Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

Abstract

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

“…The octoploid strawberry genome has been described as "notoriously complex" and an "extreme example of difficulty" for study (Folta and Davis, 2006;Hirsch and Buell, 2013;Hirakawa et al, 2014;Koskela et al, 2016). While GBS, GWAS, and NGS-reliant applications are relatively straightforward in organisms with well-characterized reference genomes, such approaches were previously difficult or intractable in octoploid strawberry Tennessen et al, 2014;Bassil et al, 2015;Vining et al, 2017). Genetic studies in octoploid strawberry previously relied on the genome of woodland strawberry (F. vesca), an extant relative to one of four diploid subgenomes contained in F. × ananassa (Shulaev et al, 2011;Edger et al, 2017).…”

“…Genetic studies in octoploid strawberry previously relied on the genome of woodland strawberry (F. vesca), an extant relative to one of four diploid subgenomes contained in F. × ananassa (Shulaev et al, 2011;Edger et al, 2017). For nearly a decade, the F. vesca genome was the only framework available for DNA variant discovery, gene discovery, genetic mapping, and genome-wide association studies in octoploid strawberry (Tennessen et al, 2014;Bassil et al, 2015;Davik et al, 2015;Vining et al, 2017;Pincot et al, 2018). The development of a chromosome-scale reference genome for F. × ananassa (Edger et al, 2019b) provided the physical framework needed to overcome previous barriers, and explore the organization and evolution of its progenitor genomes.…”

A roadmap for research in octoploid strawberry

“…Underlying computational challenges associated with genotyping by sequencing (GBS) and other nextgeneration sequencing (NGS) facilitated approaches have limited their widespread application in octoploid strawberry thus far 36,37 . The challenges are similar across species, but obviously exacerbated in allogamous polyploids: uneven and inadequate sequencing depth, copy number uncertainty, heterozygote miscalling, missing data, sequencing errors, etc., all of which challenge the integration of DNA variant information across studies [38][39][40] .…”

“…The challenges are similar across species, but obviously exacerbated in allogamous polyploids: uneven and inadequate sequencing depth, copy number uncertainty, heterozygote miscalling, missing data, sequencing errors, etc., all of which challenge the integration of DNA variant information across studies [38][39][40] . As with the other DNA marker genotyping approaches reviewed here, the first GBS study in octoploid strawberry utilized the diploid F. vesca reference genome in combination with a phylogenetic approach (POLiMAPS) for aligning, classifying, and calling DNA variants 9,36 .…”

Chromosome Evolution of Octoploid Strawberry

“…Fragaria relative to the diploid ancestral genomes would have occurred early 433 on, before the speciation of F. chiloensis and F. virginiana Vining et al, 2017)…”