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

Authors: DENOYES, BEATRICE - University Of Bordeaux; AMAYA, IRAIDA - Instituto De Investigacion Y Formacion Agraria Y Pesquera; LISTON, AARON - Oregon State University; TENNESSEN, JACOB - Oregon State University; ASHMAN, TIA-LYNN - University Of Pittsburgh; WHITAKER, VANCE - University Of Florida; HYTÖNEN, TIMO - University Of Helsinki; VAN DE WEG, ERIC - Plant Research International - Netherlands; OSORIO, SONIA - University Of Malaga; FOLTA, KEVIN - University Of Florida; Slovin, Janet; HARRISON, RICHARD - East Malling Research; MONFORT, AMPARO - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); Bassil, Nahla

Submitted to: Acta Horticulturae
Publication Type: Review Article
Publication Acceptance Date: 8/15/2016
Publication Date: 9/30/2016
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. 2016. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come. Acta Horticulturae. https://doi.org/10.17660/ActaHortic.2017.1156.3.
DOI: https://doi.org/10.17660/ActaHortic.2017.1156.3

Interpretive Summary: Strawberry is an agronomically important crop grown throughout the world for its distinctive sweet and nutritious berry. This review is a compendium of information from laboratories around the world about the recent advances in genetics and molecular biology that have made the diploid woodland strawberry an excellent plant model for studying fruit quality, how these plants grow and develop, how they respond to and resist infection by fungi, bacteria, and viruses, and how they tolerate stresses such as drought and heat. The information gained from the woodland strawberry has led to advances in our understanding of the more complex commercial dessert strawberry that will benefit breeders, growers, processors, and researchers interested in improving strawberry production.

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.