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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

Author
item Denoyes, Beatrice - University Of Bordeaux
item Amaya, Iraida - Ifapa Centro Alameda Del Obispo
item Liston, Aaron - Oregon State University
item Tennessen, Jacob - Oregon State University
item Ashman, Tia-lynn - University Of Pittsburgh
item Whitaker, Vance - University Of Florida
item Hytönen, Timo - University Of Helsinki
item Van De Weg, Eric - University Of Wurzburg
item Osorio, Sonia - University Of Malaga
item Folta, Kevin - University Of Florida
item Slovin, Janet
item Harrison, Richard - East Malling Research
item Monfort, Amparo - Institute De Recerca I Tecnologia Agroalimentaries (IRTA)
item Bassil, Nahla

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2016
Publication Date: 4/20/2017
Citation: Denoyes, B., Amaya, I., Liston, A., Tennessen, J., Ashman, T., Whitaker, V., Hytönen, T., van de Weg, E., Osorio, S., Folta, K., Slovin, J.P., Harrison, R., Monfort, A., Bassil, N.V. 2017. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. Acta Horticulturae. 1156:13-24. doi: 10.17660/ActaHortic.2017.1156.3.

Interpretive Summary: In the last decade, new genomic tools have promised to bridge the gap between plant physiology and plant sciences. In strawberry, the woodland strawberry was the first reference genome sequence obtained in the Rosoideae sub-family. This genome has a high level of similarity to genomes of other species of strawberry, and it also provides a reference for closely related plants like brambles and roses. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses have appeared in addition to the classical segregating biparental population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. In this article, selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.

Technical Abstract: In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.