D. W. Simpson

Comparative Genetic Mapping Between Octoploid and Diploid Fragaria Species Reveals a High Level of Colinearity Between Their Genomes and the Essentially Disomic Behavior of the Cultivated Octoploid Strawberry

Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. ×ananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. ×ananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry.

Simple Sequence Repeat Marker Development and Mapping Targeted to Previously Unmapped Regions of the Strawberry Genome Sequence

The genome sequence of the woodland strawberry (Fragaria vesca L.) is an important resource providing a reference for comparative genomics studies and future sequenced rosaceous species and has great utility as a model for the development of markers for mapping in the cultivated strawberry Fragaria ×ananassa Duchesne ex Rozier. A set of 152 microsatellite simple sequence repeat (SSR) primer pairs was developed and mapped, along with 42 previously published but unmapped SSRs, permitting the precise assignment of 28.2 Mbp of previously unanchored genome sequence scaffolds (13% of the F. vesca genome sequence). The original ordering of F. vesca sequence scaffolds was performed without a physical map, using predominantly SSR markers to order scaffolds via anchoring to a comprehensive linkage map. This report complements and expands resolution of the Fragaria spp. reference map and refines the scaffold ordering of the F. vesca genome sequence using newly devised tools. The results of this study provide two significant resources: (i) the concurrent validation of a substantial set of SSRs associated with these previously unmapped regions of the Fragaria spp. genome and (ii) the precise placement of previously orphaned genomic sequence. Together, these resources improve the resolution and completeness of the strawberry genome sequence, making it a better resource for downstream studies in Fragaria spp. and the family Rosaceae.

Expression of Fragaria vesca PIP aquaporins in response to drought stress: PIP down-regulation correlates with the decline in substrate moisture content.

PIP aquaporin responses to drought stress can vary considerably depending on the isoform, tissue, species or level of stress; however, a general down-regulation of these genes is thought to help reduce water loss and prevent backflow of water to the drying soil. It has been suggested therefore, that it may be necessary for the plant to limit aquaporin production during drought stress, but it is unknown whether aquaporin down-regulation is gradual or triggered by a particular intensity of the stress. In this study, ten Fragaria PIP genes were identified from the woodland strawberry (Fragaria vesca L.) genome sequence and characterised at the sequence level. The water relations of F. vesca were investigated and the effect of different intensities of drought stress on the expression of four PIP genes, as well as how drought stress influences their diurnal transcription was determined. PIP down-regulation in the root corresponded to the level of drought stress. Moreover, transcript abundance of two genes highly expressed in the root (FvPIP1;1 and FvPIP2;1) was strongly correlated to the decline in substrate moisture content. The amplitude of diurnal aquaporin expression in the leaves was down-regulated by drought without altering the pattern, but showing an intensity-dependent effect. The results show that transcription of PIP aquaporins can be fine-tuned with the environment in response to declining water availability.

A genetic linkage map of an inter-specific diploid Fragaria BC1 mapping population and its comparison with the Fragaria reference map (FV FN)

Summary We have produced a reduced linkage map of a diploid Fragaria backcross progeny (F. vesca [F. vesca F. viridis]) denoted 815 x 903BC from 31 microsatellite (SSR) and two gene-specific markers selected from the diploid Fragaria reference map FV FN. The 33 sequence tagged-site (STS) markers selected, segregated in seven linkage groups, and marker order was conserved between FV FN and 815 x 903BC. Significant segregation distortion, observed on three of the seven linkage groups, was accompanied by a reduction in observed recombination frequency and, therefore, genetic distance between markers mapped in these linkage groups. However, this distortion did not affect marker order compared to FV FN and may indicate non-random chromosomal divergence during speciation in Fragaria. Our findings indicate that no major genome reorganisation has occurred during speciation in the genus, and suggest that STS linkage maps of other Fragaria populations, including those of the cultivated strawberry F. ananassa, could be constructed using the diploid Fragaria reference map FV FN as a standard reference point.

Meristem culture for the elimination of the strawberry crown rot pathogen Phytophthora cactorum

Two methods to induce a symptomless infection of crown rot (Phytophthora cactorum) in stolons of three strawberry (Fragaria×ananassa) cultivars were evaluated. Spraying a 10 −4 ml zoospore suspension was the most effective method, producing a mean infection rate of 12%. Meristem cultures were subsequently established from all of the inoculated stolons and tested eight weeks later for the presence of P. cactorum using a PCR-based assay. A total of 784 meristems were excised and DNA was successfully extracted from 505 viable meristem cultures, 46 of which had been excised from stolons that were shown to have a symptomless infection of crown rot. No viable meristems were found to be infected with the pathogen. This investigation confirmed the suitability and reliability of meristem culture for the production of strawberry plants free from crown rot.

Identification of powdery mildew resistance QTL in Fragaria x ananassa

The obligate biotrophic fungus Podosphaera aphanis is the causative agent of powdery mildew on cultivated strawberry (Fragaria x ananassa). Genotypes from two bi-parental mapping populations ‘Emily’ x ‘Fenella’ and ‘Redgauntlet’ x ‘Hapil’ were phenotyped for powdery mildew disease severity in a series of field trials. Here we report multiple QTL associated with resistance to powdery mildew, identified in ten phenotyping events conducted across different years and locations. Seven QTL show a level of stable resistance across multiple phenotyping events however many other QTL were represented in a single phenotyping event and therefore must be considered transient. One of the identified QTL was closely linked to an associated resistance gene across the wider germplasm. Furthermore, a preliminary association analysis identified a novel conserved locus for further investigation. Our data suggests that resistance is highly complex and that multiple additive sources of quantitative resistance to powdery mildew exist across strawberry germplasm. Implementation of the reported markers in marker-assisted breeding or genomic selection would lead to improved powdery mildew resistant strawberry cultivars, particularly where the studied parents, progeny and close pedigree material are included in breeding germplasm. Key Message Powdery mildew resistance in two strawberry mapping populations is controlled by both stable and transient novel QTL of moderate effect. Some transferability of QTL across wider germplasm was observed.

Identification of powdery mildew resistance QTL in strawberry (Fragaria × ananassa)

AbstractKey MessagePowdery mildew resistance in two strawberry mapping populations is controlled by both stable and transient novel QTL of moderate effect. Some low transferability of QTL across wider germplasm was observed.Abstract The obligate biotrophic fungus Podosphaera aphanis is the causative agent of powdery mildew on cultivated strawberry (Fragaria × ananassa). Genotypes from two bi-parental mapping populations ‘Emily’ × ‘Fenella’ and ‘Redgauntlet’ × ‘Hapil’ were phenotyped for powdery mildew disease severity in a series of field trials. Here, we report multiple QTL associated with resistance to powdery mildew, identified in ten phenotyping events conducted across different years and locations. Six QTL show a level of stable resistance across multiple phenotyping events; however, many other QTL were represented in a single phenotyping event and therefore must be considered transient. Subsequent screening of identified QTL across a validation set determined whether identified QTL remained closely linked to the associated resistance gene in the wider germplasm. Furthermore, a preliminary association analysis identified a novel conserved locus for further investigation. Our data suggest that resistance is highly complex and that multiple, primarily additive, sources of quantitative resistance to powdery mildew exist across strawberry germplasm. Utilisation of the reported markers in marker-assisted breeding or genomic selection would lead to improved powdery mildew-resistant strawberry cultivars, particularly where the studied parents, progeny and close pedigree material are included in breeding germplasm.