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

The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance,including the soft fruit species strawberry(Fragaria 3ananassa),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.

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.