Narrowing down the single homoeologous FaPFRU locus controlling flowering in cultivated octoploid strawberry using a selective mapping strategy

Abstract

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 FaPFRU 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 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.

Keywords: Fragaria; bin mapping; marker-assisted selection; perpetual flowering; polyploidy.

Figure 1

The overall strategy in seven steps based on selective mapping using a reduced sample of individuals and combined with QTL identification and fine mapping.

Figure 2

Representation of the bins on (a) the four female and (b) male linkage groups (LG) belonging to the homoeologous group IV. Bins consist of groups of markers separated by recombinational crossover sites. The position of each bin is shown by a black or white rectangle on the LG, and the name of each bin is indicated in italic. The targeted bins overlapping the FaPFRU locus are framed in red.

Figure 3

QTLs linked to perpetual flowering (PF) trait identified in ‘Capitola’: (a) in Gaston et al. (2013) and (b) in this study and (c) in ‘Mara des Bois’ on the Linkage Group LGIVb. The blue bar represents the position of the scaffold scf0513158_v1.0. Phenotypic data analysed for QTL identification are the number of newly emerged inflorescences from the end of May to the beginning of August, representing the PF trait, for 6 and 3 years, respectively ‘Capitola’ × ‘CF1116’ −(a) and (b)− and ‘Mara des Bois’ × ‘Pajaro’ −(c)− segregating populations. Markers added in this study are in italic.

Figure 4

Genotype (H and A for the presence and absence of the markers), phenotype (PF and SF for perpetual and seasonal flowering) and the number of recombinants according to genotype and phenotype. The individuals presenting a recombination (framed in blue) between the markers Bx083_206 and Bx215_131 present both PF and SF behaviours (in bold), indicating that the FaPFRU locus controlling the trait of interest is localized between these two markers, which represent the two flanking markers of the reduced FaPFRU locus (bracket in red).

Figure 5

Comparison between physical and genetic distances for all informative markers (SSRs) localized on the four homoeologous (a) female and (b) male linkage groups (LG) IV. Physical distance was identified thanks to the pseudochromosome‐4 sequence of the F. vesca reference genome v2.0.a1. Genetic distances are identified thanks to linkage maps of the octoploid population ‘Capitola’ × ‘CF1116’. The two flanking markers of the reduced FaPFRU locus on the LGIVb‐f are framed in black. In grey, genomic region without SSR markers in our study.

Figure 6

The number of inflorescences and stolons of individuals belonging to four populations scored in 2012 according to their flowering behaviour, perpetual flowering (PF) or seasonal flowering (SF).

Figure 7

Dose effect of the co‐dominant markers Bx089_215c/Bx089_220r localized in the FaPFRU locus. Phenotyping was performed on ‘Mara des Bois’‐S₁ population. Double Dose indicates homozygous individuals for Bx089_215c (linked in coupling to the FaPFRU allelic variant), Single Dose indicates heterozygous individuals for Bx089_215c/Bx089_220r and Nulli Dose indicates homozygous individuals for Bx089_220r. Asterisks indicate significant differences by Student's t‐test: *, **, *** for statistical significance at P ≤ 0.05, 0.01, 0.001, respectively.