) family proteins, receptor-like proteins, and toll-interleukin-like receptor (TIR)-nucleotide-binding site (NBS)-LRR class proteins] and members of the signaling receptor kinase family [LRR proteins, kinases domain of unknown function 26 (DUF26) and wheat leucine-rich repeat receptor-like kinase10 (LRK10)-like kinases] are related to early flowering in alfalfa. Additionally, those involved in secondary metabolism (2-oxoglutarate/Fe (II)-dependent dioxygenases and UDP-glycosyltransferase) and the proteasome degradation pathway [really interesting new gene (RING)/U-box superfamily proteins and F-box family proteins] are also related to early flowering in alfalfa. Conclusions Integrated phenotypical, physiological, and transcriptomic analyses demonstrate that hormone biosynthesis and signaling pathways, pathogenesis-related genes, signaling receptor kinase family genes, secondary metabolism genes, and proteasome degradation pathway genes are responsible for the early flowering phenotype in alfalfa. This will provide new insights into future studies of flowering time in alfalfa and inform genetic improvement strategies for optimizing this important trait.

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The inheritance of flowering time in Townsville stylo (Stylosanthes humilis)

Australian Journal of Agricultural Research ◽

10.1071/ar9760825 ◽

1976 ◽

Vol 27 (6) ◽

pp. 825 ◽

Cited By ~ 7

Author(s):

DF Cameron

Keyword(s):

Flowering Time ◽

Dominant Gene ◽

Diallel Cross ◽

Early Flowering ◽

Multiple Alleles ◽

Locus Model ◽

Stylosanthes Humilis ◽

Townsville Stylo ◽

Maturity Groups ◽

Early Flowering Phenotype

The inheritance of flowering time was studied in F1, F2 and F3 populations derived from a diallel cross among nine naturalized Australian lines of Townsville stylo (Stylosnnthes humilis) and in F1 and F2 populations from a small number of crosses between naturalized Australian lines and introductions from Mexico and Brazil. Strong dominance for lateness of flowering was observed in both the (Australian x Australian) and the (Australian x Mexican/Brazilian introductions) crosses, and some F2 and F3 progenies included small numbers of extremely early plants, flowering up to 55 days earlier than the earliest parent. The flowering time distributions of the (Australian x Australian) crosses could be explained by a three-locus model with multiple alleles at two loci. Proposed genotypes for the four maturity groups are as follows: late, LLM2M2EE; late-midseason, LLmmEE; mid-season, l2l2M2M2EE; early, l1l1M1M1EE; very early, LLM2M2ee. Only one major dominant gene for lateness of flowering could be detected from the distribution of the two (Australian x introduced line) F2 populations, but the segregation of extremely early types and the low recovery of the early-flowering phenotype suggested that other gene loci were segregating.

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Circadian clock components in Arabidopsis I. The terminal flower 1 enhances the early flowering phenotype of a mutant, Ihy cca1

Plant Biotechnology ◽

10.5511/plantbiotechnology.22.311 ◽

2005 ◽

Vol 22 (4) ◽

pp. 311-317 ◽

Cited By ~ 4

Author(s):

Sumire Fujiwara ◽

Mayu Nakagawa ◽

Hiroshi Kamada ◽

George Coupland ◽

Tsuyoshi Mizoguchi

Keyword(s):

Circadian Clock ◽

Early Flowering ◽

Terminal Flower ◽

Terminal Flower 1 ◽

Early Flowering Phenotype

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Double loss-of-function mutation in EARLY FLOWERING 3 and CRYPTOCHROME 2 genes delays flowering under continuous light but accelerates it under long days and short days: an important role for Arabidopsis CRY2 to accelerate flowering time in continuous light

Journal of Experimental Botany ◽

10.1093/jxb/erq450 ◽

2011 ◽

Vol 62 (8) ◽

pp. 2731-2744 ◽

Cited By ~ 12

Author(s):

Rim Nefissi ◽

Yu Natsui ◽

Kana Miyata ◽

Atsushi Oda ◽

Yoshihiro Hase ◽

...

Keyword(s):

Flowering Time ◽

Continuous Light ◽

Early Flowering ◽

Loss Of Function ◽

Cryptochrome 2 ◽

Short Days

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Analysis of early-flowering genes at barley chromosome 2H expands the repertoire of mutant alleles at the Mat-c locus

Plant Cell Reports ◽

10.1007/s00299-019-02472-4 ◽

2019 ◽

Vol 39 (1) ◽

pp. 47-61

Author(s):

Izabela Matyszczak ◽

Marta Tominska ◽

Shakhira Zakhrabekova ◽

Christoph Dockter ◽

Mats Hansson

Keyword(s):

Pericentromeric Region ◽

Early Flowering ◽

Antirrhinum Majus ◽

Optimal Timing ◽

Near Isogenic Lines ◽

Loss Of Function ◽

Yield Improvement ◽

X Ray ◽

Nonsynonymous Substitutions ◽

Flowering Genes

Abstract Key message Analyses of barley mat-c loss of function mutants reveal deletions, splice-site mutations and nonsynonymous substitutions in a key gene regulating early flowering. Abstract Optimal timing of flowering is critical for reproductive success and crop yield improvement. Several major quantitative trait loci for flowering time variation have been identified in barley. In the present study, we analyzed two near-isogenic lines, BW507 and BW508, which were reported to carry two independent early-flowering mutant loci, mat-b.7 and mat-c.19, respectively. Both introgression segments are co-localized in the pericentromeric region of chromosome 2H. We mapped the mutation in BW507 to a 31 Mbp interval on chromosome 2HL and concluded that BW507 has a deletion of Mat-c, which is an ortholog of Antirrhinum majus CENTRORADIALIS (AmCEN) and Arabidopsis thaliana TERMINAL FLOWER1 (AtTFL1). Contrary to previous reports, our data showed that both BW507 and BW508 are Mat-c deficient and none of them are mat-b.7 derived. This work complements previous studies by identifying the uncharacterized mat-c.19 mutant and seven additional mat-c mutants. Moreover, we explored the X-ray structure of AtTFL1 for prediction of the functional effects of nonsynonymous substitutions caused by mutations in Mat-c.

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