Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype

Cockram, James; Chiapparino, Elena; Taylor, Scott A.; Stamati, Konstantina; Donini, Paolo; Laurie, D. A.; O’Sullivan, Donal M.

doi:10.1007/s00122-007-0626-x

Cited by 114 publications

(159 citation statements)

References 26 publications

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“…Photoperiod sensitivity also plays an important role in the seasonal timing of grain production, but this usually marks differences in varieties sown in the same season but in different geographical regions. As one moves north, sensitivity to photoperiod results in yield losses in the Mediterranean-adapted winter wheat (Worland et al 1998;Cockram et al 2007a). In the south, flowering and heading under lengthening days allow plants to avoid the dry conditions of summer, but in the north, the lower temperatures and wetter summers mean that early flowering induced by lengthening days results in flowering at smaller size and with less productivity.…”

Section: Seasonal Cues Regulating Plant Phenologymentioning

confidence: 99%

Genetic and physiological bases for phenological responses to current and predicted climates

Wilczek

Burghardt

Cobb

et al. 2010

Phil. Trans. R. Soc. B

191

178

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We are now reaching the stage at which specific genetic factors with known physiological effects can be tied directly and quantitatively to variation in phenology. With such a mechanistic understanding, scientists can better predict phenological responses to novel seasonal climates. Using the widespread model species Arabidopsis thaliana, we explore how variation in different genetic pathways can be linked to phenology and life-history variation across geographical regions and seasons. We show that the expression of phenological traits including flowering depends critically on the growth season, and we outline an integrated life-history approach to phenology in which the timing of later life-history events can be contingent on the environmental cues regulating earlier life stages. As flowering time in many plants is determined by the integration of multiple environmentally sensitive gene pathways, the novel combinations of important seasonal cues in projected future climates will alter how phenology responds to variation in the flowering time gene network with important consequences for plant life history. We discuss how phenology models in other systems-both natural and agricultural-could employ a similar framework to explore the potential contribution of genetic variation to the physiological integration of cues determining phenology.

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Section: Seasonal Cues Regulating Plant Phenologymentioning

confidence: 99%

Genetic and physiological bases for phenological responses to current and predicted climates

Wilczek

Burghardt

Cobb

et al. 2010

Phil. Trans. R. Soc. B

191

178

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“…1E), suggesting that the presence of H3K27me3 at HvVRN1 chromatin is associated with repression of the gene before vernalization. In some varieties of wheat and barley, deletions within the first intron of VRN1 are associated with activation of VRN1 expression without vernalization treatment (23,(32)(33)(34). The barley variety Morex contains a large (5.2 kb) deletion in the first intron of HvVRN1 (i.e., regions 4 and 5 are absent) (see Fig.…”

Section: Repression Of Hvvrn1 Expression Before Vernalization Is Assomentioning

confidence: 99%

“…Levels of H3K4me3, a modification associated with epigenetic inheritance of active gene transcription (27)(28)(29)(30), and H3K27me3, a modification associated with long-term gene repression (28,30,31), were analyzed. The HvVRN1 gene has a large (10.8 kb) first intron containing regions associated with regulation of HvVRN1 expression (23,(32)(33)(34). We analyzed 6 regions across the 5Ј end of the HvVRN1 gene: the promoter (2 kb upstream of the translational start, region 1), exon 1 (region 2), and 4 sites along the length of the first intron (regions 3-6) (Fig.…”

mentioning

confidence: 99%

Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene

Oliver

Finnegan²,

Dennis³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

219

210

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Prolonged exposure to low temperatures (vernalization) accelerates the transition to reproductive growth in many plant species, including the model plant Arabidopsis thaliana and the economically important cereal crops, wheat and barley. Vernalizationinduced flowering is an epigenetic phenomenon. In Arabidopsis, stable down-regulation of FLOWERING LOCUS C (FLC) by vernalization is associated with changes in histone modifications at FLC chromatin. In cereals, the vernalization response is mediated by stable induction of the floral promoter VERNALIZATION1 (VRN1), which initiates reproductive development at the shoot apex. We show that in barley (Hordeum vulgare), repression of HvVRN1 before vernalization is associated with high levels of histone 3 lysine 27 trimethylation (H3K27me3) at HvVRN1 chromatin. Vernalization caused increased levels of histone 3 lysine 4 trimethylation (H3K4me3) and a loss of H3K27me3 at HvVRN1, suggesting that vernalization promotes an active chromatin state at VRN1. Levels of these histone modifications at 2 other floweringtime genes, VERNALIZATION2 and FLOWERING LOCUS T, were not altered by vernalization. Our study suggests that maintenance of an active chromatin state at VRN1 is likely to be the basis for epigenetic memory of vernalization in cereals. Thus, regulation of chromatin state is a feature of epigenetic memory of vernalization in Arabidopsis and the cereals; however, whereas vernalizationinduced flowering in Arabidopsis is mediated by epigenetic regulation of the floral repressor FLC, this phenomenon in cereals is mediated by epigenetic regulation of the floral activator, VRN1.epigenetic ͉ MADS ͉ intron ͉ barley ͉ chromatin P lants respond to seasonal cues, such as temperature and day-length, to ensure that flowering coincides with favorable conditions. Prolonged exposure to low winter temperatures (vernalization) accelerates the progression from vegetative to reproductive growth in many plant species, including the temperate cereals (such as wheat and barley) and dicot species (such as Arabidopsis) (1-3). In both these lineages, plants retain a ''memory'' of the prolonged cold of winter, which stimulates flowering when days lengthen during spring (1-3). The memory of cold is then reset in the next sexual generation to ensure progeny are competent to respond to vernalization (1-3).In Arabidopsis, the vernalization response is mediated by epigenetic regulation of the floral repressor, FLOWERING LOCUS C (FLC), which encodes a MADS-box transcription factor that represses genes involved in floral initiation, including SUPPRESSOR OF CONSTANS 1 and FLOWERING LOCUS T (FT) (1,(4)(5)(6). FLC is expressed before vernalization and delays flowering, but its expression is repressed by vernalization (1, 4). FLC remains repressed when plants are subsequently exposed to warm temperatures, allowing activation of FT, which promotes flowering (1, 4). The stable down-regulation of FLC by vernalization is associated with an increase in the levels of repressive histone modifications at FLC chromat...

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“…Sequences in the first intron might also regulate processing of the VRN1 transcript 15 . Several active alleles of VRN1 with deletions or insertions in the first intron have been identified in barley [16][17][18][19] . These reduce the vernalization requirement to different extents and have been used to breed varieties that flower without vernalization, which are grown where winters are warm or where crops are sown in spring 19,20 .…”

mentioning

confidence: 99%

Direct links between the vernalization response and other key traits of cereal crops

et al. 2015

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Transcription of the VERNALIZATION1 gene (VRN1) is induced by prolonged cold (vernalization) to trigger flowering of cereal crops, such as wheat and barley. VRN1 encodes a MADS box transcription factor that promotes flowering by regulating the expression of other genes. Here we use transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to identify direct targets of VRN1. Over 500 genomic regions were identified as potential VRN1-binding targets by ChIP-seq. VRN1 binds the promoter of FLOWERING LOCUS T-like 1, a promoter of flowering in vernalized plants. VRN1 also targets VERNALIZATION2 and ODDSOC2, repressors of flowering that are downregulated in vernalized plants. RNA-seq identified additional VRN1 targets that might play roles in triggering flowering. Other targets of VRN1 include genes that play central roles in low-temperature-induced freezing tolerance, spike architecture and hormone metabolism. This provides evidence for direct regulatory links between the vernalization response pathway and other important traits in cereal crops.

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Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype

Cited by 114 publications

References 26 publications

Genetic and physiological bases for phenological responses to current and predicted climates

Genetic and physiological bases for phenological responses to current and predicted climates

Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene

Direct links between the vernalization response and other key traits of cereal crops

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