Vernalization Response Research Articles

Proteomic Analysis of Vernalization Responsive Proteins in Winter Wheat Jing841.

Vernalization is one of the pivotal ways for plants to flower. The twodimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-offlight/ time-of-flight mass spectrometry (MALDI-TOF/TOF MS) were applied to analyze the changes in protein expression profiles in responding to vernalization in leaves of wheat seedling before (0d) and after (30d) of vernalization. The main objective of this study was to analyze the vernalization-responsive proteins in winter wheat after vernalization. Winter wheat seedling leaf proteins were extracted by phenol extraction coupled with ammonium acetate in methanol. 2-DE was conducted according to procedures described in the manual given by the GE manufacture. The selected protein spots were identified by MALDITOF/ TOF MS. Gene ontology (GO) classification was applied to classify the functions of the differentially expressed proteins. Pathway enrichment analysis identified significantly enriched metabolic pathways or signal transduction pathways relative to the whole proteins background. The results of 2-DE and MALDI-TOF/TOF MS showed that among the 65 differentially expressed proteins that were successfully identified under vernalization, 30 were up-regulated whereas 35 were down-regulated after vernalization, respectively. These vernalization-responsive proteins were found to play roles in carbohydrate metabolism, protein metabolism, photosynthesis, defense and stress-resistance and may therefore participate in many biological processes in responding to vernalization. The enhanced accumulation of proteins after vernalization, such as thiamine thiazole synthase, late embryogenesis abundant protein, and glutathione-S-transferase, probably play vital roles in the mechanisms underlying vernalization response in wheat. Our results indicated these vernalization-responsive proteins were found to be involved in protein metabolism, carbohydrate metabolism, photosynthesis, and stress resistance/ defense. The responses of plants to low temperature were very complex, involving in a wide range of cellular pathways for signal transduction, gene regulation, protein modifications, and metabolic regulation. Studying on wheat proteomic profiles in response to vernalization can improve our understanding the molecular mechanisms underlying vernalization in cereals. The results obtained in this study have provided a novel insight into the mechanisms underlying vernalization in cereal crops.

Ability of alleles of PPD1 and VRN1 genes to predict flowering time in diverse Australian wheat (Triticum aestivum) cultivars in controlled environments

Flowering time of wheat (Triticum aestivum L.) is a critical determinant of grain yield. Frost, drought and heat stresses from either overly early or overly late flowering can inflict significant yield penalties. The ability to predict time of flowering from different sowing dates for diverse cultivars across environments in Australia is important for maintaining yield as autumn rainfall events become less reliable. However, currently there are no models that can accurately do this when new cultivars are released. Two major Photoperiod1 and three Vernalisation1 development genes, with alleles identified by molecular markers, are known to be important in regulating phasic development and therefore time to anthesis, in response to the environmental factors of temperature and photoperiod. Allelic information from molecular markers has been used to parameterise models that could predict flowering time, but it is uncertain how much variation in flowering time can be explained by different alleles of the five major genes. This experiment used 13 elite commercial cultivars of wheat, selected for their variation in phenology and in turn allelic variation at the major development genes, and 13 near-isogenic lines (NILs) with matching multi-locus genotypes for the major development genes, to quantify how much response in time to flowering could be explained by alleles of the major genes. Genotypes were grown in four controlled environments at constant temperature of 22°C with factorial photoperiod (long or short day) and vernalisation (±) treatments applied. NILs were able to explain a large proportion of the variation of thermal time to flowering in elite cultivars in the long-day environment with no vernalisation (97%), a moderate amount in the short-day environment with no vernalisation (62%), and less in the short-day (51%) and long-day (47%) environments with vernalisation. Photoperiod was found to accelerate development, as observed in a reduction in phyllochron, thermal time to heading, thermal time to flowering, and decreased final leaf numbers. Vernalisation response was not as great, and rates of development in most genotypes were not significantly increased. The results indicate that the alleles of the five major development genes alone cannot explain enough variation in flowering time to be used to parameterise gene-based models that will be accurate in simulating flowering time under field conditions. Further understanding of the genetics of wheat development, particularly photoperiod response, is required before a model with genetically based parameter estimates can be deployed to assist growers to make sowing-time decisions for new cultivars.

A high-density consensus linkage map of white lupin highlights synteny with narrow-leafed lupin and provides markers tagging key agronomic traits

White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L. angustifolius L.) genomes. Mapping of white lupin quantitative trait loci (QTLs) revealed polygenic control of vernalization responsiveness and anthracnose resistance, as well as a single locus regulating seed alkaloid content. We found high sequence collinearity between white and narrow-leafed lupin genomes. Interestingly, the white lupin QTLs did not correspond to previously mapped narrow-leafed lupin loci conferring vernalization independence, anthracnose resistance, low alkaloids and Phomopsis stem blight resistance, highlighting different genetic control of these traits. Our suite of allele-sequenced and PCR validated markers tagging these QTLs is immediately applicable for marker-assisted selection in white lupin breeding. The consensus map constitutes a platform for synteny-based gene cloning approaches and can support the forthcoming white lupin genome sequencing efforts.

Differences in vernalisation responses in onion cultivars

ABSTRACTOnions normally form bulbs in the first year of growth; however, exposure to low temperatures can induce flowering (vernalisation) before bulbs are produced. Based on the cultivation data of onions grown in Japan, we evaluated and validated a reported model describing the onion vernalisation response. The observed bolting rates of ‘Sapporoki’, which was used in the construction of a previous model, were a good fit to the model, whereas, the bolting rates of one of the overwinter-type cultivars, ‘Momiji No.3ʹ, were lower than the predicted value. The difference between the predicted and observed bolting rates in ‘Momiji No.3ʹ was caused by a larger VD0.5, the coefficient in vernalisation response models that represents the time point when half of the plants have bolted. Overwinter-type and/or bolting resistant cultivars can have parameters that indicate a further vernalisation requirement for bolting. The parameters in our model can be customised to the cultivar being investigated, and our study suggests the viability of modelling onion bolting by using air temperature.

Altered regulation of TERMINAL FLOWER 1 causes the unique vernalisation response in an arctic woodland strawberry accession.

Vernalisation requirement is an agriculturally important trait that postpones the development of cold-sensitive floral organs until the spring. The family Rosaceae includes many agriculturally important fruit and berry crops that suffer from crop losses caused by frost injury to overwintering flower buds. Recently, a vernalisation-requiring accession of the Rosaceae model woodland strawberry (Fragaria vesca) has been identified in northern Norway. Understanding the molecular basis of the vernalisation requirement in this accession would advance the development of strawberry cultivars better adapted to temperate climate. We use gene silencing, gene expression analysis, genetic mapping and population genomics to study the genetic basis of the vernalisation requirement in woodland strawberry. Our results indicate that the woodland strawberry vernalisation requirement is endemic to northern Norwegian population, and mapping data suggest the orthologue of TERMINAL FLOWER1 (FvTFL1) as the causal floral repressor. We demonstrate that exceptionally low temperatures are needed to downregulate FvTFL1 and to make these plants competent to induce flowering at low postvernalisation temperatures in the spring. We show that altered regulation of FvTFL1 in the northern Norwegian woodland strawberry accession postpones flower induction until the spring, allowing plants to avoid winter injuries of flower buds that commonly occur in temperate regions.

Fine-tuning timing: natural variation informs the mechanistic basis of the switch to flowering in Arabidopsis thaliana.

The evolution of diverse life history strategies has allowed Arabidopsis thaliana to adapt to worldwide locations, spanning a range of latitudinal and environmental conditions. Arabidopsis thaliana accessions are either vernalization-requiring winter annuals or rapid cyclers, with extensive natural variation in vernalization requirement and response. Genetic and molecular analysis of this variation has enhanced our understanding of the mechanisms involved in life history determination, with translation to both natural and crop systems in the Brassicaceae and beyond.

Modular function of long noncoding RNA, COLDAIR, in the vernalization response.

The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C (FLC) during vernalization in Arabidopsis thaliana. The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 (PRC2) and subsequent trimethylation of Histone H3 Lysine 27 (H3K27me3) at FLC chromatin. In this study we found that the association of COLDAIR with chromatin occurs only at the FLC locus and that the central region of the COLDAIR transcript is critical for this interaction. A modular motif in COLDAIR is responsible for the association with PRC2 in vitro, and the mutations within the motif that reduced the association of COLDAIR with PRC2 resulted in vernalization insensitivity. The vernalization insensitivity caused by mutant COLDAIR was rescued by the ectopic expression of the wild-type COLDAIR. Our study reveals the molecular framework in which COLDAIR lncRNA mediates the PRC2-mediated repression of FLC during vernalization.

Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization.

Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during vernalization. More than 36 million clean reads were generated for each sample and the portions mapped to the reference genome were all above 67.0%. Our results show that the differentially expressed genes (DEGs) between room temperature and the early stage of vernalization (4,845) are the most in all treatments pairs. A series of vernalization related genes, including two FLOWERING LOCUS C (FLC) genes, were screened according to the annotations. A total of 775 genes were also filtered as the vernalization related candidates based on their expression profiles. Cold stress responsive genes were also analyzed to further confirm the sequencing result. Several key genes in vernalization or cold stress response were validated by quantitative RT-PCR (RT-qPCR). This study identified a number of genes that may be involved in vernalization, which are useful for other functional genomics research in radish.

Accelerated vernalization response by an altered PHD-finger protein in Arabidopsis

ABSTRACTVernalization is a response to the winter cold to acquire the competence to flower in next spring. VERNALIZATION INSENSITIVE 3 (VIN3) is a PHD-finger protein that binds to modified histones in vitro. VIN3 is induced by long-term cold and is necessary for Polycomb Repression Complex 2 (PRC2)-mediated tri-methylation of Histone H3 Lysine 27 (H3K27me3) at the FLC locus in Arabidopsis. An alteration in the PHD-finger domain of VIN3 changes the binding specificity of the PHD-finger domain of VIN3 in vitro and results in an accelerated vernalization response in vivo. The acceleration in vernalization response is achieved by increased enrichments of VIN3 and tri-methylation of Histone H3 Lysine 27 (H3K27me3) at the FLC locus without invoking the increased enrichment of Polycomb Repressive Complex 2. This result indicates that the binding specificity of the PHD-finger domain of VIN3 plays a role in mediating a proper vernalization response in Arabidopsis. Furthermore, this work shows a potential that the alteration of PHD-finger domains could be applied to alter various developmental processes in plants.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.).

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP “hotspots,” and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r2 = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

Effects of ambient temperature and photoperiod on flowering time in faba bean (Vicia faba L.)

Flowering time is a vulnerable stage of plant development and is therefore a significant determinant of adaptation and grain yield in faba bean (Vicia faba L.). It is largely controlled by genotype, environmental factors of temperature and photoperiod, and genotype-by-environment interactions. The aim of this study was to evaluate variation in flowering time and the responses of flowering time to ambient temperature and photoperiod in Australian faba bean. Time of sowing experiments were carried out to assess variation among lines for flowering time (measured in days to flowering, thermal time to flowering and node of first flower) and to determine plant sensitivities to ambient temperature and photoperiod by regression analysis in the field, while four controlled environment experiments of differing temperature and photoperiod were undertaken to further analyse the variation in responses. Results showed significant variation in responses to both ambient temperature and photoperiod. Photoperiod was the main factor influencing variation in flowering time, with lines grouped as sensitive, intermediate or insensitive. The responses to ambient temperature were more complex. Most lines fit the traditional linear model, but with possible variation in optimal temperature and/or vernalisation response, while some lines showed temperature insensitivity.

A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat.

Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2 Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2 Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.

The Binding Specificity of the PHD-Finger Domain of VIN3 Moderates Vernalization Response.

Vernalization is a response to winter cold to initiate flowering in spring. VERNALIZATION INSENSITIVE3 (VIN3) is induced by winter cold and is essential to vernalization response in Arabidopsis (Arabidopsis thaliana). VIN3 encodes a PHD-finger domain that binds to modified histones in vitro. An alteration in the binding specificity of the PHD-finger domain of VIN3 results in a hypervernalization response. The hypervernalization response is achieved by increased enrichments of VIN3 and trimethylation of Histone H3 Lys 27 at the FLC locus without invoking the increased enrichment of Polycomb Repressive Complex 2. Our result shows that the binding specificity of the PHD-finger domain of VIN3 plays a role in mediating a proper vernalization response in Arabidopsis.

Vernalisation and photoperiod sensitivity in wheat: Impact on canopy development and yield components

Genetic variation in the VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) genes, which control the vernalisation and photoperiod response, underpin wheat adaptation to different environments. Near isogenic lines were used to investigate the role of allelic combinations of VRN1 and PPD-D1, including new alleles for VRN1-A1, on the length of developmental phases, dynamics of leaf and tiller appearance and yield components in complementary irrigated field trials relevant to low latitude wheat growing areas and controlled conditions. Allelic differences in VRN1 had a stronger effect on the duration of the vegetative phase, while photoperiod sensitivity at PPD-D1 lengthened the stem elongation phase (SE) by up to 23%. If a phase was lengthened, flowering was delayed. The level of response to daylength during stem elongation (SE) introduced by photoperiod sensitive alleles was dependent on the VRN1 composition and vernalisation status. A longer SE under short days was achieved by PPD1 sensitive genotypes when one VRN1 spring allele was present and plants were vernalised. The duration of SE was weakly related to spike dry weight m−2 at DC65 in the field but did not translate into higher grain number m−2. In the field, lines with two to three VRN1 spring alleles had shortest development phases, including SE, close flowering dates, sampled similar temperature environments at different stages, and achieved high yields. Yield advantage was explained by higher biomass, harvest index, grain number m−2 and thousand kernel weight. Genotypes with three winter VRN1 alleles were comparatively disadvantaged, with a longer vegetative phase placing SE under higher temperatures. Allelic differences in both genes caused large variation in leaf and tiller number generation but also in tiller mortality and individual leaf size, lessening the impact on leaf area. Changes in plant morphology and yield components that did not seem mediated via the influence of development genes on the duration of different stages and their impact on resource capture deserve further investigation.

Identifying the North American Plum Species Phylogenetic Signal Using Nuclear, Mitochondrial, and Chloroplast DNA Markers

Prunus phylogeny has been extensively studied using chloroplast DNA (cpDNA) sequences. Chloroplast DNA has a slow rate of evolution, which is beneficial to determine species relationships at a deeper level. The chloroplast-based phylogenies have a limitation due to the transfer of this organelle by interspecific hybridization. This creates difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been reported, which creates a problem when using cpDNA-based phylogenies to determine species relationships. The main goal of this project was to identify nuclear gene regions that could provide an improved phylogenetic signal at the species level in Prunus. A total of 11 species in Prunus and within section Prunocerasus were used. Two peach (Prunus persica) haploids were used to test the reliability of the molecular markers developed in this project to amplify single-copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and 3 with isozymes, were tested. Similarly, 41 simple sequence repeat (SSR) markers, seven cpDNA regions, and the internal transcribed spacer (ITS) region, were used. Multiple gene regions were identified and provided the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 are recommended for a phylogenetic analysis with a larger number of taxa. The use of potentially informative characters (PICS) as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. This will allow selecting the region(s), which can be used in phylogenetic studies with higher number of taxa.

Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2.

BackgroundThe Arabidopsis FLOWERING LOCUS T (FT) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality. In legumes, FT evolved into three, functionally diversified clades, FTa, FTb and FTc. A milestone achievement in narrow-leafed lupin (Lupinus angustifolius L.) domestication was the loss of vernalization responsiveness at the Ku locus. Recently, one of two existing L. angustifolius homologs of FTc, LanFTc1, was revealed to be the gene underlying Ku. It is the first recorded involvement of an FTc homologue in vernalization. The evolutionary basis of this phenomenon in lupin has not yet been deciphered.ResultsBacterial artificial chromosome (BAC) clones carrying LanFTc1 and LanFTc2 genes were localized in different mitotic chromosomes and constituted sequence-specific landmarks for linkage groups NLL-10 and NLL-17. BAC-derived superscaffolds containing LanFTc genes revealed clear microsyntenic patterns to genome sequences of nine legume species. Superscaffold-1 carrying LanFTc1 aligned to regions encoding one or more FT-like genes whereas superscaffold-2 mapped to a region lacking such a homolog. Comparative mapping of the L. angustifolius genome assembly anchored to linkage map localized superscaffold-1 in the middle of a 15 cM conserved, collinear region. In contrast, superscaffold-2 was found at the edge of a 20 cM syntenic block containing highly disrupted collinearity at the LanFTc2 locus. 118 PEBP-family full-length homologs were identified in 10 legume genomes. Bayesian phylogenetic inference provided novel evidence supporting the hypothesis that whole-genome and tandem duplications contributed to expansion of PEBP-family genes in legumes. Duplicated genes were subjected to strong purifying selection. Promoter analysis of FT genes revealed no statistically significant sequence similarity between duplicated copies; only RE-alpha and CCAAT-box motifs were found at conserved positions and orientations.ConclusionsNumerous lineage-specific duplications occurred during the evolution of legume PEBP-family genes. Whole-genome duplications resulted in the origin of subclades FTa, FTb and FTc and in the multiplication of FTa and FTb copy number. LanFTc1 is located in the region conserved among all main lineages of Papilionoideae. LanFTc1 is a direct descendant of ancestral FTc, whereas LanFTc2 appeared by subsequent duplication.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3150-z) contains supplementary material, which is available to authorized users.

Identification of Earliness Per Se Flowering Time Locus in Spring Wheat through a Genome‐Wide Association Study

Identification of earliness per se (Eps) flowering time loci in spring wheat are troublesome due to confounding effects of vernalization and photoperiod responses. The Wheat Association Mapping Initiative panel of 287 elite lines was assessed to identify genomic regions associated with Eps and to understand the effects of vernalization and photoperiod treatments in spring wheat. The panel was grown under field conditions with four different treatments: (i) vernalization, where 1‐d germinated seeds were kept at 4°C for 6 to 8 wk; (ii) extended photoperiod treatment, from seedling emergence to 10 d after anthesis in the field; (iii) treatments (i) and (ii) in combination; and (iv) a control treatment without either (i) or (ii). The combined vernalization and photoperiod treatments had the greatest effect in advancing the flowering time (4 d). Genome‐wide association study in this panel on treatment (iii) detected a locus for Eps in chromosome 1D at 163 to 167 cM. An analysis of the flowering time data on this panel from 19 international environments did not show the presence of Eps in chromosome 1D, indicating the possible masking effect of vernalization and photoperiod genes. This study also validated the diagnostic marker—a transcription factor in the circadian clock input pathway called Triticum aestivum EARLY FLOWERING 3—that is associated with Eps in chromosome 1D and can be used for marker‐assisted selection.

Transcriptome comparison reveals key candidate genes in response to vernalization of Oriental lily.

BackgroundOriental hybrid lily ‘Sorbonne’, a very important cut flower for lily, is enjoyed great popularity in the world, but it must experience a period of low winter temperature to initiate or accelerate the flowering process. To gain a better understanding of the temperature signaling pathway and the molecular metabolic reactions involved in the vernalization response, a genome-wide transcriptional analysis using RNA-Seq was performed.Results188,447,956 sequencing reads was assembled into 66,327 unigenes and showed similarity to known proteins in the Swiss-Prot protein database, and 2,893, 30,406 and 60,737 unigenes aligned to existing sequences in the KEGG, COG, and GO databases. Based on qRT-PCR results, we studied the expression of three signal regulation pathways genes–the plant hormones signal transduction (LoAP2, LoIAA1, LoARF10), the DNA methylation (LoCMT, LoFLD), and vernalizatin pathway (LoFLC, LoVRN1, LoVRN2, LoFT, LoSOC1, LoLFY, LoSVP) in the immature flower buds of Oriental hybrid lily. In addition, we identified two vernalizaiton–related genes (LoSVP and LoVRN1) from the cDNA library, which appear to be promising candidates for playing key roles in the development and response of flowering in Oriental lily plants, and LoSVP had a function in delaying flowering but LoVRN1could promote flowering early.ConclusionsWe collected a sample for transcriptome sequencing and comparison when the bulb’s apical meristem was in the time of floral transition when the apical meristem had not converted into the morphological differentiation process, which helped to obtain more genes playing key roles in the floral induction pathways. The upstream and downstream relationship between different genes were forecasted by the analysis of genes’ expression levels in a wide range of time. Future research that is targeted towards how genes interact on each other, which will promote establishing and perfecting the molecular mechanisms of floral induction pathway by vernalization.

Genotype × environment interactions for phenological adaptation in narrow-leafed lupin: A simulation study with a parameter optimized model

An understanding of genotype×environment (G×E) interactions for phenological adaptation in crops can help identify traits that facilitate genetic improvement and cultivar selection. Such understanding is also necessary to identify environments that facilitate identification of cultivars with better environmental adaptation. Process-based crop simulation models including APSIM are valuable tools to investigate G×E interactions and traits conferring adaption to particular conditions. However cultivar parameters relating to crop phenology in crop model are difficult to determine directly through field experiments. Within this paper, we present a simulation study to explore the environmental and genotypic control of time to flowering and maturity in lupin and its grain yield, by using the APSIM model. In the model, lupin cultivar parameters were optimized by combining prior knowledge and PEST (Parameter ESTimation), a model-independent parameter optimiser. The parameterisation was for nine lupin cultivars with contrasting maturity (early vs late) and vernalization requirement (non-responsive vs responsive) across 13 sites×years across Australia. We showed that phenological differences among the cultivars were well explained by the optimized set of parameters, mainly reflected in vernalization response and photoperiodic sensitivity before flowering. Simulated flowering days and grain yield agreed well with the observations, with RMSEs (root mean squared error) of 4days and 0.34tha−1 for all cultivars together. The simulation results showed that lupin yield was significantly affected by temperature and water availability. An early-maturity cultivar would yield better than the late-maturity one at the warm and low rainfall region, while at high rainfall or long-season regions, cultivar types should be chosen tactically based on the climatic conditions for that season. Thus, lupin breeding in Australia should therefore focus on temperature regimes and rainfall gradients. These results indicate that the parameter-optimized APSIM model could be used to explore the adaptation of genotypes to a particular environment to provide guidance for a more efficient breeding program and develop optimal agronomic management practices.

Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants.

BackgroundMany genes involved in responses to photoperiod and vernalization have been characterized or predicted in Arabidopsis (Arabidopsis thaliana), Brachypodium (Brachypodium distachyon), wheat (Triticum aestivum) and barley (Hordeum vulgare). However, little is known about the transcription regulation of these genes, especially in the large, complex genomes of wheat and barley.ResultsWe identified 68, 60, 195 and 61 genes that are known or postulated to control pathways of photoperiod (PH), vernalization (VE) and pathway integration (PI) in Arabidopsis, Brachypodium, wheat and barley for predicting transcription factor binding sites (TFBSs) in the promoters of these genes using the FIMO motif search tool of the MEME Suite. The initial predicted TFBSs were filtered to confirm the final numbers of predicted TFBSs to be 1066, 1379, 1528, and 789 in Arabidopsis, Brachypodium, wheat and barley, respectively. These TFBSs were mapped onto the PH, VE and PI pathways to infer about the regulation of gene expression in Arabidopsis and cereal species. The GC contents in promoters, untranslated regions (UTRs), coding sequences and introns were higher in the three cereal species than those in Arabidopsis. The predicted TFBSs were most abundant for two transcription factor (TF) families: MADS-box and CSD (cold shock domain). The analysis of publicly available gene expression data showed that genes with similar numbers of MADS-box and CSD TFBSs exhibited similar expression patterns across several different tissues and developmental stages. The intra-specific Tajima D-statistics of TFBS motif diversity showed different binding specificity among different TF families. The inter-specific Tajima D-statistics suggested faster TFBS divergence in TFBSs than in coding sequences and introns. Mapping TFBSs onto the PH, VE and PI pathways showed the predominance of MADS-box and CSD TFBSs in most genes of the four species, and the difference in the pathway regulations between Arabidopsis and the three cereal species.ConclusionOur approach to associating the key flowering genes with their potential TFs through prediction of putative TFBSs provides a framework to explore regulatory mechanisms of photoperiod and vernalization responses in flowering plants. The predicted TFBSs in the promoters of the flowering genes provide a basis for molecular characterization of transcription regulation in the large, complex genomes of important crop species, wheat and barley.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2916-7) contains supplementary material, which is available to authorized users.