Altered regulation of TERMINAL FLOWER 1 causes the unique vernalisation response in an arctic woodland strawberry accession

Acclimation of circadian rhythms in woodland strawberries (Fragaria vesca L.) to Arctic and mid-latitude photoperiods

BACKGROUND

Though many abiotic factors are constantly changing, the photoperiod is a predictable factor that enables plants to time many physiological responses. This timing is regulated by the circadian clock, yet little is known about how the clock adapts to the differences in photoperiod between mid-latitudes and high latitudes. The primary objective of this study was to compare how clock gene expression is modified in four woodland strawberry (Fragaria vesca L.) accessions originating from two different populations in Italy (IT1: Tenno, Italy, 45°N, IT4: Salorno, Italy, 46°N) and two in Northern Norway (NOR2: Alta, Norway, 69°N, NOR13: Indre Nordnes, Norway 69°N) when grown under simulated daylength conditions of an Arctic or mid-latitude photoperiod. The second objective was to investigate whether population origin or the difference in photoperiod influenced phytohormone accumulation.

RESULTS

The Arctic photoperiod induced lower expression in IT4 and NOR13 for six clock genes (FvLHY, FvRVE8, FvPRR9, FvPRR7, FvPRR5, and FvLUX), in IT1 for three genes (FvLHY, FvPRR9, and FvPRR5) and in NOR2 for one gene (FvPRR9). Free-running rhythms for FvLHY in IT1 and IT4 were higher after the Arctic photoperiod, while the free-running rhythm for FvLUX in IT4 was higher after the mid-latitude photoperiod. IT1 showed significantly higher expression of FvLHY and FvPRR9 than all other accessions, as well as significantly higher expression of the circadian regulated phytohormone, abscisic acid (ABA), but low levels of salicylic acid (SA). NOR13 had significantly higher expression of FvRVE8, FvTOC1, and FvLUX than all other accessions. NOR2 had extremely low levels of auxin (IAA) and high levels of the jasmonate catabolite, hydroxyjasmonic acid (OH-JA).

CONCLUSIONS

Our study shows that circadian rhythms in Fragaria vesca are driven by both the experienced photoperiod and genetic factors, while phytohormone levels are primarily determined by specific accessions' genetic factors rather than the experienced photoperiod.

Diversity of woodland strawberry inflorescences arises from heterochrony regulated by TERMINAL FLOWER 1 and FLOWERING LOCUS T

A vast variety of inflorescence architectures have evolved in angiosperms. Here, we analyze the diversity and development of the woodland strawberry (Fragaria vesca) inflorescence. Contrary to historical classifications, we show that it is a closed thyrse: a compound inflorescence with determinate primary monopodial axis and lateral sympodial branches, thus combining features of racemes and cymes. We demonstrate that this architecture is generated by 2 types of inflorescence meristems differing in their geometry. We further show that woodland strawberry homologs of TERMINAL FLOWER 1 (FvTFL1) and FLOWERING LOCUS T (FvFT1) regulate the development of both the racemose and cymose components of the thyrse. Loss of functional FvTFL1 reduces the number of lateral branches of the main axis and iterations in the lateral branches but does not affect their cymose pattern. These changes can be enhanced or compensated by altering FvFT1 expression. We complement our experimental findings with a computational model that captures inflorescence development using a small set of rules. The model highlights the distinct regulation of the fate of the primary and higher-order meristems, and explains the phenotypic diversity among inflorescences in terms of heterochrony resulting from the opposite action of FvTFL1 and FvFT1 within the thyrse framework. Our results represent a detailed analysis of thyrse architecture development at the meristematic and molecular levels.

TEMPRANILLO homologs in apple regulate flowering time in the woodland strawberry Fragaria vesca

The long juvenile period of fruit trees makes their breeding costly and time-consuming. Therefore, flowering time engineering and shortening the juvenile phase have become a breeding priority for the genetic improvement of fruit tree crops. Many economically valuable fruit trees belong to the Rosaceae family including apples and strawberries. TEMPRANILLO (TEM) acts as a key player in flowering time control through inhibiting FT function. Two genes with high sequence similarity with the Arabidopsis TEM genes were isolated from apple (Malus domestica). Due to the complexity of carrying out functional studies in apple, we characterized their function in woodland strawberry as well as their expression in apple. The expression of MdTEM genes in apple tissues from juvenile plants was dramatically higher than that in the tissues from adult trees. In woodland strawberry, the overexpression of MdTEM genes down-regulated FvFT1, FvGA3OX1, and FvGA3OX2 genes in strawberry. The MdTEM-overexpressing lines exhibited delayed flowering, in terms of days to flowering and the number of leaves at flowering. While, RNAi-mediated silencing of TEM resulted in five days earlier flowering, with a lower number of leaves, a higher trichome density, and in some cases, caused in vitro flowering. According to these results and in silico analyses, it can be concluded that MdTEM1 and MdTEM2 can be considered as orthologs of FvTEM and probably AtTEM genes, which play an important role in regulating the juvenile phase and flowering time through regulating FT and GA biosynthetic pathway.

Expression Profiling of Four Mango FT/TFL1-Encoding Genes under Different Fruit Load Conditions, and Their Involvement in Flowering Regulation

Plant flowering is antagonistically modulated by similar FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1) proteins. In mango (Mangifera indica L.), flowering is induced by cold temperatures, unless the tree is juvenile or the adult tree had a high fruit load (HFL) in the summer. Here, we studied the effects of juvenility and fruit load on the expression of four MiFT/TFL1 genes cloned from the mango ‘Shelly’ cultivar. Ectopic expression of MiFT1 in Arabidopsis resulted in early flowering, whereas over-expression of MiFT2 and the two cloned MiTFL1 genes repressed flowering. Moreover, juvenility was positively correlated with higher transcript levels of MiFT2 and both MiTFL1s. In trees with a low fruit load, leaf MiFT1 expression increased in winter, whereas HFL delayed its upregulation. MiFT2 expression was upregulated in both leaves and buds under both fruit load conditions. Downregulation of both MITFL1s in buds was associated with a decrease in regional temperatures under both conditions; nevertheless, HFL delayed the decrease in their accumulation. Our results suggest that cold temperature has opposite effects on the expression of MiFT1 and the MiTFL1s, thereby inducing flowering, whereas HFL represses flowering by both suppressing MiFT1 upregulation and delaying MiTFL1s downregulation. The apparent flowering-inhibitory functions of MiFT2 are discussed.

Role of FaSOC1 and FaCO in the seasonal control of reproductive and vegetative development in the perennial crop Fragaria × ananassa

The diploid woodland strawberry (F. vesca) represents an important model for the genus Fragaria. Significant advances in the understanding of the molecular mechanisms regulating seasonal alternance of flower induction and vegetative reproduction has been made in this species. However, this research area has received little attention on the cultivated octoploid strawberry (F. × ananassa) despite its enormous agronomical and economic importance. To advance in the characterization of this intricated molecular network, expression analysis of key flowering time genes was performed both in short and long days and in cultivars with seasonal and perpetual flowering. Analysis of overexpression of FaCO and FaSOC1 in the seasonal flowering 'Camarosa' allowed functional validation of a number of responses already observed in F. vesca while uncovered differences related to the regulation of FaFTs expression and gibberellins (GAs) biosynthesis. While FvCO has been shown to promote flowering and inhibit runner development in the perpetual flowering H4 accession of F. vesca, our study showed that FaCO responds to LD photoperiods as in F. vesca but delayed flowering to some extent, possibly by induction of the strong FaTFL1 repressor in crowns. A contrasting effect on runnering was observed in FaCO transgenic plants, some lines showing reduced runner number whereas in others runnering was slightly accelerated. We demonstrate that the role of the MADS-box transcription factor FaSOC1 as a strong repressor of flowering and promoter of vegetative growth is conserved in woodland and cultivated strawberry. Our study further indicates an important role of FaSOC1 in the photoperiodic repression of FLOWERING LOCUS T (FT) genes FaFT2 and FaFT3 while FaTFL1 upregulation was less prominent than that observed in F. vesca. In our experimental conditions, FaSOC1 promotion of vegetative growth do not require induction of GA biosynthesis, despite GA biosynthesis genes showed a marked photoperiodic upregulation in response to long days, supporting GA requirement for the promotion of vegetative growth. Our results also provided insights into additional factors, such as FaTEM, associated with the vegetative developmental phase that deserve further characterization in the future.

Time-Course Transcriptomic Profiling of Floral Induction in Cultivated Strawberry

The initiation and quality of flowering directly affect the time to market and economic benefit of cultivated strawberries, but the underlying mechanisms of these processes are largely unknown. To investigate the gene activity during the key period of floral induction in strawberries, time-course transcriptome analysis was performed on the shoot apex of the strawberry cultivar ‘Benihoppe.’ A total of 7177 differentially expressed genes (DEGs) were identified through pairwise comparisons. These DEGs were grouped into four clusters with dynamic expression patterns. By analyzing the key genes in the potential flowering pathways and the development of the leaf and flower, at least 73 DEGs that may be involved in the regulatory network of floral induction in strawberries were identified, some of which belong to the NAC, MYB, MADS, and SEB families. A variety of eight hormone signaling pathway genes that might play important roles in floral induction were analyzed. In particular, the gene encoding DELLA, a key inhibitor of the gibberellin signaling pathway, was found to be significantly differentially expressed during the floral induction. Furthermore, the differential expression of some important candidate genes, such as TFL1, SOC1, and GAI-like, was further verified by qRT-PCR. Therefore, we used this time-course transcriptome data for a preliminary exploration of the regulatory network of floral induction and to provide potential candidate genes for future studies of flowering in strawberries.

Natural Variation in the Control of Flowering and Shoot Architecture in Diploid Fragaria Species

In perennial fruit and berry crops of the Rosaceae family, flower initiation occurs in late summer or autumn after downregulation of a strong repressor TERMINAL FLOWER1 (TFL1), and flowering and fruiting takes place the following growing season. Rosaceous fruit trees typically form two types of axillary shoots, short flower-bearing shoots called spurs and long shoots that are, respectively, analogous to branch crowns and stolons in strawberry. However, regulation of flowering and shoot architecture differs between species, and environmental and endogenous controlling mechanisms have just started to emerge. In woodland strawberry (Fragaria vesca L.), long days maintain vegetative meristems and promote stolon formation by activating TFL1 and GIBBERELLIN 20-OXIDASE4 (GA20ox4), respectively, while silencing of these factors by short days and cool temperatures induces flowering and branch crown formation. We characterized flowering responses of 14 accessions of seven diploid Fragaria species native to diverse habitats in the northern hemisphere and selected two species with contrasting environmental responses, Fragaria bucharica Losinsk. and Fragaria nilgerrensis Schlecht. ex J. Gay for detailed studies together with Fragaria vesca. Similar to F. vesca, short days at 18°C promoted flowering in F. bucharica, and the species was induced to flower regardless of photoperiod at 11°C after silencing of TFL1. F. nilgerrensis maintained higher TFL1 expression level and likely required cooler temperatures or longer exposure to inductive treatments to flower. We also found that high expression of GA20ox4 was associated with stolon formation in all three species, and its downregulation by short days and cool temperature coincided with branch crown formation in F. vesca and F. nilgerrensis, although the latter did not flower. F. bucharica, in contrast, rarely formed branch crowns, regardless of flowering or GA20ox4 expression level. Our findings highlighted diploid Fragaria species as rich sources of genetic variation controlling flowering and plant architecture, with potential applications in breeding of Rosaceous crops.

Axillary Bud Fate Shapes Plant Architecture in Horticultural Crops

Above-ground plant architecture is dictated to a large extent by the fates and growth rates of aerial plant meristems. Shoot apical meristem gives rise to the fundamental plant form by generating new leaves. However, the fates of axillary meristems located in leaf axils have a great influence on plant architecture and affect the harvest index, yield potential and cultural practices. Improving plant architecture by breeding facilitates denser plantations, better resource use efficiency and even mechanical harvesting. Knowledge of the genetic mechanisms regulating plant architecture is needed for precision breeding, especially for determining feasible breeding targets. Fortunately, research in many crop species has demonstrated that a relatively small number of genes has a large effect on axillary meristem fates. In this review, we select a number of important horticultural and agricultural plant species as examples of how changes in plant architecture affect the cultivation practices of the species. We focus specifically on the determination of the axillary meristem fate and review how plant architecture may change even drastically because of altered axillary meristem fate. We also explain what is known about the genetic and environmental control of plant architecture in these species, and how further changes in plant architectural traits could benefit the horticultural sector.

Woodland strawberry axillary bud fate is dictated by a crosstalk of environmental and endogenous factors

Plant architecture is defined by fates and positions of meristematic tissues and has direct consequences on yield potential and environmental adaptation of the plant. In strawberries (Fragaria vesca L. and F. × ananassa Duch.), shoot apical meristems can remain vegetative or differentiate into a terminal inflorescence meristem. Strawberry axillary buds (AXBs) are located in leaf axils and can either remain dormant or follow one of the two possible developmental fates. AXBs can either develop into stolons needed for clonal reproduction or into branch crowns (BCs) that can bear their own terminal inflorescences under favorable conditions. Although AXB fate has direct consequences on yield potential and vegetative propagation of strawberries, the regulation of AXB fate has so far remained obscure. We subjected a number of woodland strawberry (F. vesca L.) natural accessions and transgenic genotypes to different environmental conditions and growth regulator treatments to demonstrate that strawberry AXB fate is regulated either by environmental or endogenous factors, depending on the AXB position on the plant. We confirm that the F. vesca GIBBERELLIN20-oxidase4 (FvGA20ox4) gene is indispensable for stolon development and under tight environmental regulation. Moreover, our data show that apical dominance inhibits the outgrowth of the youngest AXB as BCs, although the effect of apical dominance can be overrun by the activity of FvGA20ox4. Finally, we demonstrate that the FvGA20ox4 is photoperiodically regulated via FvSOC1 (F. vesca SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1) at 18°C, but at higher temperature of 22°C an unidentified FvSOC1-independent pathway promotes stolon development.

The FveFT2 florigen/FveTFL1 antiflorigen balance is critical for the control of seasonal flowering in strawberry while FveFT3 modulates axillary meristem fate and yield

Plant architecture is central in determining crop yield. In the short-day species strawberry, a crop vegetatively propagated by daughter-plants produced by stolons, fruit yield is further dependent on the trade-off between sexual reproduction (fruits) and asexual reproduction (daughter-plants). Both are largely dependent on meristem identity, which establishes the development of branches, stolons and inflorescences. Floral initiation and plant architecture are modulated by the balance between two related proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). We explored in woodland strawberry the role of the uncharacterised FveFT2 and FveFT3 genes and of the floral repressor FveTFL1 through gene expression analyses, grafting and genetic transformation (overexpression and gene editing). We demonstrate the unusual properties of these genes. FveFT2 is a nonphotoperiodic florigen permitting short-day (SD) flowering and FveTFL1 is the long-hypothesised long-day systemic antiflorigen that contributes, together with FveFT2, to the photoperiodic regulation of flowering. We additionally show that FveFT3 is not a florigen but promotes plant branching when overexpressed, that is likely to be through changing axillary meristem fate, therefore resulting in a 3.5-fold increase in fruit yield at the expense of stolons. We show that our findings can be translated into improvement of cultivated strawberry in which FveFT2 overexpression significantly accelerates flowering.

Applying the Solanaceae Strategies to Strawberry Crop Improvement

Strawberry is a fruit crop species of major horticultural importance, for which fruit quality and the control of flowering (for fruit yield), runnering (for vegetative propagation), and the trade-off between the two are main breeding targets. The octoploid cultivated strawberry has a limited genetic basis. This raises the question of how to identify important gene targets and successfully exploit them for strawberry improvement. In this Opinion article we propose to apply to woodland strawberry, a wild diploid species displaying wide diversity, the strategies successfully employed in recent years for the identification of genetic variations underlying fruit quality and fruit yield traits in solanaceous crops (tomato, potato). Next we propose to use gene editing technologies to translate the findings to cultivated strawberry.

EjTFL1 Genes Promote Growth but Inhibit Flower Bud Differentiation in Loquat

TERMINAL FLOWER1 (TFL1), a key factor belonging to the phosphatidyl ethanolamine-binding protein (PEBP) family, controls flowering time and inflorescence architecture in some plants. However, the role of TFL1 in loquat remains unknown. In this study, we cloned two TFL1-like genes (EjTFL1-1 and EjTFL1-2) with conserved deduced amino acid sequences from cultivated loquat (Eriobotrya japonica Lindl.). First, we determined that flower bud differentiation occurs at the end of June and early July, and then comprehensively analyzed the temporal and spatial expression patterns of these EjTFL1s during loquat growth and development. We observed the contrasting expression trends for EjTFL1s and EjAP1s (APETALA 1) in shoot apices, and EjTFL1s were mainly expressed in young tissues. In addition, short-day and exogenous GA₃ treatments promoted the expression of EjTFL1s, and no flower bud differentiation was observed after these treatments in loquat. Moreover, EjTFL1s were localized to the cytoplasm and nucleus, and both interacted with another flowering transcription factor, EjFD, in the nucleus, and EjTFL1s-EjFD complex significantly repressed the promoter activity of EjAP1-1. The two EjTFL1s were overexpressed in wild-type Arabidopsis thaliana Col-0, which delayed flowering time, promoted stem elongation, increased the number of branches, and also affected flower and silique phenotypes. In conclusion, our results suggested that EjTFL1-1 and EjTFL1-2 do not show the same pattern of expression whereas both are able of inhibiting flower bud differentiation and promoting vegetative growth in loquat by integrating GA₃ and photoperiod signals. These findings provide useful clues for analyzing the flowering regulatory network of loquat and provide meaningful references for flowering regulation research of other woody fruit trees.

Turning Meristems into Fortresses

TERMINAL FLOWER1 (TFL1) was named from knockout Arabidopsis thaliana mutants in which the inflorescence abnormally terminates into a flower. In wild type plants, the expression of TFL1 in the center of the inflorescence meristem represses the flower meristem identity genes LEAFY (LFY) and APETALA1 (AP1) to maintain indeterminacy. LFY and AP1 are activated by flowering signals that antagonize TFL1. Its characterization in numerous species revealed that the TFL1-mediated regulation of meristem fate has broader impacts on plant development than originally depicted in A. thaliana. By blocking floral transition, TFL1 genes participate in the control of juvenility, shoot growth pattern, inflorescence architecture, and the establishment of life history strategies. Here, we contextualize the role of the TFL1-mediated protection of meristem indeterminacy throughout plant development.

Developmental Pathways Are Blueprints for Designing Successful Crops

Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.