Characterization of genes associated with TGA7 during the floral transition

Background The TGACG-binding (TGA) family has 10 members that play vital roles in Arabidopsis thaliana defense responses and development. However, their involvement in controlling flowering time remains largely unknown and requires further investigation. Results To study the role of TGA7 during floral transition, we first investigated the tga7 mutant, which displayed a delayed-flowering phenotype under both long-day and short-day conditions. We then performed a flowering genetic pathway analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal the differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 days after germination. For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences, with the majority (84.55 %) of mRNAs being between 500 and 3,000 nt. In total, 325 differentially expressed genes were identified between WT and tga7 mutant seedlings. Among them, four genes were associated with flowering time control. The differential expression of these four flowering-related genes was further validated by qRT-PCR. Conclusions Among these four differentially expressed genes associated with flowering time control, FLC and MAF5 may be mainly responsible for the delayed-flowering phenotype in tga7, as TGA7 expression was regulated by autonomous pathway genes. These results provide a framework for further studying the role of TGA7 in promoting flowering.

Plant long non-coding RNAs in the regulation of transcription

Eukaryotic genomes are pervasively transcribed, producing large numbers of non-coding RNAs (ncRNAs), including tens of thousands of long ncRNAs (lncRNAs), defined as ncRNAs longer than 200 nucleotides. Recent studies have revealed the important roles lncRNAs play in the regulation of gene expression at various levels in all eukaryotes; moreover, emerging research in plants has identified roles for lncRNAs in key processes such as flowering time control, root organogenesis, reproduction, and adaptation to environmental changes. LncRNAs participate in regulating most steps of gene expression, including reshaping nuclear organization and chromatin structure; governing multiple steps of transcription, splicing, mRNA stability, and translation; and affecting post-translational protein modifications. In this review, I present the latest progress on the lncRNA-mediated regulatory mechanisms modulating transcription in Arabidopsis thaliana, focusing on their functions in regulation of gene expression via chromatin structure and interactions with the transcriptional machinery.

A Trimethylguanosine Synthase1-like (TGS1) homologue is implicated in vernalisation and flowering time control

Key message A plant-specificTrimethylguanosine Synthase1-likehomologue was identified as a candidate gene for theeflmutation in narrow-leafed lupin, which alters phenology by reducing vernalisation requirement. Abstract The vernalisation pathway is a key component of flowering time control in plants from temperate regions but is not well understood in the legume family. Here we examined vernalisation control in the temperate grain legume species, narrow-leafed lupin (Lupinus angustifolius L.), and discovered a candidate gene for an ethylene imine mutation (efl). The efl mutation changes phenology from late to mid-season flowering and additionally causes transformation from obligate to facultative vernalisation requirement. The efl locus was mapped to pseudochromosome NLL-10 in a recombinant inbred line (RIL) mapping population developed by accelerated single seed descent. Candidate genes were identified in the reference genome, and a diverse panel of narrow-leafed lupins was screened to validate mutations specific to accessions with efl. A non-synonymous SNP mutation within an S-adenosyl-L-methionine-dependent methyltransferase protein domain of a Trimethylguanosine Synthase1-like (TGS1) orthologue was identified as the candidate mutation giving rise to efl. This mutation caused substitution of an amino acid within an established motif at a position that is otherwise highly conserved in several plant families and was perfectly correlated with the efl phenotype in F2 and F6 genetic population and a panel of diverse accessions, including the original efl mutant. Expression of the TGS1 homologue did not differ between wild-type and efl genotypes, supporting altered functional activity of the gene product. This is the first time a TGS1 orthologue has been associated with vernalisation response and flowering time control in any plant species.

The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis thaliana

Pre-mRNA splicing is a crucial step of gene expression whereby the spliceosome produces constitutively and alternatively spliced transcripts that not only diversify the transcriptome but also play essential functions during plant development and responses to environmental changes. Numerous evidences indicate that regulation at the pre-mRNA splicing step is important for flowering time control, however the components and detailed mechanism underlying this process remain largely unknown. Here, we identified a previously unknown splicing factor in Arabidopsis thaliana, RNA BINDING PROTEIN 45d (RBP45d), a member of the RBP45/47 family. Using sequence comparison and biochemical analysis, we determined that RBP45d is a component of the U1 small nuclear ribonucleoprotein (U1 snRNP) with functions distinct from other family members. RBP45d associates with the U1 snRNP by interacting with pre-mRNA-processing factor 39a (PRP39a) and directly regulates alternative splicing (AS) for a specific set of genes. Plants with loss of RBP45d function exhibit defects in temperature-induced flowering potentially due to the mis-regulation of temperature-sensitive AS by RBP45d and PRP39a of the key flowering gene FLOWERING LOCUS M. Taken together, we report that RBP45d is a novel U1 snRNP component in plants that functions together with PRP39a in temperature-mediated flowering.

Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.)

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Repeated rearrangement of the GSL‐AOP locus contributed to spatio‐temporal variation in defense chemistry in Arabidopsis

Plants coordinate metabolic and developmental processes with the help of genetically variable, interconnected regulatory networks. The GSL-AOP locus in Arabidopsis thaliana encodes enzymes involved in the biosynthesis of glucosinolate defense compounds and has been attributed regulatory functions e.g. in flowering time control. To correlate genetic and phenotypic variation linked to GSL-AOP, we conducted a phylogenetic analysis across 1135 accessions and found that the available short-read sequencing data does not fully resolve the structural diversity in the locus. We analyzed a selection of 74 accessions for glucosinolate profiles and flowering time under different conditions and acquired long-read sequence information for glucosinolate and flowering time loci. Especially in the Caucasus region, structural variation in GSL-AOP was associated with conditional, tissue-specific glucosinolate profiles. Variation in FLC among the Caucasian accessions correlated with variation in the flowering time response to vernalization, suggesting that local adaptation has shaped defense and development in an orchestrated manner.

MiR396 is involved in plant response to vernalization and flower development in Agrostis stolonifera

MicroRNA396 (miR396) has been demonstrated to regulate flower development by targeting growth-regulating factors (GRFs) in annual species. However, its role in perennial grasses and its potential involvement in flowering time control remain unexplored. Here we report that overexpression of miR396 in a perennial species, creeping bentgrass (Agrostis stolonifera L.), alters flower development. Most significantly, transgenic (TG) plants bypass the vernalization requirement for flowering. Gene expression analysis reveals that miR396 is induced by long-day (LD) photoperiod and vernalization. Further study identifies VRN1, VRN2, and VRN3 homologs whose expression patterns in wild-type (WT) plants are similar to those observed in wheat and barley during transition from short-day (SD) to LD, and SD to cold conditions. However, compared to WT controls, TG plants overexpressing miR396 exhibit significantly enhanced VRN1 and VRN3 expression, but repressed VRN2 expression under SD to LD conditions without vernalization, which might be associated with modified expression of methyltransferase genes. Collectively, our results unveil a potentially novel mechanism by which miR396 suppresses the vernalization requirement for flowering which might be related to the epigenetic regulation of VRN genes and provide important new insight into critical roles of a miRNA in regulating vernalization-mediated transition from vegetative to reproductive growth in monocots.

FLOWERING LOCUS T4 delays flowering and decreases floret fertility in barley

FLOWERING LOCUS T-like (FT-like) genes control the photoperiodic regulation of flowering in many angiosperm plants. The family of FT-like genes is characterized by extensive gene duplication and subsequent diversification of FT functions which occurred independently in modern angiosperm lineages. In barley, there are 12 known FT-like genes (HvFT), but the function of most of them remains uncharacterized. This study aimed to characterize the role of HvFT4 in flowering time control and development in barley. The overexpression of HvFT4 in the spring cultivar Golden Promise delayed flowering time under long-day conditions. Microscopic dissection of the shoot apical meristem revealed that overexpression of HvFT4 specifically delayed spikelet initiation and reduced the number of spikelet primordia and grains per spike. Furthermore, ectopic overexpression of HvFT4 was associated with floret abortion and with the down-regulation of the barley MADS-box genes VRN-H1, HvBM3, and HvBM8 which promote floral development. This suggests that HvFT4 functions as a repressor of reproductive development in barley. Unraveling the genetic basis of FT-like genes can contribute to the identification of novel breeding targets to modify reproductive development and thereby spike morphology and grain yield.