GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1.

Precise regulation of flowering time is critical for cereal crops to synchronize reproductive development with optimum environmental conditions, thereby maximizing grain yield. The plant-specific gene GIGANTEA (GI) plays an important role in the control of flowering time, with additional functions on the circadian clock and plant stress responses. In this study, we show that GI loss-of-function mutants in a photoperiod-sensitive tetraploid wheat background exhibit significant delays in heading time under both long-day (LD) and short-day photoperiods, with stronger effects under LD. However, this interaction between GI and photoperiod is no longer observed in isogenic lines carrying either a photoperiod-insensitive allele in the PHOTOPERIOD1 (PPD1) gene or a loss-of-function allele in EARLY FLOWERING 3 (ELF3), a known repressor of PPD1. These results suggest that the normal circadian regulation of PPD1 is required for the differential effect of GI on heading time in different photoperiods. Using crosses between mutant or transgenic plants of GI and those of critical genes in the flowering regulation pathway, we show that GI accelerates wheat heading time by promoting FLOWERING LOCUS T1 (FT1) expression via interactions with ELF3, VERNALIZATION 2 (VRN2), CONSTANS (CO), and the age-dependent microRNA172-APETALA2 (AP2) pathway, at both transcriptional and protein levels. Our study reveals conserved GI mechanisms between wheat and Arabidopsis but also identifies specific interactions of GI with the distinctive photoperiod and vernalization pathways of the temperate grasses. These results provide valuable knowledge for modulating wheat heading time and engineering new varieties better adapted to a changing environment.

Allelic variations of Vrn-1 and Ppd-1 genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time.

The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods.

BACKGROUND: Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod. RESULTS: We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type (WT) plants. The delay in heading between WT and phy mutants was greater in LD than in SD, confirming the importance of PHYB and PHYC in accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods, PHYB regulated more genes than PHYC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genes VRN-A1 and PPD-B1 in phyB and phyC mutants compared to the WT. CONCLUSIONS: Our study confirms the major role of both PHYB and PHYC in flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.

Photoperiod-sensitivity genes (Ppd-1): quantifying their effect on the photoperiod response model in wheat.

Coupling anthesis date to the most suitable environmental conditions is critical for wheat (Triticum aestivum L.) adaptation and yield potential. Development to anthesis is controlled by temperature and photoperiod. Response to photoperiod is chiefly modulated by Ppd-1 genes, but their effect on the quantitative response to photoperiod of (i) time to anthesis and (ii) pre-anthesis phases remains largely unknown. A photoperiod-sensitive spring cultivar, Paragon, and near-isogenic lines of it carrying different combinations of Ppd-1a insensitivity alleles were tested under a wide range of photoperiods, including switches in photoperiod at the onset of stem elongation. Using multimodel inference we found that Ppd-1a alleles reduced photoperiod sensitivity of (i) emergence to anthesis and (ii) emergence to onset of stem elongation, both in a less than additive manner, while threshold photoperiod and intrinsic earliness were unaffected. Sensitivity to current photoperiod from onset of stem elongation to flag leaf and from then to anthesis was milder than for previous phases and was not related to variability in Ppd-1. However, 'memory' effects of previously experienced photoperiod on the duration from onset of stem elongation to flag leaf were related to variability in Ppd-1. The characterization and quantification provided here of the effects on development of Ppd-1 allelic combinations should help increase accuracy of genotype-to-phenotype models in predicting wheat phenology.

Photoperiod-sensitivity genes shape floret development in wheat.

Lengthening the pre-anthesis period of stem elongation (or late-reproductive phase, LRP) through altering photoperiod sensitivity has been suggested as a potential means to increase the number of fertile florets at anthesis (NFF) in wheat. However, little is known about the effects that the Ppd-1 genes modulating plant response to photoperiod may have on reproductive development. Here, five genotypes with either sensitive (b) or insensitive (a) alleles were grown in chambers under contrasting photoperiods (12 h or 16 h) to assess their effects. The genotypes consisted of the control cultivar Paragon (three Ppd-1b) and four near-isogenic lines of Paragon with Ppd-1a alleles introgressed from: Chinese Spring (Ppd-B1a), GS-100 (Ppd-A1a), Sonora 64 (Ppd-D1a), and Triple Insensitive (three Ppd-1a). Under a 12-h photoperiod, NFF in the genotypes followed the order three Ppd-1b > Ppd-B1a > Ppd-A1a > Ppd-D1a > three Ppd-1a. Under a 16-h photoperiod the differences were milder, but three Ppd-1b still had a greater NFF than the rest. As Ppd-1a alleles shortened the LRP, spikes were lighter and the NFF decreased. The results demonstrated for the first time that Ppd-1a decreases the maximum number of florets initiated through shortening the floret initiation phase, and this partially explained the variations in NFF. The most important impact of Ppd-1a alleles, however, was related to a reduction in survival of floret primordia, which resulted in the lower NFF. These findings reinforce the idea that an increased duration of the LRP, achieved through photoperiod sensitivity, would be useful for increasing wheat yield potential.

Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes.

BACKGROUND: Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a complex trait regulated by a number of genes and several gene families. Availability of the wheat genomic sequence opens new opportunities for exploring candidate genes diversity for FT. Therefore, the objectives of this study were to identity SNPs and insertion-deletion (indels) in genes known to be involved in frost tolerance and to perform association genetics analysis of respective SNPs and indels on FT. RESULTS: Here we report on the sequence analysis of 19 candidate genes for FT in wheat assembled using the Chinese Spring IWGSC RefSeq v1.0. Out of these, the tandem duplicated C-repeat binding factors (CBF), i.e. CBF-A3, CBF-A5, CBF-A10, CBF-A13, CBF-A14, CBF-A15, CBF-A18, the vernalisation response gene VRN-A1, VRN-B3, the photoperiod response genes PPD-B1 and PPD-D1 revealed association to FT in 235 wheat cultivars. Within six genes (CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1) amino acid (AA) substitutions in important protein domains were identified. The amino acid substitution effect in VRN-A1 on FT was confirmed and new AA substitutions in CBF-A3, CBF-A15, VRN-B3, PPD-B1 and PPD-D1 located at highly conserved sites were detected. Since these results rely on phenotypic data obtained at five locations in 2 years, detection of significant associations of FT to AA changes in CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1 may be exploited in marker assisted breeding for frost tolerance in winter wheat. CONCLUSIONS: A set of 65 primer pairs for the genes mentioned above from a previous study was BLASTed against the IWGSC RefSeq resulting in the identification of 39 primer combinations covering the full length of 19 genes. This work demonstrates the usefulness of the IWGSC RefSeq in specific primer development for highly conserved gene families in hexaploid wheat and, that a candidate gene association genetics approach based on the sequence data is an efficient tool to identify new alleles of genes important for the response to abiotic stress in wheat.

Effects of ambient temperature in association with photoperiod on phenology and on the expressions of major plant developmental genes in wheat (Triticum aestivum L.).

In addition to its role in vernalization, temperature is an important environmental stimulus in determining plant growth and development. We used factorial combinations of two photoperiods (16H, 12H) and three temperature levels (11, 18 and 25 °C) to study the temperature responses of 19 wheat cultivars with established genetic relationships. Temperature produced more significant effects on plant development than photoperiod, with strong genotypic components. Wheat genotypes with PPD-D1 photoperiod sensitive allele were sensitive to temperature; their development was delayed by higher temperature, which intensified under non-inductive conditions. The effect of temperature on plant development was not proportional; it influenced the stem elongation to the largest extent, and warmer temperature lengthened the lag phase between the detection of first node and the beginning of intensive stem elongation. The gene expression patterns of VRN1, VRN2 and PPD1 were also significantly modified by temperature, while VRN3 was more chronologically regulated. The associations between VRN1 and VRN3 gene expression with early apex development were significant in all treatments but were only significant for later plant developmental phases under optimal conditions (16H and 18 °C). Under 16H, the magnitude of the transient peak expression of VRN2 observed at 18 and 25 °C associated with the later developmental phases.

Analysis of the Effects of the Vrn-1 and Ppd-1 Alleles on Adaptive and Agronomic Traits in Common Wheat (Triticum aestivum L.).

Wheat heading time is primarily governed by two loci: VRN-1 (response to vernalization) and PPD-1 (response to photoperiod). Five sets of near-isogenic lines (NILs) were studied with the aim of investigating the effect of the aforementioned genes on wheat vegetative period duration and 14 yield-related traits. Every NIL was sown in the hydroponic greenhouse of the Institute of Cytology and Genetics, SB RAS. To assess their allelic composition at the VRN-1 and PPD-1 loci, molecular markers were used. It was shown that HT in plants with the Vrn-A1vrn-B1vrn-D1 genotype was reduced by 29 and 21 days (p < 0.001) in comparison to HT in plants with the vrn-A1Vrn-B1vrn-D1 and the vrn-A1vrn-B1Vrn-D1 genotypes, respectively. In our study, we noticed a decrease in spike length as well as spikelet number per spike parameter for some NIL carriers of the Vrn-A1a allele in comparison to carriers of the Vrn-B1 allele. PCA revealed three first principal components (PC), together explaining more than 70% of the data variance. Among the studied genetic traits, the Vrn-A1a and Ppd-D1a alleles showed significant correlations with PCs. Regarding genetic components, significant correlations were calculated between PC3 and Ppd-B1a (-0.26, p < 0.05) and Vrn-B1 (0.57, p < 0.05) alleles. Thus, the presence of the Vrn-A1a allele affects heading time, while Ppd-D1a is associated with plant height reduction.

Fine Mapping of a Vigor QTL in Chickpea (Cicer arietinum L.) Reveals a Potential Role for Ca4_TIFY4B in Regulating Leaf and Seed Size.

Plant vigor is a complex trait for which the underlying molecular control mechanisms remain unclear. Vigorous plants tend to derive from larger seeds and have greater early canopy cover, often with bigger leaves. In this study, we delimited the size of a major vigor quantitative trait locus (QTL) on chickpea chromosome 4-104.4 kb, using recombinant association analysis in 15 different heterogeneous inbred families, derived from a Rupali/Genesis836 recombinant inbred line population. The phenotypic and molecular genetic analysis provided evidence for a role of the gene Ca4_TIFY4B, in determining leaf and seed size in chickpea. A non-synonymous single-nucleotide polymorphism (SNP) in the high-vigor parent was located inside the core motif TIFYCG, resulting in a residue change T[I/S]FYCG. Complexes formed by orthologs of Ca4_TIFY4B (PEAPOD in Arabidopsis), Novel Interactor of JAZ (CaNINJA), and other protein partners are reported to act as repressors regulating the transcription of downstream genes that control plant organ size. When tested in a yeast 2-hybrid (Y2H) assay, this residue change suppressed the interaction between Ca4_TIFY4B and CaNINJA. This is the first report of a naturally occurring variant of the TIFY family in plants. A robust gene-derived molecular marker is available for selection in chickpea for seed and plant organ size, i.e., key component traits of vigor.

Functional Analysis of the "Green Revolution" Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding.

Flowering is central to the transformation of plants from vegetative growth to reproductive growth. The circadian clock system enables plants to sense the changes in the external environment and to modify the growth and development process at an appropriate time. Photoperiod-1 (Ppd-1), which is controlled by the output signal of the circadian clock, has played an important role in the wheat "Green Revolution." In the current study, we systematically studied the relationship between Ppd-1 haplotypes and both wheat yield- and quality-related traits, using genome-wide association analysis and transgenic strategies, and found that highly appropriate haplotypes had been selected in the wheat breeding programs. Genome-wide association analysis showed that Ppd-1 is associated with significant differences in yield-related traits in wheat, including spike length (SL), heading date (HD), plant height (PH), and thousand-grain weight (TGW). Ppd-1-Hapl-A1 showed increased SL by 4.72-5.93%, whereas Ppd-1-Hapl-B1 and Ppd-1-Hapl-D1 displayed earlier HD by 0.58-0.75 and 1.24-2.93%, respectively, decreased PH by 5.64-13.08 and 13.62-27.30%, respectively, and increased TGW by 4.89-10.94 and 11.12-21.45%, respectively. Furthermore, the constitutive expression of the Ppd-D1 gene in rice significantly delayed heading date and resulted in reduced plant height, thousand-grain weight, grain width (GW), and total protein content. With reference to 40years of data from Chinese wheat breeding, it was found that the appropriate haplotypes Ppd-1-Hapl-A1, Ppd-1-Hapl-B1, and Ppd-1-Hapl-D1 had all been subjected to directional selection, and that their distribution frequencies had increased from 26.09, 60.00, and 52.00% in landraces to 42.55, 93.62, and 96.23% in wheat cultivars developed in the 2010s. A Ppd-B1 methylation molecular marker was also developed to assist molecular wheat breeding. This research is of significance for fully exploring the function of the Ppd-1 gene and its genetic resource diversity, to effectively use the most appropriate haplotypes and to improve crop yield and sustainability.

Resin based restorative dental materials: characteristics and future perspectives.

This review article compiles the characteristics of resin based dental composites and an effort is made to point out their future perspectives. Recent research studies along with few earlier articles were studied to compile the synthesis schemes of commonly used monomers, their characteristics in terms of their physical, mechanical and polymerization process with selectivity towards the input parameters of polymerization process. This review covers surface modification processes of various filler particles using silanes, wear behaviour, antimicrobial behaviour along with its testing procedures to develop the fundamental knowledge of various characteristics of resin based composites. In the end of this review, possible areas of further interests are pointed out on the basis of literature review on resin based dental materials.

The structure of a purple acid phosphatase involved in plant growth and pathogen defence exhibits a novel immunoglobulin-like fold.

Phosphatases function in the production, transport and recycling of inorganic phosphorus, which is crucial for cellular metabolism and bioenergetics, as well as in bacterial killing, since they are able to generate reactive oxygen species via Fenton chemistry. Diphosphonucleotide phosphatase/phosphodiesterase (PPD1), a glycoprotein plant purple acid phosphatase (PAP) from yellow lupin seeds, contains a bimetallic Fe-Mn catalytic site which is most active at acidic pH. Unlike other plant PAPs, PPD1 cleaves the pyrophosphate bond in diphosphonucleotides and the phosphodiester bond in various phosphodiesters. The homohexameric organization of PPD1, as revealed by a 1.65 Šresolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms. The N-terminal domain of PPD1 has an unexpected and unique fibronectin type III-like fold that is absent in other plant PAPs. Here, the in vitro DNA-cleavage activity of PPD1 is demonstrated and it is proposed that the fibronectin III-like domain, which 'overhangs' the active site, is involved in DNA selectivity, binding and activation. The degradation of DNA by PPD1 implies a role for PPD1 in plant growth and repair and in pathogen defence.