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.

OBITUARY Heinrich Rohrer, pioneer of scanning tunnelling microscopy, remembered p.30 GENES US Supreme Court patent rulings set a higher bar for innovation p.29 ART Exhibition revels in the power of unconstrained thought p.28 SPACE An elegy for the disappearing dark, banished by science p.26 Feeding the future We must mine the biodiversity in seed banks to help to overcome food shortages, urge Susan McCouch and colleagues. The International Center for Tropical Agriculture in Colombia holds 65,000 crop samples from 141 countries.

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.

The density and utility of the molecular genetic linkage map of the widespread use of RFLP markers and maps in suncultivated sunflower (Helianthus annuus L.) has been greatly inflower has been restricted by a lack of public RFLP creased by the development and mapping of several hundred simple sequence repeat (SSR) markers. Of 1089 public SSR markers de-probes, consequent lack of a dense public RFLP map, scribed thus far, 408 have been mapped in a recombinant inbred line and low-throughput nature of RFLP markers. The diffi-(RIL) mapping population (RHA280 ϫ RHA801). The goal of the culties posed by the historic lack of public, single-copy present research was to increase the density of the sunflower map by DNA markers were only weakly offset by the emerconstructing a new RIL map (PHA ϫ PHB) based on SSRs, adding gence of facile, universal DNA markers, e.g., RAPDs loci for newly developed SSR markers to the RHA280 ϫ RHA801 RIL (Williams et al., 1990, 1993) and AFLPs (Vos et al., map, and integrating the restriction fragment length polymorphism 1995). RAPDs have primarily been used for tagging (RFLP) and SSR maps of sunflower. The latter was accomplished by phenotypic loci in sunflower, e.g., rust (Puccinia helianadding 120 SSR marker loci to a backbone of 80 RFLP marker loci thi Schw.) and Orobanche cumana Wallr. resistance on the HA370 ϫ HA372 F 2 map. The map spanned 1275.4 centimorgans (cM) and had a mean density of 6.3 cM per locus. The genes (Lawson et al., 1998; Lu et al., 2000). While RAPD PHA ϫ PHB SSR map was constructed from 264 SSR marker loci, and AFLP markers have a multitude of uses, both are spanned 1199.4 cM, and had a mean density of 4.5 cM per locus. The dominant, multicopy, and often nonspecific in nature RHA280 ϫ RHA801 map was constructed by adding 118 new SSR and, as a whole, unsatisfactory for establishing a geand insertion-deletion (INDEL) marker loci to 459 previously nome-wide framework of DNA markers for anchoring mapped SSR marker loci. The 577-locus map spanned 1423.0 cM and cross referencing genetic linkage maps. Single-copy, and had a mean density of 2.5 cM per locus. The three maps were codominant DNA markers, e.g., SSRs, are preferred for constructed from 1044 DNA marker loci (701 unique SSR and 89 such purposes and, until recently, have been lacking unique RFLP or INDEL marker loci) and supply a dense genomein sunflower. wide framework of sequence-based DNA markers for molecular breeding and genomics research in sunflower.

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (F. chiloensis and F. virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication— 59-76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that Fragaria × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis, F. virginiana, and Fragaria × ananassa (π = 0.0059-0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern Fragaria × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.