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Extending the period of fruit production is a way to substantially increase crop yield in many fruit or ornamental species. In the cultivated octoploid strawberry (Fragaria x ananassa), the most consumed small fruit worldwide, fruit production season can be extended by selecting perpetual flowering (PF) cultivars. This trait is of considerable interest to growers and to the food industry. Four homoeologous loci controlling a single trait can be expected in such a complex octoploid species. However, we recently showed that the PF trait is under the control of the single dominant FaPFRU locus (Gaston et al., 2013), making it potentially amenable to marker assisted selection (MAS). Here, we report the successful use of a strategy, based on selective mapping using a reduced sample of individuals, to identify nine markers in close linkage to the FaPFRU allelic variant. Thus, this strategy can be used to fine map target homoeologous loci in other complex polyploid crop species. Recombinant analysis further enabled us to reduce the locus to a region flanked by two markers, Bx083_206 and Bx215_131, corresponding to a 1.1 Mb region in the diploid F. vesca reference genome. This region comprised 234 genes, including 15 flowering-associated genes. Among these, the FLOWERING LOCUS T (FT) is known to be a key activator of flowering. The close association between the PF trait and the FaPFRU flanking markers was validated using an additional segregating population and genetic resources. This study lays the foundation for effective and rapid breeding of PF strawberry cultivars by MAS. This article is protected by copyright. All rights reserved.

Fruit colour is central to the sensorial and nutritional quality of strawberry fruit and is therefore a major target in breeding programmes of the octoploid cultivated strawberry ( Fragaria × ananassa ). The red colour of the fruit is caused by the accumulation of anthocyanins, which are water-soluble flavonoids. To facilitate molecular breeding, here we have mapped with high resolution fruit colour quantitative trait loci (QTLs) (COLOUR, scored visually as in selection programmes) and associated flavonoid metabolic QTLs (5 anthocyanins compounds together with 8 flavonols and flavan-3-ols) to specific subgenomes of cultivated strawberry. Two main colour-related QTLs were located on the LG3A linkage group ( Fragaria vesca subgenome). Genetic mapping, transcriptome analysis and whole genome sequencing enabled the detection of a homoeo-allelic variant of ANTHOCYANIDIN REDUCTASE ( ANR) underlying the major male M3A COLOUR and pelargonidin-3-glucoside (PgGs) QTLs (up to ∼20% of explained variance). Consistent with previously published functional studies, ANR transcript abundance was inversely related with PgGs content in contrasted progeny individuals. Genetic segregation analyses further indicated that a molecular marker designed using an 18 bp deletion found in the 5′UTR of the candidate ANR homoeo-allelic variant is effective in identifying genotypes with intense red fruit colour. Our study provides insights into the genetic and molecular control of colour-related traits in strawberry and further defines a genetic marker for marker-assisted selection of new strawberry varieties with improved colour. The QTLs detected and the underlying candidate genes are different from those described to date, emphasising the importance of screening a wide diversity of genetic resources in strawberry.

• 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.

Extending the period of fruit production is a way to substantially increase crop yield in many fruit or ornamental species. In the cultivated octoploid strawberry ( Fragaria × ananassa ), the most consumed small fruit worldwide, fruit production season can be extended by selecting the perpetual flowering ( PF ) cultivars. This trait is of considerable interest to growers and to the food industry. Four homoeologous loci controlling a single trait can be expected in such a complex octoploid species. However, we recently showed that the PF trait is under the control of the single dominant Fa PFRU locus ( J. Exp. Bot ., 2013, 64 , 1837), making it potentially amenable to marker‐assisted selection ( MAS ). Here, we report the successful use of a strategy, based on a selective mapping using a reduced sample of individuals, to identify nine markers in close linkage to the FaPFRU allelic variant. Thus, this strategy can be used to fine map the target homoeologous loci in other complex polyploid crop species. Recombinant analysis further enabled us to reduce the locus to a region flanked by two markers, Bx083_206 and Bx215_131, corresponding to a 1.1 Mb region in the diploid F. vesca reference genome. This region comprises 234 genes, including 15 flowering associated genes. Among these, the FLOWERING LOCUS T ( FT ) is known to be a key activator of flowering. The close association between the PF trait and the Fa PFRU flanking markers was validated using an additional segregating population and genetic resources. This study lays the foundation for effective and rapid breeding of PF strawberry cultivars by MAS .

Perpetual-flowering (PF) is a highly desirable trait within cultivated strawberries (Fragaria ×ananassa) for the commercial and home garden markets. The most widely used source of the PF trait was originally introgressed from a wild F. virginiana subsp. glauca accession collected in the Wasatch Mountains near Salt Lake City, UT in 1955. This source is conferred by a single dominant QTL, FaPFRU, and was recently identified in multiple bi-parental populations. Multiple markers have been proposed as diagnostic tests for marker-assisted selection (MAS). These markers were proposed after looking at a relatively small sample of germplasm. To identify the best diagnostic testing procedure for MAS, the markers were evaluated individually and in combination on a training set of cultivars with known genotypes and the best test was used to determine the distribution of the FaPFRU source of PF within a large sample of octoploid Fragaria germplasm. Of the tests evaluated, the microsatellite marker Bx215 alone was found to have the best diagnostic ability for MAS with an accuracy of 93.1% in controlled conditions. When utilizing the test on 390 F. ×ananassa accessions, 164 accessions were identified to likely have the FaPFRU locus. Nine octoploid Fragaria accessions were PF and did not have this marker, indicating possible recombination events or potentially novel sources of the PF trait. Future work will be needed to dissect the PF trait in these nine individuals.

Perpetual-flowering (PF) is a highly desirable trait within cultivated strawberries (Fragaria ×ananassa) for the commercial and home garden markets. The most widely used source of the PF trait was originally introgressed from a wild F. virginiana subsp. glauca accession collected in the Wasatch Mountains near Salt Lake City, UT in 1955. This source is conferred by a single dominant QTL, FaPFRU, and was recently identified in multiple bi-parental populations. Multiple markers have been proposed as diagnostic tests for marker-assisted selection (MAS). These markers were proposed after looking at a relatively small sample of germplasm. To identify the best diagnostic testing procedure for MAS, the markers were evaluated individually and in combination on a training set of cultivars with known genotypes and the best test was used to determine the distribution of the FaPFRU source of PF within a large sample of octoploid Fragaria germplasm. Of the tests evaluated, the microsatellite marker Bx215 alone was found to have the best diagnostic ability for MAS with an accuracy of 93.1% in controlled conditions. When utilizing the test on 390 F. ×ananassa accessions, 164 accessions were identified to likely have the FaPFRU locus. Nine octoploid Fragaria accessions were PF and did not have this marker, indicating possible recombination events or potentially novel sources of the PF trait. Future work will be needed to dissect the PF trait in these nine individuals.

Extending the period of fruit production is a way to substantially increase crop yield in many fruit or ornamental species. In the cultivated octoploid strawberry (Fragaria x ananassa), the most consumed small fruit worldwide, fruit production season can be extended by selecting perpetual flowering (PF) cultivars. This trait is of considerable interest to growers and to the food industry. Four homoeologous loci controlling a single trait can be expected in such a complex octoploid species. However, we recently showed that the PF trait is under the control of the single dominant FaPFRU locus (Gaston et al., 2013), making it potentially amenable to marker assisted selection (MAS). Here, we report the successful use of a strategy, based on selective mapping using a reduced sample of individuals, to identify nine markers in close linkage to the FaPFRU allelic variant. Thus, this strategy can be used to fine map target homoeologous loci in other complex polyploid crop species. Recombinant analysis further enabled us to reduce the locus to a region flanked by two markers, Bx083_206 and Bx215_131, corresponding to a 1.1 Mb region in the diploid F. vesca reference genome. This region comprised 234 genes, including 15 flowering-associated genes. Among these, the FLOWERING LOCUS T (FT) is known to be a key activator of flowering. The close association between the PF trait and the FaPFRU flanking markers was validated using an additional segregating population and genetic resources. This study lays the foundation for effective and rapid breeding of PF strawberry cultivars by MAS. This article is protected by copyright. All rights reserved.

In strawberry, the axillary bud (AXB) can produce either an elongated stem called stolon giving a daughter-plant (asexual reproduction) or an inflorescence-bearing branch crown (BC) (sexual reproduction). The fate of the AXB depends on node position on the axis and on genetic and environmental factors. Here, in Fragaria vesca, we addressed the largely unanswered question of how molecular factors determine AXB fate. To get insights into the mechanisms already at play in a morphologically indistinguishable (undifferentiated) AXB, depending on its fate, we combined (1) the phenotypic characterization of AXB development throughout plant growth with (2) the RNA-seq analysis of undifferentiated AXBs, using three different genotypes producing either BCs or stolons (fvetfl1 and fvega20ox mutants, FveFT3 overexpressor). Results allowed the identification of genes regulating AXB fate and outgrowth, among which FveBRC1. The analysis of FveBRC1 expression in genotypes combining various traits (perpetual/seasonal flowering; runnering/runneless) and the generation of CRISPR/Cas9 brc1 mutants further demonstrated that FveBRC1 plays a central role in the determination of AXB fate in strawberry, in addition to its well-known function in BC outgrowth. These original results provide new insights into the determination of AXB fate and, consequently, the control of fruit yield in strawberry.

The flowering time, which determines when the fruits or seeds can be harvested, is known to be sensitive to plasticity, i.e. the ability of a genotype to display different phenotypes in response to environmental variations. In the context of climate change, strawberry breeding can take advantage of phenotypic plasticity to create high-performing varieties adapted either to local conditions or to a wide range of climates. To decipher how the environment affects the genetic architecture of flowering time in cultivated strawberry (Fragaria × ananassa) and modify its QTL effects, we used a bi-parental segregating population grown for two years at widely divergent latitudes (5 European countries) and combined climatic variables with genomic data (Affymetrix® SNP array). We detected 10 unique flowering time QTL and demonstrated that temperature modulates the effect of plasticity-related QTL. We propose candidate genes for the three main plasticity QTL, including FaTFL1 which is the most relevant candidate in the interval of the major temperature-sensitive QTL (6D_M). We further designed and validated a genetic marker for the 6D_M QTL which offers great potential for breeding programs, for example for selecting of early-flowering strawberry varieties well adapted to different environmental conditions.Competing Interest StatementThe authors have declared no competing interest.

Flavonoids are products from specialized metabolism that contribute to fruit sensorial (colour) and nutritional (antioxidant properties) quality. Here, using a pseudo full-sibling F1 progeny previously studied for fruit sensorial quality of cultivated strawberry (Fragaria x ananassa), we explored over two successive years the genetic architecture of flavonoid-related traits using LC-ESI-MS (13 compounds including anthocyanins, flavonols and flavan-3-ols) and colorimetric assays (anthocyanins, flavonoids, phenolics, FRAP and TEAC antioxidant capacity). Network correlation analysis highlighted the high connectivity of flavonoid compounds within each chemical class and low correlation with colorimetric traits except anthocyanins. Mapping onto the female and male linkage maps of 152 flavonoid metabolic QTLs (mQTLs) and of 26 colorimetric QTLs indicated co-localization on few linkage groups of major flavonoid- and taste-related QTLs previously uncovered. These results pave the way for the discovery of genetic variations underlying flavonoid mQTLs and for marker-assisted selection of strawberry varieties with improved sensorial and nutritional quality.