850K SNP array for the cultivated strawberry Fragaria x ananassa

Overview
Analysis Name850K SNP array for the cultivated strawberry Fragaria x ananassa
MethodSNP discovery and filtering pipelines using various programs and strategies
Sourcethe Camaraso v1.0 genome and a diversity panel of 93 strawberry individuals
Date performed2020-02-07

Abstract

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.

Publication

Hardigan Michael A., Feldmann Mitchell J., Lorant Anne, Bird Kevin A., Famula Randi, Acharya Charlotte, Cole Glenn, Edger Patrick P., Knapp Steven J. Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution. Front. Plant Sci., 07 February 2020 | https://doi.org/10.3389/fpls.2019.01789

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All supplementary data files are also available in the DRYAD database (dryad.org). DOI https://doi.org/10.25338/B8R31Q
File  File Description
Affymetrix_FanaSNP_probe_info.txt  
SNPcalls.50K_genotypes.txt  
SNPcalls.850K_genotypes.txt  
Supplementary_Dataset_01.xlsx Summary of octoploid genetic maps generated by WGS sequencing, 50K SNP array, and DNA capture datasets
Supplementary_Dataset_02.xlsx 850K screening array diversity panel of octoploid strawberry cultivars and wild accessions
 
Supplementary_Dataset_03.zip Panel of 446,644 validated marker probes from the 850K SNP screening array.
 
Supplementary_Dataset_04.xlsx Panel of 49,483 marker probes selected for populating the 50K SNP production array.
 
genetic_maps.xlsx.zip