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Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE232430 | GEO | 2024/07/22

REPOSITORIES: GEO

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Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (RNA-Seq)

Project description:Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. What’s more, important core regulatory elements and corresponding transcription factors were discovered, and the complex regulatory network of wheat vernalization was analyzed.

2024-07-22 | GSE232428 | GEO

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ChIP-Seq)

2024-07-22 | GSE232426 | GEO

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq)

2024-07-22 | GSE232424 | GEO

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat

Project description:Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat

| PRJNA971967 | ENA

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq)

Project description:Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq)

| PRJNA971968 | ENA

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (RNA-Seq)

Project description:Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (RNA-Seq)

| PRJNA971969 | ENA

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ChIP-Seq)

Project description:Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ChIP-Seq)

| PRJNA971970 | ENA

Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat.

Project description:BACKGROUND: Certain temperate species require prolonged exposure to low temperature to initiate transition from vegetative growth to flowering, a process known as vernalization. In wheat, winter cultivars require vernalization to initiate flowering, making vernalization requirement a trait of key importance in wheat agronomy. The genetic bases of vernalization response have been largely studied in wheat, leading to the characterization of a regulation pathway that involves the key gene VERNALIZATION1 (VRN1). While previous studies in wheat and barley have revealed the functional role of histone modification in setting VRN1 expression, other mechanisms might also be involved. Here, we were interested in determining whether the cold-induced expression of the wheat VRN-A1 gene is associated with a change in DNA methylation. RESULTS: We provide the first DNA methylation analysis of the VRN-A1 gene, and describe the existence of methylation at CG but also at non CG sites. While CG sites show a bell-shape profile typical of gene-body methylation, non CG methylation is restricted to the large (8.5 kb) intron 1, in a region harboring fragments of transposable elements (TEs). Interestingly, cold induces a site-specific hypermethylation at these non CG sites. This increase in DNA methylation is transmitted through mitosis, and is reset to its original level after sexual reproduction. CONCLUSIONS: These results demonstrate that VRN-A1 has a particular DNA methylation pattern, exhibiting rapid shift within the life cycle of a winter wheat plant following exposure to particular environmental conditions. The finding that this shift occurs at non CG sites in a TE-rich region opens interesting questions onto the possible consequences of this type of methylation in gene expression.

| S-EPMC3890506 | biostudies-literature

Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat.

Project description:Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in 'Triple Dirk C' has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence, whereas the derived 'Jagger' allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P?<?0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 days difference) and after 3-weeks of vernalization (11 days difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 days, P?<?0.001) and one experiment under field conditions (21 d, P?<?0.0001). The RIP3 polymorphisms can be used by wheat breeders to develop winter wheat varieties adapted to regions with different duration or intensity of the cold season.

| S-EPMC6153499 | biostudies-literature

Vernalization requirement duration in winter wheat is controlled by TaVRN-A1 at the protein level.

Project description:Winter wheat requires a period of low temperatures to accelerate flowering (vernalization). This requirement could make winter wheat more vulnerable to elevated global temperature via insufficient vernalization. All known vernalization genes are cloned according to qualitative variation in vernalization requirement between spring and winter wheat, but the genes controlling quantitative variation for more or less vernalization requirement among winter wheat cultivars remain unknown. We report here that the gene for the vernalization requirement duration in winter wheat was cloned using a BC(1)F(2:3) population that segregated in a 3:1 ratio of early-flowering plants and late-flowering plants after vernalization for 3 weeks. The positional cloning of the gene for vernalization requirement duration demonstrated that this trait is controlled by TaVRN-A1 at the protein level. The Ala(180) in vrn-A1a, encoded by the dominant allele for 3-week vernalization, was mutated to Val(180) in vrn-A1b, encoded by the recessive allele for 6-week vernalization. Further studies with in vitro protein pull-down assays and immunoprecipitation analyses indicated that the mutated Val(180) in vrn-A1b protein decreased the ability to bind with TaHOX1 (the first homeobox protein in Triticum aestivum). The direct binding of TaVRN-A1 and TaHOX1 proteins was confirmed in the nucleus of living plant cells by bimolecular fluorescence complementation (BiFC) analyses. The TaHOX1 gene was found to be upregulated by low temperatures, and to have a significant genetic effect on heading date, suggesting that TaHOX1 functions in the flowering pathway in winter wheat.

| S-EPMC4282524 | biostudies-literature

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