scholarly journals Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 288
Author(s):  
Zhihui Guo ◽  
Meilan Xu ◽  
Hironori Nagano ◽  
Lindsay V. Clark ◽  
Erik J. Sacks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Flowering Time ◽  
Heading Date ◽  
Biomass Accumulation ◽  
Initial Step ◽  
Day Length ◽  
Miscanthus Sinensis ◽  
Sequence Characterization ◽  
Mini Core Collection ◽  
Trait Locus

The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensisGhd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A. The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus.

scholarly journals O-linked N-acetylglucosamine transferase is involved in fine regulation of flowering time in winter wheat

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Min Fan ◽  
Fang Miao ◽  
Haiyan Jia ◽  
Genqiao Li ◽  
Carol Powers ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Flowering Time ◽  
Heading Date ◽  
Wheat Cultivars ◽  
Gene Encoding ◽  
Constitutive Overexpression ◽  
Winter Wheat Cultivars ◽  
Fine Regulation ◽  
Trait Locus ◽  
Glcnac Transferase

AbstractVernalization genes underlying dramatic differences in flowering time between spring wheat and winter wheat have been studied extensively, but little is known about genes that regulate subtler differences in flowering time among winter wheat cultivars, which account for approximately 75% of wheat grown worldwide. Here, we identify a gene encoding anO-linkedN-acetylglucosamine (O-GlcNAc) transferase (OGT) that differentiates heading date between winter wheat cultivars Duster and Billings. We clone thisTaOGT1gene from a quantitative trait locus (QTL) for heading date in a mapping population derived from these two bread wheat cultivars and analyzed in various environments. Transgenic complementation analysis shows that constitutive overexpression ofTaOGT1bfrom Billings accelerates the heading of transgenic Duster plants.TaOGT1 is able to transfer anO-GlcNAc group to wheat proteinTaGRP2. Our findings establish important roles forTaOGT1in winter wheat in adaptation to global warming in the future climate scenarios.

Loci affecting flowering time in oat under short-day conditions

Genome ◽  
2006 ◽  
Vol 49 (12) ◽  
pp. 1528-1538 ◽  
Author(s):  
Ana B. Locatelli ◽  
Luiz C. Federizzi ◽  
Sandra C. K. Milach ◽  
Charlene P. Wight ◽  
Stephen J. Molnar ◽  
...  
Keyword(s):  
Flowering Time ◽  
Comparative Mapping ◽  
Bulked Segregant Analysis ◽  
Recombinant Inbred Lines ◽  
Rice Genome ◽  
Reference Population ◽  
Day Length ◽  
Short Day ◽  
Growing Seasons ◽  
Trait Locus

Flowering time (or days to heading) is an important characteristic in crop plants that affects adaptation to cropping cycles and growing seasons. The objectives of this study were to identify molecular markers associated with flowering time in 3 oat populations developed from Brazilian oat varieties, and to compare their map locations with those of other loci that might influence flowering time. Flowering time was studied in recombinant inbred lines from 3 hexaploid oat populations: UFRGS 8 × Pc68/5*Starter; UFRGS 881971 × Pc68/5*Starter; and UFRGS 8 × UFRGS 930605. Bulked segregant analysis, using amplified fragment length polymorphism, was followed by selective mapping in each population and in a reference population, ‘Kanota’ × ‘Ogle’ (K×O). One quantitative trait locus (QTL) with major effects on flowering time was identified in each cross. Comparative mapping showed that a major QTL, with earliness alleles originating from UFRGS 8 and UFRGS 881971, is in a region with close homology to K×O linkage group 17 and to a locus that reportedly confers day-length insensitivity in oat (Di1). This is the first report to identify the map location of the Di1 locus, and putatively confirm the presence of Di1 alleles in new germplasm. Further comparative mapping and the alignment of mapped oat markers with the sequenced rice genome suggest that this QTL and (or) Di1 is orthologous to the Hd1 locus in rice and the CONSTANS gene in Arabidopsis and other species. A different QTL with major effects segregated in the UFRGS 8 × UFRGS 930605 cross, where the early-flowering allele for Di1 was probably fixed. Two additional QTLs with smaller effects were identified in the UFRGS 8 × Pc68/5*Starter population. These results suggest that the Brazilian oat line UFRGS 8 contains an optimal set of alleles conditioning earliness under the short-day conditions of the Brazilian winter growing season, and that molecular selection could be used to introgress these alleles into other breeding material.

scholarly journals RNA-Seq Analysis of Gene Expression Changes Related to Delay of Flowering Time under Drought Stress in Tropical Maize

2021 ◽  
Vol 11 (9) ◽  
pp. 4273
Author(s):  
Kyung-Hee Kim ◽  
Kitae Song ◽  
Jeong-Min Park ◽  
Jae-Yoon Kim ◽  
Byung-Moo Lee
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Flowering Time ◽  
De Novo ◽  
Expression Profiles ◽  
Heading Date ◽  
Tropical Maize ◽  
Short Day ◽  
Stress Changes ◽  
Delayed Flowering

Few studies have reported on the flowering time mechanism of tropical maize under short-day conditions. Drought, another important factor that affects flowering time, has been reported to delay the silking date in tropical maize. However, due to the lack of genetic information related to flowering in maize, the mechanism by which drought delays flowering is unclear. To further understand this process, we analyzed drought-responsive genes using RNA sequencing and identified genes related to flowering time, including contigs from de novo assembly. The results revealed changes in the expression of flowering-time genes, including INDETERMINATE1 (ID1), Heading date 3a (Hd3a), CONSTANS-like genes, and ZEA MAYS CENTRORADIALES8 (ZCN8), which are known to be crucial factors in flowering. In particular, Hd3a, CONZ1, and ZCN8, which have been reported to accelerate flowering under short-day conditions, were downregulated by drought stress. Changes in gene expression appear to play an important role in changes in flowering time under drought. These expression profiles will help to further understand the flowering-time genes of tropical maize and the delayed flowering time resulting from drought.

Quantitative genetic analysis of flowering time in tomato

Genome ◽  
2007 ◽  
Vol 50 (3) ◽  
pp. 303-315 ◽  
Author(s):  
José M. Jiménez-Gómez ◽  
Carlos Alonso-Blanco ◽  
Alicia Borja ◽  
Germán Anastasio ◽  
Trinidad Angosto ◽  
...  
Keyword(s):  
Flowering Time ◽  
Solanum Species ◽  
Day Length ◽  
Leaf Number ◽  
Phenotypic Variance ◽  
Days To Flowering ◽  
Solanum Lycopersicum L ◽  
Close Relationship ◽  
Genetic Mechanisms ◽  
Trait Locus

Artificial selection of cultivated tomato ( Solanum lycopersicum L.) has resulted in the generation of early-flowering, day-length-insensitive cultivars, despite its close relationship to other Solanum species that need more time and specific photoperiods to flower. To investigate the genetic mechanisms controlling flowering time in tomato and related species, we performed a quantitative trait locus (QTL) analysis for flowering time in an F2 mapping population derived from S. lycopersicum and its late-flowering wild relative S. chmielewskii . Flowering time was scored as the number of days from sowing to the opening of the first flower (days to flowering), and as the number of leaves under the first inflorescence (leaf number). QTL analyses detected 2 QTLs affecting days to flowering, which explained 55.3% of the total phenotypic variance, and 6 QTLs for leaf number, accounting for 66.7% of the corresponding phenotypic variance. Four of the leaf number QTLs had not previously been detected for this trait in tomato. Colocation of some QTLs with flowering-time genes included in the genetic map suggests PHYB2, FALSIFLORA, and a tomato FLC-like sequence as candidate genes that might have been targets of selection during the domestication of tomato.

scholarly journals Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan Brassac ◽  
Quddoos H. Muqaddasi ◽  
Jörg Plieske ◽  
Martin W. Ganal ◽  
Marion S. Röder
Keyword(s):  
Flowering Time ◽  
Aspartic Acid ◽  
Synonymous Substitution ◽  
Minor Effect ◽  
Phenotypic Variance ◽  
Spikelet Number ◽  
Wheat Varieties ◽  
Trait Locus ◽  
A Minor ◽  
Spikelet Number Per Spike

AbstractTotal spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.

scholarly journals Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yuxin Yang ◽  
Xueying Zhang ◽  
Lifen Wu ◽  
Lichao Zhang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Flowering Time ◽  
Heading Date ◽  
Yield Component ◽  
Potential Candidate ◽  
Rna Seq ◽  
Nucleotide Synthesis ◽  
Light Reaction ◽  
Grain Number Per Spike ◽  
Double Ridge

Abstract Background Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. Results In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. Conclusions RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date.

scholarly journals Optimizing expression quantitative trait locus mapping workflows for single-cell studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna S. E. Cuomo ◽  
Giordano Alvari ◽  
Christina B. Azodi ◽  
Davis J. McCarthy ◽  
Marc Jan Bonder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait Locus ◽  
Single Cell ◽  
Quantitative Trait ◽  
Cell Types ◽  
Expression Quantitative Trait Locus ◽  
Eqtl Mapping ◽  
Trait Locus ◽  
The Impact

Abstract Background Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for sample multiplexing improving, population-scale scRNA-seq, and thus single-cell expression quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping of sc-eQTL provides additional resolution to study the regulatory role of common genetic variants on gene expression across a plethora of cell types and states and promises to improve our understanding of genetic regulation across tissues in both health and disease. Results While previously established methods for bulk eQTL mapping can, in principle, be applied to sc-eQTL mapping, there are a number of open questions about how best to process scRNA-seq data and adapt bulk methods to optimize sc-eQTL mapping. Here, we evaluate the role of different normalization and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines. We use both real and simulated datasets across single-cell technologies to systematically assess the impact of these different statistical approaches. Conclusion We provide recommendations for future single-cell eQTL studies that can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.

scholarly journals Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
S. F. Prewitt ◽  
A. Shalit-Kaneh ◽  
S. N. Maximova ◽  
M. J. Guiltinan
Keyword(s):  
Gene Expression ◽  
Tissue Culture ◽  
Gene Family ◽  
Flowering Time ◽  
Molecular Mechanisms ◽  
Regulatory Pathways ◽  
Late Flowering ◽  
Precocious Flowering ◽  
Transition To Flowering

Abstract Background In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant’s transition to flowering could lead to strategies to accelerate cacao breeding. Results BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates. Conclusion We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao’s single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.

scholarly journals Gene body methylation mediates epigenetic inheritance of plant traits

2021 ◽  
Author(s):  
Zaigham Shahzad ◽  
Jonathan D. Moore ◽  
Daniel Zilberman
Keyword(s):  
Gene Expression ◽  
Flowering Time ◽  
Cytosine Methylation ◽  
Plant Traits ◽  
Phenotypic Diversity ◽  
Strong Association ◽  
Epigenetic Inheritance ◽  
Evolutionary Significance ◽  
Gene Body ◽  
Gene Body Methylation

AbstractCytosine methylation is an epigenetically heritable DNA modification common in plant and animal genes, but the functional and evolutionary significance of gene body methylation (gbM) has remained enigmatic. Here we show that gbM enhances gene expression in Arabidopsis thaliana. We also demonstrate that natural gbM variation influences drought and heat tolerance and flowering time by modulating gene expression, including that of Flowering Locus C (FLC). Notably, epigenetic variation accounts for as much trait heritability in natural populations as DNA sequence polymorphism. Furthermore, we identify gbM variation in numerous genes associated with environmental variables, including a strong association between flowering time, spring atmospheric NO2 – a by-product of fossil fuel burning – and FLC epialleles. Our study demonstrates that gbM is an important modulator of gene expression, and its natural variation fundamentally shapes phenotypic diversity in plant populations. Thus, gbM provides an epigenetic basis for adaptive evolution independent of genetic polymorphism.

Sign in / Sign up

Export Citation Format

Share Document