Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives

Abstract

The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array

“…65,66 Our synteny analysis indicated a high level of conservation between the rose and strawberry genomes. The majority of the markers that mapped on one linkage group in rose had their highest sequence similarity with the sequence of a single pseudochromosome of strawberry, with the exception of rose linkage groups 2 and 3: their markers corresponded to both strawberry pseudochromosomes 1 and 6, indicating that translocations have occurred.…”

Fragaria: A genus with deep historical roots and ripe for evolutionary and ecological insights

“…Fragaria vesca has several attributes that made it an attractive target for genome sequencing. It is a diploid with a relatively small 206‐Mbp genome (Longhi et al, 2014). Compared with most other cultivated perennials, the plants are compact, easily grown under controlled conditions, and can be propagated both sexually and asexually (Slovin and Michael, 2011).…”

“…An efficient transformation system for F. vesca has been developed (Oosumi et al, 2006) and transposon‐tagged mutants are available for reverse genetics applications (Veilleux et al, 2012). The genome sequence of F. vesca has already facilitated significant progress in functional genomics of flowering (Mouhu et al, 2013; Hollender et al, 2014) and fruiting (Kang et al, 2013), and these advances will ultimately be applied to crop improvement efforts (Folta, 2013; Longhi et al, 2014). More immediate progress is anticipated from the vast numbers of genetic markers developed from the genome sequence of F. vesca that can be used in genetic linkage mapping (Tennessen et al, 2013) and high‐throughput assays for marker‐assisted breeding (Chambers et al, 2013).…”

HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry ( Fragaria×ananassa )

“…It is a genetically-complex species with an allo-octoploid genome (2n=8x=56) with an approximate size of 830 Mbp [1] (adjusted in relation to the 240 Mbp genome size of F. vesca reported by Shulaev et al [2]. Well-established breeding programs exist for its genetic improvement, many of which employ, to a greater or lesser extent, molecular marker technology to facilitate the breeding process [3].…”