A High-Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae, Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing

Fragaria iinumae Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for F. iinumae. The F. iinumae linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter “Array”), and genotyping by sequencing (GBS). The F2 generation mapping population was derived by selfing F. iinumae hybrid F1D, the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the Fragaria vesca ssp. vesca L. ‘Hawaii 4’ pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between F. iinumae and F. vesca, and/or to F. vesca genomic assembly errors. The Fii map provides a basis for anchoring a F. iinumae genome assembly as a prerequisite for constructing a second diploid reference genome for Fragaria

Strawberry breeding for disease resistance in Dresden

Verticillium resistance is one of the most important breeding goals in strawberry resistance breeding at Dresden-Pillnitz. Resistance evaluation of cultivars, advanced selections and seedlings is realized under natural conditions at a provocation field and by artificial inoculation in the greenhouse. Introgression of Fragaria chiloensis L. (Miller) into Fragaria ×ananassa Duch. resulted in highly tolerant breeding selections. After back-crossing with cultivars of F. ×ananassa first genotypes were selected which can be evaluated in experimental cultivar trials at different locations in Germany

Aroma map in European woodland strawberry

Woodland strawberry (Fragaria vesca, 2x) is the diploid closest ancestor of the cultivated strawberry (Fragaria ´ annassa, 8x) and the model species for genetic studies in the Fragaria genus. It is naturally distributed all across Europe and it is appreciated for their delicate aroma and flavor. Aiming to describe the genetic and organoleptic diversity of European woodland strawberry and decipher the genetic control of its characteristic volatile compounds, we have sequenced and metabolically-phenotyped a diverse collection of 199 geographically distant European accessions. The metabolic profiling of the lines includes a set of 100 unambiguosly identified volatiles. This study has revealed genetic and metabolic differences between subpopulations with different geographical origin. In addition, Genome Wide Association Analysis points to several candidate genetic regions controlling the accumulation of volatiles compounds sharing common biosynthetic pathways. Specifically, we have detected SNPs associated to the accumulation of methyl ketones and their corresponding alcohols mapping to a small region of chromosome 4 with a reduced set of candidate genes.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Characterization of an allotriploid strawberry Fragaria × bifera Duchesne (Rosaceae) from Europe

Peer reviewedPostprin

A Phylogenetic Analysis of the Genus Fragaria (Strawberry) Using Intron-Containing Sequence from the ADH-1 Gene

The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae

Origin and evolution of the octoploid strawberry genome.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry

アントシアニジン合成系遺伝子DFRの系統解析

Plants have various color pigments. Many plants have fruits and flowers of vivid colors such as orange, red, purple and blue. Anthocyanins with anthocyanidins as aglycone are one group of plant pigments. Each type of anthocyanidins is determined by the substrate specificity of dihydroflavonol 4-reductase (DFR) in its biosynthetic pathway and has a major influence on the determination of plant color. We performed a phylogenetic analysis of DFR genes, which are key enzymes of this anthocyanidin biosynthesis pathway. We collected 170 DFR clones in various plants by browsing database (NCBI). The collected DFRs were classified into ten groups according tosequence similarity. The consensus sequences within each group were aligned, and amino acids involved in the responsible region for determination of the substrate specificity of DFR have been shown. In addition, DFR's intron sites were highly conserved. These results would be useful to unveil the relationship between DFR and plant pigments

Production of bioactive phenolic compounds by berry cell cultures

The production of phenolic compounds by berry cell cultures of strawberry (Fragaria x ananassa) was studied and the biosynthesis of phenolic compounds was stimulated by elicitation

High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa

Background: Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. Results: Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. Conclusions: High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae

Molecular diversity of anthracnose pathogen populations associated with UK strawberry production suggests multiple introductions of three different Colletotrichum species.

Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production