ABR-PG: The Use of Pentaploid Surrogates for Assembly and Anchoring of Octoploid Strawberry Genomes

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The cultivated strawberry (Fragaria x ananassa) and its immediate ancestors, F. chiloensis and F. virginiana, are an important and intriguing crop plant system from evolutionary, genomic and horticultural perspectives. Having originated from a cross between its two immediate ancestors in the mid-1700s, the cultivated strawberry is one of the youngest crop species. It has four genomes, each present in two copies, making a total of eight genomes. These were passed down from as many as four ancestors, thus making the cultivated strawberry among the most genomically complex crop plants. As yet, it has not been possible to get a genome sequence for the cultivated strawberry, primarily because of the great complexity of having eight genomes. This challenge is addressed in this project by implementation of a new strategy that reduces the number of genomes to be sequenced from eight to four. The approach is to get a hybrid with five genomes - called a pentaploid - by first crossing a well-studied variety with two genomes (termed a diploid) to one with eight. After sequencing the pentaploid, the genome of the diploid is subtracted out bioinformatically, leaving only four genomes to be assembled. The result will be the first assembled genome sequence for one of the immediate ancestors of the cultivated strawberry, which will be a resource of immense value to strawberry researchers and breeders interested in further improving this economically important and healthful fruit crop.No reference genome has yet been established for an octoploid strawberry. Challenges facing such efforts include those inherent to polyploidy, as well as those associated with heterozygosity. The octoploid strawberry species, including the cultivated Fragaria x ananassa and its immediate ancestors F. chiloensis and F. virginiana, are subject to inbreeding depression, and doubled haploid clones as used for genome assembly in the peach and apple genome projects have not been an available option in strawberry. A bold approach will be implemented to solve this problem by using pentaploid hybrids as "modified haploid" subjects for whole genome sequencing and linkage mapping. The project goals are to construct a high resolution, pentaploid-based linkage map and use it to anchor a pentaploid-based genome assembly, from which the known diploid genome copy has been digitally subtracted out. Linkage mapping will be accomplished using markers from the Axiom IStraw90 SNP array. The specific project objectives are to: 1) construct a high resolution, octoploid linkage map based upon a novel, pentaploid mapping population; 2) construct an octoploid genome assembly based upon newly generated DNA sequence and optical mapping data derived from a single pentaploid plant; 3) anchor the genome assembly to the linkage map; and, 4) compare the utility of the newly assembled octoploid genome to that of the existing diploid genome as references in relation to an expanded program of SNP discovery in octoploid germplasm. The project will establish a needed knowledge foundation for subsequent research aimed at defining the subgenome composition(s) of the octoploid Fragaria species. Only within this knowledge framework will it be possible to define the homoeologues and subgenomic specificities of genes of economic and basic scientific interest. The employment of a pentaploid progeny population for linkage map construction will provide detailed insight into patterns of allele segregation that might otherwise be obscured by the challenges of genotype calling in an octoploid, thereby offering the potential to differentiate disomic and polysomic inheritance patterns and to finally establish whether the latter do in fact occur at the octoploid level in strawberry. The genomic resources to be developed, including the first octoploid reference genome, will be rapidly disseminated via the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) and Genome Database for Rosaceae (http://www.rosaceae.org/) public databases. The research products will advance both basic and applied research in strawberry, and will reinforce efforts to implement marker-assisted breeding in strawberry.