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

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.

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

“…While diploid models have a logical place in biological studies ( Gaston et al. 2020 ), our findings and many others highlight the feasibility and simplicity with which genetic and genomic approaches can be applied in allo-octoploid populations to discover genotype-to-phenotype associations, identify causal loci and mutations, understand and exploit natural genetic variation, and apply genome-informed breeding approaches ( Liston et al.2014 ; Denoyes et al. 2017 ; Oh et al.…”

Genome‐wide diversity analysis suggests divergence among Upper Guinea and the Dahomey Gap populations of the Sisrè berry (Syn: miracle fruit) plant (Synsepalum dulcificum [Schumach. & Thonn.] Daniell) in West Africa

“…Compared with moreheavily invested berry crops, however, such as strawberry ( Fragaria × ananassa ) (Barbey et al., 2020; Denoyes et al., 2016; Nelson et al., 2021), blueberry ( Vaccinium corymbosum ) (Die & Rowland, 2013; Qi et al., 2021), cranberry ( Vaccinium macrocarpon ) (Covarrubias‐Pazaran et al., 2016; Diaz‐Garcia et al., 2021), and blackberry ( Rubus spp.) (Foster et al., 2019; Garcia‐Seco et al., 2015), all of which benefit from long breeding histories and extensive genomic resources, Sisrè berry is an orphan crop with no systematic history of breeding or readily available genetic resources or information to facilitate its improvement.…”