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.
Highlights
Fragaria is an important soft fruit genus, primarily due to the cultivation of the genetically complex garden strawberry (Fragaria ×ananassa Duch; 2n = 8x = 56)
This resulted in a list of 1,098 SNPcontaining stacks that were used for mapping
The final linkage map produced contained a total of 902 sequence characterized single nucleotide polymorphisms (SNPs) markers in 650 mapping bins spanning 1,581.5 cM across 31 linkage group fragments that corresponded to the full complement of 28 chromosomes of the F. ×ananassa genome (Fig 1)
Summary
Fragaria is an important soft fruit genus, primarily due to the cultivation of the genetically complex garden strawberry (Fragaria ×ananassa Duch; 2n = 8x = 56). In 2012, the world production of strawberries exceeded 5 million tons and the crop was valued in excess of US$10 billion [1]. In addition to its aesthetic qualities and nutritional value, strawberry is appreciated for its flavor, aroma, and content of ‘health-benefitting’ antioxidant compounds [2]. The cultivated strawberry is a genetically complex allo-octoploid (2n = 8x = 56). Very recent studies of the sub-genome structure of the species have determined that at least three diploid donors have contributed to the extant genome composition.
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