Aa<i>TFL1</i>Confers an Age-Dependent Response to Vernalization in Perennial<i>Arabis alpina</i>

Wang, Renhou; Albani, Maria C.; Vincent, Coral; Bergonzi, Sara; Luan, Ming; Bai, Yan; Kiefer, Christiane; Castillo, Rosa Menéndez; Coupland, George

doi:10.1105/tpc.111.083451

Cited by 125 publications

(146 citation statements)

References 51 publications

(79 reference statements)

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“…Furthermore, annual and perennial species in the Brassicaceae also differ in the age at which they acquire competence to flower in response to vernalization (Wang et al . 2011; Bergonzi et al . 2013; Zhou et al .…”

Section: Discussionmentioning

confidence: 99%

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Divergence of annual and perennial species in the Brassicaceae and the contribution of cis‐acting variation at FLC orthologues

Kiefer

Severing

Karl³

et al. 2017

Molecular Ecology

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Variation in life history contributes to reproductive success in different environments. Divergence of annual and perennial angiosperm species is an extreme example that has occurred frequently. Perennials survive for several years and restrict the duration of reproduction by cycling between vegetative growth and flowering, whereas annuals live for 1 year and flower once. We used the tribe Arabideae (Brassicaceae) to study the divergence of seasonal flowering behaviour among annual and perennial species. In perennial Brassicaceae, orthologues of FLOWERING LOCUS C (FLC), a floral inhibitor in Arabidopsis thaliana, are repressed by winter cold and reactivated in spring conferring seasonal flowering patterns, whereas in annuals, they are stably repressed by cold. We isolated FLC orthologues from three annual and two perennial Arabis species and found that the duplicated structure of the A. alpina locus is not required for perenniality. The expression patterns of the genes differed between annuals and perennials, as observed among Arabidopsis species, suggesting a broad relevance of these patterns within the Brassicaceae. Also analysis of plants derived from an interspecies cross of A. alpina and annual A. montbretiana demonstrated that cis‐regulatory changes in FLC orthologues contribute to their different transcriptional patterns. Sequence comparisons of FLC orthologues from annuals and perennials in the tribes Arabideae and Camelineae identified two regulatory regions in the first intron whose sequence variation correlates with divergence of the annual and perennial expression patterns. Thus, we propose that related cis‐acting changes in FLC orthologues occur independently in different tribes of the Brassicaceae during life history evolution.

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Section: Discussionmentioning

confidence: 99%

“…These mechanisms of flowering control have been studied in several perennial species and compared to that of the well‐established annual model species Arabidopsis thaliana (Albani & Coupland 2010; Wang et al . 2011; Andres & Coupland 2012; Iwata et al . 2012; Koskela et al .…”

Section: Introductionmentioning

confidence: 99%

Divergence of annual and perennial species in the Brassicaceae and the contribution of cis‐acting variation at FLC orthologues

Kiefer

Severing

Karl³

et al. 2017

Molecular Ecology

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“…Our results on FvTFL1 and earlier findings that seasonal changes in the expression of two Populus FTlike genes regulate the perennial growth cycle in Populus (Hsu et al, 2011) highlight the importance of CETS proteins in the control of perennialism. Also, in A. alpina, TFL1 contributes to perennialism by regulating the age-dependent sensitivity of meristems to vernalization; but transient silencing of the FLC ortholog, PEP1, by vernalization has a major role in the cycling between vegetative and generative phases in this species (Wang et al, 2009(Wang et al, , 2011.…”

Section: Regulation Of Fvtfl1 Mrna Expression Controls Photoperiodic mentioning

confidence: 99%

“…and F. vesca (Brown and Wareing, 1965;Iwata et al, 2012). Furthermore, TFL1 homologs have been shown to repress flowering and to control the length of the juvenile phase in apple (Malus domestica), Populus, and A. alpina (Kotoda et al, 2006;Mohamed et al, 2010;Wang et al, 2011).…”

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confidence: 99%

Mutation inTERMINAL FLOWER1Reverses the Photoperiodic Requirement for Flowering in the Wild StrawberryFragaria vesca

et al. 2012

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Photoperiodic flowering has been extensively studied in the annual short-day and long-day plants rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), whereas less is known about the control of flowering in perennials. In the perennial wild strawberry, Fragaria vesca (Rosaceae), short-day and perpetual flowering long-day accessions occur. Genetic analyses showed that differences in their flowering responses are caused by a single gene, SEASONAL FLOWERING LOCUS, which may encode the F. vesca homolog of TERMINAL FLOWER1 (FvTFL1). We show through high-resolution mapping and transgenic approaches that FvTFL1 is the basis of this change in flowering behavior and demonstrate that FvTFL1 acts as a photoperiodically regulated repressor. In short-day F. vesca, long photoperiods activate FvTFL1 mRNA expression and short days suppress it, promoting flower induction. These seasonal cycles in FvTFL1 mRNA level confer seasonal cycling of vegetative and reproductive development. Mutations in FvTFL1 prevent long-day suppression of flowering, and the early flowering that then occurs under long days is dependent on the F. vesca homolog of FLOWERING LOCUS T. This photoperiodic response mechanism differs from those described in model annual plants. We suggest that this mechanism controls flowering within the perennial growth cycle in F. vesca and demonstrate that a change in a single gene reverses the photoperiodic requirements for flowering.

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“…Six of the pep1-1 mutations overlapped with the annotation of genes. Among those, we identified the known causal mutation, aligned to a splice donor site of the PEP1 ortholog FLC 27,31 (Fig. 2c).…”

Section: Fde1 Is the Ortholog Of A Thaliana Ap2mentioning

confidence: 99%

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

et al. 2013

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Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F 2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M 3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.Forward genetic screens have been of fundamental importance in elucidating biological mechanisms in model species 1 . Their success, however, has relied on the feasibility of mutant gene isolation. Identification of causal mutations typically begins with genetic mapping, followed by candidate gene sequencing and complementation studies using transformation. Advances in DNA sequencing technologies have tremendously accelerated genetic mapping by combining bulk segregant analysis, that is, pooling recombinant genomes, with whole-genome sequencing, usually referred to as mapping by sequencing 2,3 . This approach is now becoming standard for mutation mapping and identification in many model species 3-12 and has even been applied to decipher quantitative traits with complex genetic architectures 13,14 . Recently, mutagen-induced changes have been used as novel markers, allowing mapping of mutations using isogenic mapping populations 10,15 . Nevertheless, all mapping-by-sequencing methods rely on resequencing, a method for whole-genome reconstruction based on aligning sequences to a reference sequence. Therefore, this requirement restricts the application of the technique to species for which such a reference genome sequence is available.Many reference-sequence assembly projects are currently in progress, including ones for most of the major crop species and breeding animals. However, even with an existing reference sequence, extending mapping-by-sequencing methods beyond the sequenced reference accessions has proved technically challenging. Mutant alleles of genes that are not present in the reference sequence cannot be identified within resequencing data alone. In particular, fast-evolving genes, such as those involved in disease resistance, might not always be represented in the reference sequence 16,17 .Alternative solutions for mapping-by-sequencing in species without reference sequences have been proposed, such ...

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AaTFL1Confers an Age-Dependent Response to Vernalization in PerennialArabis alpina

Cited by 125 publications

References 51 publications

Divergence of annual and perennial species in the Brassicaceae and the contribution of cis‐acting variation at FLC orthologues

Divergence of annual and perennial species in the Brassicaceae and the contribution of cis‐acting variation at FLC orthologues

Mutation inTERMINAL FLOWER1Reverses the Photoperiodic Requirement for Flowering in the Wild StrawberryFragaria vesca

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

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