Early Flowering Research Articles

Genome-wide identification of the monovalent cation/proton antiporter (CPA) superfamily and expression analysis in tomato

The cation/proton antiporter (CPA) superfamily, crucial for regulating Na+, K+, and pH equilibrium in plant cells, plays an essential role in plant growth and stress adaptation. However, limited research has been conducted on the CPA gene superfamily in tomatoes. In this study, a total of 31 SlCPA members were identified in the tomato genome, comprising 18 cation/H+ exchangers (SlCHXs), 7 Na+/H+ exchangers (SlNHXs), and 6 K+ efflux antiporters (SlKEAs). A comprehensive analysis encompassing their chromosomal locations, gene structures, phylogenetic relationships, collinearity, tissue-specific expression profiles, and responses to abiotic stress was undertaken. Collinearity and phylogenetic analyses unveiled two groups, represented by Solyc08g081810, Solyc01g008190, Solyc12g056160, and Solyc06g060630, Solyc08g078880, suggesting potential redundancy resulting from duplication events. Tissue-specific expression analysis revealed SlNHXs and SlKEAs expression at multiple developmental stages, while SlCHXs were predominantly expressed during early flower and fruit development, indicating their likely involvement in these processes. Salt treatment notably induced the expression of SlSOS1 (Solyc01g005020) and Solyc04g056600, implicating their role in responding to salt stress. Under drought stress, the expression of Solyc01g005020 and Solyc08g081820 was also significantly induced, supported by promoter element analyses indicating the presence of drought response-related cis-elements like ABRE and MYB binding sites. This study establishes a foundation for further elucidating the gene functions of individual members within the tomato SlCPA family.

Nuclear factor Y-A3b binds to the SINGLE FLOWER TRUSS promoter and regulates flowering time in tomato.

The control of flowering time is essential for reproductive success and has a major effect on seed and fruit yield and other important agricultural traits in crops. Nuclear factors Y (NF-Ys) are transcription factors that form heterotrimeric protein complexes to regulate gene expression required for diverse biological processes, including flowering time control in plants. However, to our knowledge, there has been no report on mutants of individual NF-YA subunits that promote early flowering phenotype in plants. In this study, we identified SlNF-YA3b, encoding a member of the NF-Y transcription factor family, as a key gene regulating flowering time in tomato. Knockout of NF-YA3b resulted in an early flowering phenotype in tomato, whereas overexpression of NF-YA3b delayed flowering in transgenic tomato plants. NF-YA3b was demonstrated to form heterotrimeric protein complexes with multiple NF-YB/NF-YC heterodimers in yeast three-hybrid assays. Biochemical evidence indicated that NF-YA3b directly binds to the CCAAT cis-elements of the SINGLE FLOWER TRUSS (SFT) promoter to suppress its gene expression. These findings uncovered a critical role of NF-YA3b in regulating flowering time in tomato and could be applied to the management of flowering time in crops.

Floral colour variation across life history and geography in Mimulus ringens (Phrymaceae)

Abstract Floral and life history traits play important roles in plant speciation. The genus Mimulus is a model system for studying speciation. It includes examples of species in which floral colour facilitates isolation through pollinator shifts, as well as life history changes that result in temporal or ecogeographic isolation. We investigate the possibility that both floral colour and life history have shifted together in a recently described, genetically distinct group within the species Mimulus ringens. Using a large, range-wide citizen science dataset, we test for geographic trends in flower colour and flowering time. We combine this with greenhouse studies in populations of known life history to test for differences in flower colour with life history. We show that darker-flowered plants are more common at higher latitudes, that annual-like populations have darker flowers, and that flowering time varies with latitude only in the subset of populations that have lighter flowers. This suggests that annual-like populations (with the earlier flowering time typical of this life history) are restricted to the northern part of the species range and may have distinct trends in flowering date.

Добив и качество на тютюн Виржиния в зависимост от генотипа и агротехничски практики

The effects of three N rates (0, 20 and 40 kg N ha-1) and time of topping (topping at early flowering and topping at full flowering) on yield and quality (percentage of first, second and third grade dried tobacco, and chemical composition) of Virginia tobacco genotypes (Virginia 0514, Hybrid 33, Hybrid 27) were studied in field experiment in 2015-2016. The experimental design was a randomized complete block replicated three times. The most important factor that affects leaf yield was N rate. Genotype differences and time of topping also had a significant effect on the yield. The application of 20 and 40 kg N ha-1 improved the leaf yield by 12.6%, and 17.8%, respectively, in comparison with unfertilized plants. When tobacco was topped at early flowering stage, the yields of the different genotypes increased by 4.3%-10.1% compared to the topping at full flowering. Nitrogen fertilization and topping had almost the same effect on the quality of the tobacco (as determined by the percentage of first grade dried tobacco). The genotype effect was weaker but also statistically significant. The quantity of the first class was also determined by the interaction of topping and nitrogen rate. Topping at early flowering increased the concentrations of nicotine and total nitrogen in tobacco. The reducing sugars/nicotine ratio was higher, and in this case more favorable, when tobacco plants were topped at full flowering stage. Nicotine content (2.33%-3.53%) increased when the rate of nitrogen increased. There was a negative relationship between increasing N levels and reducing sugars content.

Integrated transcriptomic and metabolomic analysis reveals the regulation mechanism of early bolting and flowering in two cultivars of Angelica sinensis

The root of Angelica sinensis is utilized in Traditional Chinese medicine to enhance blood replenishment and facilitate blood circulation. The early bolting and flowering (EBF) of A. sinensis, however, compromises the quality of the roots and restricts the yield of medicinal substances. The study was conducted to compare the transcriptomic and metabolomic profiles between EBF plants and normal plants of two cultivars of A. sinensis, followed by validation of the transcriptome results using qRT-PCR. There were 3677 DEGs in EBF plants compared to normal plants of cultivar 2 (Mingui No.2), and cultivar 4 (Mingui No.4) was 3354. The main differential metabolites in the EBF and normal plants were phenolic acids, flavonoids, lignans, and coumarins. The analysis of 5 EBF-related pathways revealed 28 genes exhibiting differential expression and 5 metabolites showing differential accumulation. The expression of the Lhcb5, Lhcb2, Lhcb6, Lhcb1, Lhca4, ATPG1, EGLC, CELB, AMY, glgA, CYCD3, SnRK2, PYL, AHK2, AUX1, BSK, FabI/K, ACACA and FabV decreased and the expression of the PsbR, PsbA, LHY, FT, CO, malQ, HK, GPI and DELLA increased in EBF plants. In addition, the Abscisic acid, d-Glucose-6P, α-d-Glucose-1P, NADP+, and ADP were more significantly enriched in EBF plants. The findings offer novel perspectives on the EBF mechanisms in A. sinensis and other medicinal plants of the Apiaceae family.

A Long-Lived Alpine Perennial Advances Flowering under Warmer Conditions but Not Enough to Maintain Reproductive Success.

AbstractAssessing whether phenological shifts in response to climate change confer a fitness advantage requires investigating the relationships among phenology, fitness, and environmental drivers of selection. Despite widely documented advancements in phenology with warming climate, we lack empirical estimates of how selection on phenology varies in response to continuous climate drivers or how phenological shifts in response to warming conditions affect fitness. We leverage an unusual long-term dataset with repeated, individual measurements of phenology and reproduction in a long-lived alpine plant. We analyze phenotypic plasticity in flowering phenology in relation to two climate drivers, snowmelt timing and growing degree days (GDDs). Plants flower earlier with increased GDDs and earlier snowmelt, and directional selection also favors earlier flowering under these conditions. However, reproduction still declines with warming and early snowmelt, even when flowering is early. Furthermore, the steepness of this reproductive decline increases dramatically with warming conditions, resulting in very little fruit production regardless of flowering time once GDDs exceed approximately 225 degree days or snowmelt occurs before May 15. Even though advancing phenology confers a fitness advantage relative to stasis, these shifts are insufficient to maintain reproduction under warming, highlighting limits to the potential benefits of phenological plasticity under climate change.

A shorter inverted repeat length in a hairpin RNA results in a stronger silencing efficacy

RNA interference (RNAi), particularly hairpin RNA (hpRNA) constructs, is a potent genetic manipulation tool, influencing traits that are crucial for crop improvement. Typical hpRNA constructs consist of inverted repeat sequences derived from the mRNA of the target gene, separated by a non-complementary spacer. This configuration initiates the formation of a double-stranded RNA structure due to the complementary nature of sense and antisense sequences in the transcribed RNA. In this research, two hpRNA constructs, namely hp-TFL1-S and hp-TFL1-L, with distinct lengths of inverted repeats, were designed to target TFL1, a pivotal regulator of both flowering timing and inflorescence structure. hp-TFL1-L construct encompasses all the 150 nucleotide sequences of the hp-TFL1-S construct and an extra 135 nucleotides. These constructs included a chalcone synthase intron as a spacer, resulting in hairpin double-stranded RNA molecules of 150 and 285 base pair after transcription. The PCR and qRT-PCR analysis results confirmed the accurate design of both constructs and their successful suppression of TFL1 mRNA expression in transgenic Arabidopsis. Interestingly, Arabidopsis lines carrying hp-TFL1-S and hp-TFL1-L exhibited distinct phenotypic features. hp-TFL1-S induced more pronounced phenotypic changes, resulting in earlier flowering compared to the hp-TFL1-L and control group. Moreover, hp-TFL1-S had a significant impact on inflorescence architecture, distinguishing it from both hp-TFL1-L and control plants. This study provides an example where inverted repeat length alters the efficacy of silencing, and in this case, surprisingly the shorter construct appears to have a stronger silencing efficacy. This argues multiple sized hpRNAs should be tested in RNAi-based gene silencing experiments.

Flower opening dynamics, pollen-ovule ratio, stigma receptivity and stigmatic pollen germination (in-vivo) in Chaenomeles speciosa (Sweet) Nakai

Although Chaenomeles is widely used in horticulture, traditional Chinese medicine and landscape greening, insufficient research has hindered its breeding and seed selection. This study investigated the floral phenology, floral organ characteristics, palynology, and breeding systems of Chaenomeles speciosa (Sweet) Nakai. The floral characteristics of C. speciosa were observed both visually and stereoscopically. The microstructures of the flower organs were observed using scanning electron microscopy. Pollen stainability was determined using triphenyl tetrazolium chloride staining. Stigma receptivity was determined using the benzidine-H2O2 method and the post-artificial pollination pollen germination method. The breeding system was assessed based on the outcrossing index and pollen–ovule ratio. The flowers of C. speciosa were bisexual with a flowering period from March to April. The flowering periods of single flowers ranged from 8 to 19 d, and those of single plants lasted 18–20 d. The anthers were cylindrical, with the base attached to the filament, and were split longitudinally to release pollen. The flower had five styles, with a connate base. The ovaries had five carpels and five compartments. The inverted ovules were arranged in two rows on the placental axis. The stigma of C. speciosa was dry and had many papillary protrusions. In the early flowering stage (1–2 d of flowering), the pollen exhibited high stainability (up to 84.24%), but all stainability was lost at 7 d of flowering. Storage at – 20 °C effectively delayed pollen inactivation. The stigma receptivity of C. speciosa lasted for approximately 7 days, and the breeding system was classified as outcrossing with partial self-compatibility.

Drought stress induces early flowering and the stress tolerance of offspring in Petunia hybrida.

Petunia hybrida (Solanaceae) exhibits high sensitivity to water scarcity, especially during flowering. This study investigated changes in the flowering time of P. hybrida in response to water deficit over a 7-week period. Various levels of water stress-i.e., light, moderate, and severe-were imposed on plants grown in a greenhouse, and these were compared to a control group grown alongside. Remarkably, early flowering was observed under severe stress in P. hybrida for the first time, occurring 5.3 days earlier than in the control group. Furthermore, seeds collected from control and treatment plants were then used to assess drought stress memory in offspring. Seedlings were cultivated in a dehydration medium containing either PEG 8000 or a control MS medium. In the PEG 8000 medium, seedlings from parents exposed to moderate and severe drought stresses exhibited higher drought tolerance than those from well-watered conditions. Moreover, they also displayed significantly longer roots, more leaves, and a lower ion leakage rate. Taken together, these findings demonstrated the presence of positive transgenerational effects on progeny. Thus, while parental drought stress during reproduction stage may affect seed quality, it can enhance drought tolerance in the next generation via induction of stress memory.

Identification and functional analysis of the LEAFY gene in longan flower induction

BackgroundFlowering at the right time is a very important factor affecting the stable annual yield of longan. However, a lack of knowledge of the regulatory mechanism and key genes of longan flowering restricts healthy development of the longan industry. Therefore, identifying relevant genes and analysing their regulatory mechanism are essential for scientific research and longan industry development.ResultsDlLFY (Dimocarpus longan LEAFY) contains a 1167 bp open reading frame and encodes 388 amino acids. The amino acid sequence has a typical LFY/FLO family domain. DlLFY was expressed in all tissues tested, except for the leaf, pericarp, and pulp, with the highest expression occurring in flower buds. Expression of DlLFY was significantly upregulated at the early flower induction stage in “SX” (“Shixia”). The results of subcellular localization and transactivation analysis showed that DlLFY is a typical transcription factor acting as a transcriptional activator. Moreover, overexpression of DlLFY in Arabidopsis promoted early flowering and restrained growth, resulting in reduced plant height and rosette leaf number and area in transgenic plants. DNA affinity purification sequencing (DAP-Seq) analysis showed that 13 flower-related genes corresponding to five homologous genes of Arabidopsis may have binding sites and be putative target genes. Among these five flower-related genes, only AtTFL1 (terminal flower 1) was strongly inhibited in transgenic lines.ConclusionTaken together, these results indicate that DlLFY plays a pivotal role in controlling longan flowering, possibly by interacting with TFL1.

Transcriptome Analysis of Intermittent Light Induced Early Bolting in Flowering Chinese Cabbage.

In flowering Chinese cabbage, early booting is one of the most important characteristics that is linked with quality and production. Through fixed light intensity (280 μmol·m-2·s-1) and fixed intermittent lighting in flowering Chinese cabbage, there was early bolting, bud emergence, and flowering. Moreover, the aboveground fresh weight, blade area, dry weight of blade, and quantification of the leaves in flowering Chinese cabbage were significantly reduced, while the thickness of tillers, tillers height, dry weight of tillers, and tillers weight were significantly increased. The chlorophyll contents and soil-plant analysis and development (SPAD) value decreased in the early stage and increased in the later stage. The nitrate content decreased, while the photosynthetic rate, vitamin C content, soluble sugar content, soluble protein content, phenolic content, and flavonoid content increased, and mineral elements also accumulated. In order to explore the mechanism of intermittent light promoting the early bolting and flowering of '49d' flowering Chinese cabbage, this study analyzed the transcriptional regulation from a global perspective using RNA sequencing. A total of 17,086 differentially expressed genes (DEGs) were obtained and 396 DEGs were selected that were closely related to early bolting. These DEGs were mainly involved in pollen wall assembly and plant circadian rhythm pathways, light action (34 DEGs), hormone biosynthesis and regulation (26 DEGs), development (21 DEGs), and carbohydrate synthesis and transport (6 DEGs). Three hub genes with the highest connectivity were identified through weighted gene co-expression network analysis (WGCNA): BrRVE, BrLHY, and BrRVE1. It is speculated that they may be involved in the intermittent light regulation of early bolting in flowering Chinese cabbage. In conclusion, intermittent light can be used as a useful tool to regulate plant growth structure, increase planting density, enhance photosynthesis, increase mineral accumulation, accelerate growth, and shorten the breeding cycle.

Study of the peculiarities of the main phenological growth and development phases, as well as commercial qualities of fruits of rare citrus taxa under conditions of humid subtropics of Russia

The citrus collection of the FRC Subtropical Research Center of the RAS includes 144 genotypes and contains rare species and cultivars that are of great interest for use in production, breeding, and ornamental horticulture. The research examined 13 rare taxa: Citrus aurantifolia, C. aurantifolia ‘Foro’, C.×latifolia, C.×bergamia, C. ichangensis, C. limon ‘Del Brasil’, C.×limonelloides, C.×limetta ‘Chontipico’, C. maxima ‘Sambokan’, C. medica, C. medica var. sarcodactylus, C.×meyeri, C.×myrtifolia. The research established the times and differences in the passage of the main phenological phases, namely bud opening and flower-bud formation, flowering, second and third active growth, fruit ripening. The beginning of the growing season of the studied objects was registered in the second and third decades of March; the difference between the early onset for C. aurantifolia (16.03) and the late onset for C. ichangensis (01.04) is 14–20 days. Two active growth periods were established for C. ichangensis, C. limon ‘Del Brasil’, C. maxima ‘Sambokan’, and C. medica, while the other citrus taxa under study had three periods of active growth. According to their flowering dates, taxa with early (April 11–13), middle (April 18–19), and late (April 23–28) flowering time were identified. Long flowering (29–36 days) is typical for taxa with early flowering. Remontant taxa, i. e. C. aurantifolia, C. aurantifolia ‘Foro’, C.×latifolia, C.×bergamia, C.×limonelloides, C.×limetta ‘Chontipico’, C. limon ‘Del Brasil’, C.×meyeri were identified. From the beginning of the growing season to fruit ripening, the effective heat summation was determined to be 4710–5250 ℃. The study also identified taxa with late fruit ripening, namely C. medica and C.×myrtifolia (third decade of December – first decade of January). The taxa with the best commercial qualities and biochemical composition of fruits were C. maxima ‘Sambokan’, C.×meyeri, and C.×limetta ‘Chontipico’.

Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean

BackgroundMung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr) and Arabidopsis (Arabidopsis thaliana).ResultsThe most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene (AT3G51550), has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3, Glyma.19G224200, and GmPhyA2, Glyma.20G090000). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea.ConclusionThe top two identified SNPs accounted for a significant proportion (~ 65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.

Transcriptomics Reveal an Integrated Gene Regulation Network of Early Flowering Development in an Oil Sunflower Mutant Induced by Heavy Ion Beam

The oil sunflower is an important oil crop and ornamental plant. Flowering time affects the environmental adaptability and final yield of oil sunflowers. Floral induction is one of the important events that determines subsequent reproductive growth and seed setting, but there has been no systematic study on the regulation of gene expression during the transition from vegetative growth to reproductive growth in oil sunflowers. In this study, an oil sunflower mutant displaying early flowering (ef) was obtained by heavy ion beam irradiation. This mutant had a stable genetic trait, and its flowering time was 15 days earlier than the wild type (WT) in the field. The histology result showed that the ef mutant induced floral meristem at 6-leaf stage earlier than WT. The shoot apical meristems (SAMs) of the ef mutant and WT at 4-leaf, 6-leaf, 8-leaf, 10-leaf and budding periods were collected for RNA sequencing. The results showed that the transition from the leaf meristem to the floral meristem resulted in significant changes in the transcriptional landscape. Overall, 632, 1825, 4549, 5407 and 2164 differentially expressed genes (DEGs) were identified at 4-leaf, 6-leaf, 8-leaf, 10-leaf and budding periods, respectively. These DEGs were mainly enriched in biological pathways, including plant hormone signal transduction, carbon metabolism, protein processing in endoplasmic reticulum, secondary metabolism, and photosynthesis. We also found significant differences in the expression levels of starch and sucrose metabolism-related genes in the ef mutant and WT, indicating that sugar signaling plays an important role in the early flowering of oil sunflowers, especially SUC9 and sugar synthesis and degradation enzyme genes. In addition to hormone and sugar signals, flowering integration genes SOC1, AP1, FUL and LFY were upregulated in the ef mutant, and genes in photoperiod, aging, autonomous and temperature pathways were also involved in the regulation of floral transition. The results showed that plant hormones, sucrose metabolism, and flowering genes synergistically cause the early flowering of oil sunflowers. Our study provided important information for understanding flowering and is helpful for the genetic improvement of sunflowers.

Transcriptome-Based Identification of Candidate Flowering-Associated Genes of Blueberry in a Plant Factory with Artificial Lighting (PFAL) under Short-Day-Length Conditions.

In blueberry (Vaccinium corymbosum L.), a perennial shrub, flower bud initiation is mediated by a short-day (SD) photoperiod and buds bloom once the chilling requirement is satisfied. A plant factory with artificial lighting (PFAL) is a planting system that can provide a stable and highly efficient growing environment for blueberry production. However, the characteristics of bud differentiation of blueberry plants inside PFAL systems are poorly understood. To better understand flower bud initiation and the flowering mechanism of blueberry in PFAL systems, the anatomical structure of apical buds under SD conditions in a PFAL system was observed using the southern highbush cultivar 'Misty' and a transcriptomic analysis was performed to identify the candidate flowering genes. The results indicated that the apical bud of 'Misty' differentiated gradually along with SD time course and swelled obviously when chilling was introduced. A total of 39.28 Gb clean data were generated, and about 20.31-24.11 Mb high-quality clean reads were assembled, yielding a total of 17370 differentially expressed genes (DEGs), of which 9637 were up-regulated and 7733 were down-regulated. Based on the functional annotation, 26 DEGs were identified including 20 flowering-related and 6 low-temperature DEGs, out of which the expressive level of four flowering-related DEGs (VcFT2, VcFPA, VcFMADS1, and VcCOP1) and two low-temperature-induced DEGs (VcTIL-1 and VcLTI 65-like) were confirmed by qRT-PCR with a good consistency with the pattern of transcriptome. Functional analysis indicated that VcFT2 was highly conserved with nuclear and cytoplasmic subcellular localization and was expressed mainly in blueberry leaf tissue. In Arabidopsis, ectopic overexpression of VcFT2 results in an early flowering phenotype, indicating that VcFT2 is a vital regulator of the SD-mediated flowering pathway in blueberry. These results contribute to the investigation of photoperiod-mediated flowering mechanisms of blueberry in PFAL systems.

Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation.

Molecular genetic understanding of flowering time regulation is crucial for sorghum development. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGhd7) is one of the six classical loci conferring photoperiod sensitivity of sorghum flowering. However, its functions remain poorly studied. The molecular functions of SbGhd7 were characterized. The gene regulatory network controlled by SbGhd7 was constructed and validated. The biological roles of SbGhd7 and its major targets were studied. SbGhd7 overexpression (OE) completely prevented sorghum flowering. Additionally, we show that SbGhd7 is a major negative regulator of flowering, binding to the promoter motif TGAATG(A/T)(A/T/C) and repressing transcription of the major florigen FLOWERING LOCUS T 10 (SbFT10) and floral activators EARLY HEADING DATE (SbEhd1), FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (SbFKF1) and EARLY FLOWERING 3 (SbELF3). Reinforcing the direct effect of SbGhd7, SbEhd1 OE activated the promoters of three functional florigens (SbFT1, SbFT8 and SbFT10), dramatically accelerating flowering. Our studies demonstrate that SbGhd7 is a major repressor of sorghum flowering by directly and indirectly targeting genes for flowering activation. The mechanism appears ancient. Our study extends the current model of floral transition regulation in sorghum and provides a framework for a comprehensive understanding of sorghum photoperiod response.

ATX1 and HUB1/2 promote recruitment of the transcription elongation factor VIP2 to modulate the floral transition in Arabidopsis.

Histone 2B ubiquitination (H2Bub) and trimethylation of H3 at lysine 4 (H3K4me3) are associated with transcription activation. However, the function of these modifications in transcription in plants remains largely unknown. Here, we report that coordination of H2Bub and H3K4me3 deposition with the binding of the RNA polymerase-associated factor VERNALIZATION INDEPENDENCE2 (VIP2) to FLOWERING LOCUS C (FLC) modulates flowering time in Arabidopsis. We found that RING domain protein HISTONE MONOUBIQUITINATION1 (HUB1) and HUB2 (we refer as HUB1/2), which are responsible for H2Bub, interact with ARABIDOPSIS TRITHORAX1 (ATX1), which is required for H3K4me3 deposition, to promote the transcription of FLC and repress the flowering time. The atx1-2 hub1-10 hub2-2 triple mutant in FRIGIDIA (FRI) background displayed early flowering like FRI hub1-10 hub2-2 and overexpression of ATX1 failed to rescue the early flowering phenotype of hub1-10 hub2-2. Mutations in HUB1 and HUB2 reduced the ATX1 enrichment at FLC, indicating that HUB1 and HUB2 are required for ATX1 recruitment and H3K4me3 deposition at FLC. We also found that the VIP2 directly binds to HUB1, HUB2, and ATX1 and that loss of VIP2 in FRI hub1-10 hub2-2 and FRI atx1-2 plants resulted in early flowering like that observed in FRI vip2-10. Loss of function of HUB2 and ATX1 impaired VIP2 enrichment at FLC, and reduced the transcription initiation and elongation of FLC. In addition, mutations in VIP2 reduced HUB1 and ATX1 enrichment and H2Bub and H3K4me3 levels at FLC. Together, our findings revealed that HUB1/2, ATX1, and VIP2 coordinately modulate H2Bub and H3K4me3 deposition, FLC transcription, and flowering time.

Novel SNP markers for flowering and seed quality traits in faba bean (Vicia faba L.): characterization and GWAS of a diversity panel.

Faba bean (Vicia faba L.) is a legume crop grown in diverse climates worldwide. It has a high potential for increased cultivation to meet the need for more plant-based proteins in human diets, a prerequisite for a more sustainable food production system. Characterization of diversity panels of crops can identify variation in and genetic markers for target traits of interest for plant breeding. In this work, we collected a diversity panel of 220 accessions of faba bean from around the world consisting of gene bank material and commercially available cultivars. The aims of this study were to quantify the phenotypic diversity in target traits to analyze the impact of breeding on these traits, and to identify genetic markers associated with traits through a genome-wide association study (GWAS). Characterization under field conditions at Nordic latitude across two years revealed a large genotypic variation and high broad-sense heritability for eleven agronomic and seed quality traits. Pairwise correlations showed that seed yield was positively correlated to plant height, number of seeds per plant, and days to maturity. Further, susceptibility to bean weevil damage was significantly higher for early flowering accessions and accessions with larger seeds. In this study, no yield penalty was found for higher seed protein content, but protein content was negatively correlated to starch content. Our results showed that while breeding advances in faba bean germplasm have resulted in increased yields and number of seeds per plant, they have also led to a selection pressure towards delayed onset of flowering and maturity. DArTseq genotyping identified 6,606 single nucleotide polymorphisms (SNPs) by alignment to the faba bean reference genome. These SNPs were used in a GWAS, revealing 51 novel SNP markers significantly associated with ten of the assessed traits. Three markers for days to flowering were found in predicted genes encoding proteins for which homologs in other plant species regulate flowering. Altogether, this work enriches the growing pool of phenotypic and genotypic data on faba bean as a valuable resource for developing efficient breeding strategies to expand crop cultivation.

Harnessing weedy rice as functional food and source of novel traits for crop improvement.

A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.

RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak

BackgroundHere, we investigated the underlying transcriptional-level evidence behind phytochemical differences between two metabolically extreme genotypes of Thymus daenensis. The genotypes ‘Zagheh-11’ (thymol/carvacrol type, poor in essential oil [EO] [2.9%] but rich in triterpenic acids) and ‘Malayer-21’ (thymol type and rich in EO [3.8%]) were selected from an ongoing breeding program and then clonally propagated for further experimental use.Materials and methodsGC-MS, GC-FID, and HPLC-PDA were utilized to monitor the fluctuation of secondary metabolites at four phenological stages (vegetative, bud burst, early, and full-flowering stages). The highest phytochemical divergence was observed at early flowering stage. Both genotypes were subjected to mRNA sequencing (approximately 100 million paired reads) at the aforementioned stage. The expression patterns of four key genes involved in the biosynthesis of terpenoids were also validated using qRT-PCR.ResultsCarvacrol content in ‘Zagheh-11’ (26.13%) was approximately 23 times higher than ‘Malayer-21’ (1.12%). Reciprocally, about 10% higher thymol was found in ‘Malayer-21’ (62.15%). Moreover, the concentrations of three major triterpenic acids in ‘Zagheh-11’ were approximately as twice as those found in ‘Malayer-21’. Transcriptome analysis revealed a total of 1840 unigenes that were differentially expressed, including terpene synthases, cytochrome P450, and terpenoid backbone genes. Several differentially expressed transcription factors (such as MYB, bZIP, HB-HD-ZIP, and WRKY families) were also identified. These results suggest that an active cytosolic mevalonate (MVA) pathway may be linked to higher levels of sesquiterpenes, triterpenic acids, and carvacrol in ‘Zagheh-11’. The chloroplastic pathway of methyl erythritol phosphate (MEP) may have also contributed to a higher accumulation of thymol in Malayer-21. Indeed, ‘Zagheh-11’ showed higher expression of certain genes (HMGR, CYP71D180, β-amyrin 28-monooxygenase, and sesquiterpene synthases) in the MVA pathway, while some genes in the MEP pathway (including DXR, ispG, and γ-terpinene synthase) were distinctly expressed in Malayer-21. Future efforts in metabolic engineering of MVA/MEP pathways may benefit from these findings to produce increased levels of desired secondary metabolites at commercial scale.