Publication Highlight

Ancient Strawberry Mystery Solved: Genomics Pinpoints Ancestors of Popular Fruit

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Nature Plants

Volume 9, Page 1252–1266

August 2023


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Featured Researcher: Dr. Jeffrey Mower

Dr. Jeffrey Mower

For hundreds of years, the origins of the juicy strawberry we know and love remained a juicy mystery. Now, a landmark study including PSI’s Jeff Mower has cracked the code, revealing the evolutionary blueprint of the octoploid strawberry and its wild ancestors.

This breakthrough, published in Nature Plants, shines a light on the intricate dance of ancient tetraploids and hexaploids that ultimately led to the birth of the modern strawberry. The key players? Three key diploid species: Fragaria vesca subsp. bracteata, F. iinumae, and a now-extinct relative of F. iinumae.

Using cutting-edge genomic sequencing and analysis, the researchers unraveled the complex puzzle of the four subgenomes that make up the octoploid strawberry genome. This meticulous detective work uncovered crucial clues, confirming the long-suspected role of F. vesca subsp. bracteata and F. iinumae as the direct sources of the A and B subgenomes, respectively. For the C and D subgenomes, previously proposed ancestors, F. viridis and F. nipponica, were ruled out after facing rigorous genomic interrogation, with the evidence pointing instead to extinct relatives of F. iinumae as the likely source. Additionally, the study reshuffled the deck within the C and D subgenomes, reassigning three pairs of homoeologous chromosomes based on shared genetic fingerprints.

This discovery is more than just academic curiosity. It opens doors for strawberry breeders, guiding them towards promising wild relatives as sources of valuable genetic diversity for future cultivars. Accessions of F. vesca subsp. bracteata and F. iinumae can now be prioritized for preservation and characterization, ensuring a secure genetic library for future breeding efforts.

However, the strawberry saga isn't quite over. The exact details of the polyploid tango remain shrouded in some mystery, where clues might lie in the whispers of extinct ancestors. The C and D subgenomes, while closely related, hint at a possible ancient tetraploid ancestor. Was it an autotetraploid or an allotetraploid?

The study also suggests the existence of a vanished hexaploid containing the B, C, and D subgenomes, estimated to have emerged around 3 million years ago. Perhaps, with advances in environmental DNA sequencing, these ghostly ancestors could one day be resurrected from the fossil record, completing the captivating story of the strawberry's rise to fame.

This groundbreaking study not only unveils the intricate story of the strawberry's past but also paves the way for a brighter future for this beloved fruit. By understanding its genetic roots, we can unlock its full potential, ensuring the next bite of a juicy strawberry is not just delicious, but also a testament to the power of evolutionary genomics.

Figure A
Fig. 1 (A): Morphological features of F. chiloensis, F. virginiana, F. nipponica, and the cultivar ‘Camarosa’. Scale bar, 1 cm. Adapted from Fig S1 of Jin et al 2023 Nat Plants.
Figure 2
Fig. 2: Subgenome assignments of the octoploids and tracing the potential diploid ancestors. a, Clustering of differential k-mers (k = 13 and frequency ≥ 50) among homoeologous chromosome sets that could differentiate F. virginiana (hap1) chromosomes into four subgenomes. n is the number of specific k-mers on each subgenome. b, PCA plots of four assemblies based on differential k-mers. The values in parentheses indicate the percentage of variance explained. c, Comparison of the subgenome assignment in this study and that previously proposed for the strawberry cultivar ‘Camarosa’ by Hardigan et al.33 and Edger et al.26. d, Phylogenetic analysis of the three octoploids (each with four subgenomes) and nine diploid Fragaria species. Note: The clades where F. iinumae and F. vesca are located are shown in blue and red, respectively. e, Genetic contributions of diploid strawberry species to octoploids. The percentages of resequencing data from 22 F. chiloensis accessions, 20 F. virginiana accessions and 42 F. × ananassa cultivars that mapped to eight Fragaria diploid species (F. iinumae (Fiin), F. vesca (Fves), F. nipponica (Fnip), F. viridis (Fvir), F. nilgerrensis (Fnil), F. daltoniana (Fdal), F. pentaphylla (Fpen) and F. nubicola (Fnub)) and organelle genomes (Chlo and Mito) are shown. The data are presented as mean values ±1 s.e.m. (one-way ANOVA with Duncan’s multiple range test; d.f. = 175, 159 and 335, respectively; ***P < 0.001). f, The depth of reads of a cultivated strawberry accession (sample_023)33 mapped to the eight diploid strawberry genomes (top) and the distribution of reads contributed by diploids to each subgenome (bottom). >