Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

/pdf/the-tomato-genome-sequence-provides-insights-into-fleshy-7a55qpnrdm.pdf

The tomato genome sequence provides insights into fleshy fruit evolution

In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.

/pdf/ft-protein-movement-contributes-to-long-distance-signaling-bf6esgljfo.pdf

FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis

Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.

http://science.sciencemag.org/content/sci/309/5735/741.full.pdf

Cytokinin Oxidase Regulates Rice Grain Production

A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1, was identified by means of a map-based cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of ∼12 kb as a candidate for Hd1. Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolog of CONSTANS in Arabidopsis. Sequencing analysis revealed a 43-bp deletion in the first exon of the photoperiod sensitivity 1 (se1) mutant HS66 and a 433-bp insertion in the intron in mutant HS110. Se1 is allelic to the Hd1 QTL, as determined by analysis of two se1 mutants, HS66 and HS110. Genetic complementation analysis proved the function of the candidate gene. The amount of Hd1 mRNA was not greatly affected by a change in length of the photoperiod. We suggest that Hd1 functions in the promotion of heading under short-day conditions and in inhibition under long-day conditions.

/pdf/hd1-a-major-photoperiod-sensitivity-quantitative-trait-locus-5e0p7kbbkp.pdf

Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS

FLOWERING LOCUS T (FT) is a conserved promoter of flowering that acts downstream of various regulatory pathways, including one that mediates photoperiodic induction through CONSTANS (CO), and is expressed in the vasculature of cotyledons and leaves. A bZIP transcription factor, FD, preferentially expressed in the shoot apex is required for FT to promote flowering. FD and FT are interdependent partners through protein interaction and act at the shoot apex to promote floral transition and to initiate floral development through transcriptional activation of a floral meristem identity gene, APETALA1 (AP1). FT may represent a long-distance signal in flowering.

http://science.sciencemag.org/content/sci/309/5737/1052.full.pdf

FD, a bZIP Protein Mediating Signals from the Floral Pathway Integrator FT at the Shoot Apex

Flowering in Arabidopsis is promoted via several interacting pathways A photoperiod-dependent pathway relays signals from photoreceptors to a transcription factor gene, CONSTANS (CO), which activates downstream meristem identity genes such as LEAFY (LFY) FT, together with LFY, promotes flowering and is positively regulated by CO Loss of FT causes delay in flowering, whereas overexpression of FT results in precocious flowering independent of CO or photoperiod FT acts in part downstream of CO and mediates signals for flowering in an antagonistic manner with its homologous gene, TERMINAL FLOWER1 (TFL1)

https://science.sciencemag.org/content/sci/286/5446/1960.full.pdf

A pair of related genes with antagonistic roles in mediating flowering signals.

;Heading date 3a (Hd3a) has been detected as a heading-date-related quantitative trait locus in a cross between rice cultivars Nipponbare and Kasalath. A previous study revealed that the Kasalath allele of Hd3a promotes heading under short-day (SD) conditions. High-resolution linkage mapping located the Hd3a locus in a 20-kb genomic region. In this region, we found a candidate gene that shows high similarity to the FLOWERING LOCUS T (FT) gene, which promotes flowering in Arabidopsis. Introduction of the gene caused an early-heading phenotype in rice. The transcript levels of Hd3a were increased under SD conditions. The rice Heading date 1 (Hd1) gene, a homolog of CONSTANS (CO), has been shown to promote heading under SD conditions. By expression analysis, we showed that the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a promotes heading under the control of Hd1. These results indicate that Hd3a encodes a protein closely related to Arabidopsis FT and that the function and regulatory relationship with Hd1 and CO, respectively, of Hd3a and FT are conserved between rice (an SD plant) and Arabidopsis (a long-day plant).

/pdf/hd3a-a-rice-ortholog-of-the-arabidopsis-ft-gene-promotes-3d9iwvq5ka.pdf

Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions.

In Arabidopsis, several genetic pathways controlling the floral transition (flowering) are integrated at the transcriptional regulation of FT, LFY and SOC1. TSF is the closest homolog of FT in Arabidopsis. TSF expression was induced rapidly upon activation of CONSTANS (CO). The mRNA levels of TSF and FT showed similar patterns of diurnal oscillation and response to photoperiods: an evening peak, higher levels in long day (LD) than in short day (SD) conditions, and immediate up-regulation upon day-length extension. These observations suggest that TSF is a direct regulatory target of CO. tsf mutation delayed flowering in SD conditions and enhanced the phenotype of ft in both LD and SD conditions. TSF and FT also shared similar modes of regulation by FLC, an integrator of autonomous and vernalization pathways, and other factors such as EBS and PHYB. Consistently, TSF overexpression caused a precocious flowering phenotype independent of photoperiods or CO, or FLC. These observations suggest that TSF is a new member of the floral pathway integrators and promotes flowering largely redundantly with FT but makes a distinct contribution in SD conditions. TSF and FT seem to act independently of each other and of LFY, and partially upstream of SOC1. Interestingly, the expression patterns of TSF and FT in seedlings did not overlap, although both were expressed in the phloem tissues. Our work revealed additional complexity and spatial aspects of the regulatory network at the pathway integration level. We propose that the phloem is the site where multiple regulatory pathways are integrated at the transcriptional regulation of FT and TSF.

TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT.

Plants do not bloom randomly--but how do they know when and where to make flowers? Here, we review molecular mechanisms that integrate spatial and temporal information in day-length-dependent flowering. Primarily through genetic analyses in two species, Arabidopsis thaliana and rice, we today understand the essentials of two central issues in plant biology: how the appropriate photoperiod generates an inductive stimulus based on an external coincidence mechanism, and the nature of the mobile flowering signal, florigen, which relays photoperiod-dependent information from the leaf to the growing tip of the plant, the shoot apex.

/pdf/move-on-up-it-s-time-for-change-mobile-signals-controlling-25hrzi96wx.pdf

Yasushi Kobayashi

Papers

FD, a bZIP Protein Mediating Signals from the Floral Pathway Integrator FT at the Shoot Apex

A pair of related genes with antagonistic roles in mediating flowering signals.

Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions.

TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT.

Move on up, it’s time for change—mobile signals controlling photoperiod-dependent flowering