A ddRAD Based Linkage Map of the Cultivated Strawberry, Fragaria xananassa

Abstract

The cultivated strawberry (Fragaria ×ananassa Duch.) is an allo-octoploid considered difficult to disentangle genetically due to its four relatively similar sub-genomic chromosome sets. This has been alleviated by the recent release of the strawberry IStraw90 whole genome genotyping array. However, array resolution relies on the genotypes used in the array construction and may be of limited general use. SNP detection based on reduced genomic sequencing approaches has the potential of providing better coverage in cases where the studied genotypes are only distantly related from the SNP array’s construction foundation. Here we have used double digest restriction-associated DNA sequencing (ddRAD) to identify SNPs in a 145 seedling F1 hybrid population raised from the cross between the cultivars Sonata (♀) and Babette (♂). A linkage map containing 907 markers which spanned 1,581.5 cM across 31 linkage groups representing the 28 chromosomes of the species. Comparing the physical span of the SNP markers with the F. vesca genome sequence, the linkage groups resolved covered 79% of the estimated 830 Mb of the F. ×ananassa genome. Here, we have developed the first linkage map for F. ×ananassa using ddRAD and show that this technique and other related techniques are useful tools for linkage map development and downstream genetic studies in the octoploid strawberry.

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

“…RRS methods have been widely used in genetic mapping studies. RADseq was used to develop linkage maps and conduct QTL analysis in crops including aubergine (Barchi et al, 2011(Barchi et al, , 2012, barley (Chutimanitsakun et al, 2011) and cultivated strawberry (Davik et al, 2015). The GBS method was originally tested with 276 RILs from a maize mapping population, which led to the identification of 200 000 markers (Elshire et al, 2011).…”

Double‐digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

“…At present, Illumina HiSeq is the most commonly used platform for genome resequencing albeit the short read lengths per loci (e.g., <100 bps; but MiSeq is used by Davik et al (2015), Kess et al (2016) and Vivian and Rn (2017)). This platform has the ability to produce sufficient coverage depth per locus, given an appropriate multiplexing density, to overcome potential sequencing errors and false SNP calls as well as produce high numbers of shared loci among samples.…”

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

“…P. cactorum is a persistent pathogen of strawberry and an economically significant pathogen of apple (Erwin and Ribeiro 1996). Genomic resources are available for these hosts (Antanaviciute et al 2012; Hirakawa et al 2014; Davik et al 2015; Daccord et al 2017), and recent work has identified resistance-associated QTL for cultivated strawberry (Nellist et al 2018). Despite this, genomic resources for the pathogen are limited to identification of ESTs expressed during infection (Chen et al 2011) and transcript expression during oospore germination characterized (Chen et al 2014; Chen et al 2017).…”