The molecular underpinnings of color variation and fruit shape in Fragaria are mostly unknown or unreported, although clearly of interest for development of molecular markers for breeding purposes to meet changing consumer tastes. In strawberry, antioxidant compounds such as polyphenols and ascorbic acid are important nutritional traits. Yet these are difficult traits to assess as they are influenced not only by genotype, but by the growing environment and by developmental stage. Forexample, levels of the bio-active nonflavonoid polyphenol, ellagic acid , is higher in achenes from ripe fruit of the F. vesca cultivar Yellow Wonder than in achenes from ripe fruit of F. × ananassa cultivar Calypso. A complication for improving fruit nutrient quality is that EA levels are higher in achenes than in receptacles of all cultivars tested, and EA is found primarily at small green stage. In addition, the mode of inheritance of EA content is yet to be elucidated. Previously unidentified bio-active compounds, such as the acylphloroglucinol glucosides discovered in F. × ananassa while examining the enzymatic properties of recombinant F. vesca chalcone synthases, may also exist in Fragaria species. With the availability of modern methods in metabolomics and allied fields, discovery of additional bio-active compounds is likely, and these methods can be applied to direct molecular approaches to improving fruit quality. In the future, metabolic flux analysis should also enhance our ability to delineate what biochemical pathways are good targets for fruit quality improvement as well and to predict what modifications may influence fruit quality parameters.There has been ample progress in recent years in describing the genetic architecture of disease resistance in cultivated strawberry. Many resistances appear to be primarily conferred by one or two major loci or large-effect QTL, including to Phytophthora fragariae, Xanthomonas fragariae, Phytophthora cactorum, Fusarium oxysporum f.sp fragariae, Colletotrichum gloeosporoides, and Colletotrichum acutatum.

For P. cactorum, additional minor loci have recently been identified. On the other hand, resistances to Verticillium dahaliae and Podosphaera aphanis appear to be quite complex, grow bag with no major loci identified to date. This suggests that genomic prediction approaches for these two diseases would be most effective. However, with the advent of the “Camarosa” genome, an opportunity exists to characterize Mildew Locus O genes in strawberry toward potential gene editing solutions. Elucidating the genetics of resistance to M. phaseolina should be a high priority in the future, given the recent spread of this pathogen in important production regions and the lack of effective controls for this disease. In addition, no resistance genes have been reported against gray mold caused by Botrytis cinerea. Instead, it seems most likely that any small differences in tolerance to this disease among cultivars results from morphological variations in flower structures, fruit firmness, etc. Because strong resistance to B. cinerea is not likely to result from conventional breeding, a gene editing solution may be most viable. Where disease resistances are conferred by one or a few genes, genetic and breeding approaches to characterize and increase resistance are straightforward. In the cases where classical R genes are involved, the development of custom-capture libraries and single-molecule resequencing of captured target sequences has been quite effective for identifying causal gene variants. In fact, such a resource has now been developed for cultivated strawberry in the form of a RenSeq library based on the “Camarosa” reference and resequencing of a number of elite cultivars and breeding lines. Combining this resource with mapping and association genetics approaches should help uncover subgenome-specific variants underlying known loci and lead to the cloning of R genes in octoploid strawberry. Given the tremendous allelic diversity present in strawberry and the large copy numbers and highly repetitive coding sequences typical of R genes, assembling long reads from single-molecule realtime sequencing should be helpful to this endeavor. Hand in hand with characterization of R genes, we recommend the characterization of pathogen populations in order to understand the durability of resistances.

The paradigm of a gene-for-gene arms race has been long established, but a more accurate assessment of the durability of resistance could arise from an understanding of the selective forces operating on pathogen effectors. Dual RNA-seq technology can help uncover the dynamic interactions of pathogen and host. Both the pathogen and the host transcriptomes are simultaneously captured and analyzed in silico to distinguish species specific transcripts. For some complex interactions, single cell transcriptomics coupled with protein and metabolite analysis may be helpful. What new insights into disease resistance in strawberry could be gained simply from studying the population structures of causal pathogens? Would identifying and characterizing pathogen effectors give us meaningful insights into the control of pathogens through breeding and other means? It is intriguing that some recently discovered resistance loci in strawberry confer very strong resistances and yet have apparently been durably effective in commercial production for many decades. Cloning the first R genes and pathogen effectors involved these interactions will help us to understand why.The Genome Database for Rosaceae is the central repository and datamining resource for genomics, genetics, and breeding data of Rosaceae, including strawberry and related crops such as almond, apple, apricot, blackberry, cherry, peach, pear, plum, raspberry, and rose. The volume and type of data generated for strawberry research has markedly increased in the past ten years. This includes whole-genome assembly data, RNA-seq data, multiple SNP arrays, increased numbers of QTL, and more genotypic and phenotypic data. The massive volume of data generated by the strawberry research community, combined with active curation, integration, further analyses and tool development by the GDR team has resulted in marked expansion in the data and functionality available for strawberry. In addition to the near-complete chromosome-scale assembly for F. × ananassa, two draft genome assemblies for F. × ananassa are available. Four genome assemblies, including the newest v4.0, are also available for F. vesca. New and much improved annotation v4.0. a2, including 34,007 protein-coding genes with 98.1% complete Benchmarking Universal Single-Copy Orthologs , is available. For older assemblies F. vesca genome v1.1 and v2.0, additional annotations are also available: v1.1.a2 and v2.0.a2, respectively. The draft genome assemblies of four wild diploid Fragaria species and of Potentilla micrantha a species that does not develop fleshy fruit but is closely related to Fragaria, are also available. In addition, the whole genome of F. iinumae has recently become available. GDR now provides a reference transcriptome that combines published RNASeq and EST data sets. The GDR team provides additional computational annotation for both predicted genes of whole-genome assemblies and RefTran datasets with homology to genes of closely related or model plant species and assignment of InterPro protein domains and GO terms. The genome assembly and transcript data can be accessed through the Fragaria genus and species pages, Gene/Transcript search page, JBrowse and BLASTX. The octoploid “Camarosa” genome, F. iinumae v1.0, and both annotation versions of F. vesca Genome v4.0, are used in a synteny analysis with whole-genome assemblies from 18 Rosaceae species using MCScanX with results available to view and search through the Synteny Viewer. GDR hosts 29 genetic maps for Fragaria species, most of which contain trait loci and can be viewed and compared through the MapViewer. Detailed data on 505 QTLs and 5 MTLs for 124 horticultural traits, and 171,115 genetic markers for Fragaria that includes 154,739 SNPs are available, as well as SNP data from the iStraw 90 K array for cultivated strawberry. The SNP data is accessible through JBrowse tracks, downloadable files and can be searched and downloaded from the SNP Marker and All Marker search pages. The Marker search page now includes filtering by trait name, which allows users to search for markers that are near and/or within QTLs using the associated trait name. Phenotyping data from the public projects such as RosBREED are available from GDR. In addition to the “Search Trait Evaluation” page, the public breeding data can be queried and downloaded using the Breeders toolbox.

A new module in GDR, grow bag gardening the Breeding Information Management System , now provides breeders and breeding project teams with tools to easily store, manage, archive and analyze their private or public breeding data. The availability of whole-genome assembly and SNP array data for the cultivated octoploid strawberry, along with wealth of QTL data that are integrated in the community database with data from other related crops are expected to accelerate research and practical tools such as DNA tests. BIMS in GDR will help breeders not only to organize their data but also to utilize the tools and resources that are available for strawberry improvement.The strawberries found in markets around the world today are produced by cultivated strawberry Duchesne ex Rozier, a species domesticated over the past 300 years . F. ananassa is technically not a species but an admixed population of interspecific hybrid lineages between cross-compatible wild allo-octoploid species with shared evolutionary histories . The earliest F. ananassa cultivars originated as spontaneous hybrids between F. chiloensis and F. virginiana in Brittany, the Garden of Versailles, and other Western European gardens in the early 1700s, shortly after the migration of F. chiloensis from Chile to France in 1714 . Their serendipitous origin was discovered by the French Botanist Antoine Nicolas Duchesne and famously described in a treatise on strawberries that biologists suspect included one of the first renditions of a phylogenetic tree . Even though those studies predated both the advent of genetics and the discovery of ploidy differences in the genus, the phylogenies were remarkably close to hypotheses that emerged more than 150 years later . The early interspecific hybrids were observed to be more phenotypically variable than and horticulturally superior to their wild octoploid parents, factors that drove the domestication of F. ananassa. The increase in phenotypic variability can be directly linked to an increase in nucleotide diversity and heterozygosity, and presumably to the introduction of complementary favorable alleles that were not found in either parent. Hardigan et al. showed that hybrids between F. chiloensis and F. virginiana have nearly double the genome-wide heterozygosity of their parents. With the mysterious origin of the spontaneous interspecific hybrids solved , breeding and cultivation shifted to F. ananassa, which supplanted the cultivation of the wild relatives and forever changed strawberry production and consumption worldwide . The romanticized and widely recounted story of the origin of cultivated strawberry, while compelling, oversimplifies the complexity of the wild ancestry and 300-year history of domestication, for which we have an incomplete understanding . One of our motives for reconstructing the genealogy of cultivated strawberry was to shed light on the origin and diversity of the wild founders and the breeding history. The only pedigree-informed studies of the breeding history of cultivated strawberry focused on an analysis of the ancestry of 134 North American cultivars developed between 1960 and 1985 . They identified 53 founders in the pedigrees of those cultivars, estimated that 20 founders contributed approximately 85% of the allelic diversity, and concluded that North American cultivars had originated from a genetically narrow population . Others have reached similar conclusions , and the notion that cultivated strawberry “displays limited genetic variability” has persisted . Gaston et al. were possibly alluding to the absence of morphological diversity on par with that found in tomato . Nevertheless, the genetic narrowness hypothesis has not been supported by genome-wide analyses of DNA variants, which have shown that F. chiloensis, F. virginiana, and F. ananassa harbor massive nucleotide diversity and that a preponderance of the alleles transmitted by the wild octoploid founders have survived domestication and been preserved in the global F. ananassa population . Hardigan et al. proposed an alternative to the “limited genetic variability” hypothesis , arguing that genetic variation has not been reduced by directional selection or population bottlenecks in certain populations. One of the consequences predicted by this hypothesis is the persistence of a high frequency of unfavorable alleles in domesticated populations. The domestication of cultivated strawberry has followed a path different from that of other horticulturally important species, many of which were domesticated over millennia and traced to early civilizations, e.g., apple , olive , and wine grape . Although the octoploid progenitors were cultivated before the emergence of F. ananassa, the full extent of their cultivation is unclear and neither appears to have been intensely domesticated; e.g., Hardigan et al. did not observe changes in the genetic structure between land races and wild ecotypes of F. chiloensis, a species cultivated in Chile for at least 1,000 years .