Abstract
The octoploid strawberry (Fragaria × ananassa Duch.) is one of the most important horticultural crops in the world. However, few genomic studies have been performed in this plant due to its polyploidy nature and complex genome. In this work, we developed diallelic single-nucleotide polymorphism (SNP) markers using next-generation resequencing data and high-resolution melting (HRM) analysis. We also constructed a genetic linkage map using an F1 segregating population derived from a cross between two cultivars, F. × ananassa ‘Sulhyang’ and ‘Senga-sengana’. A previous study revealed 20,848 SNP positions that can be developed into HRM markers. In this study, 576 SNP-based and 34 simple sequence repeat (SSR)-based HRM markers were developed using 832 newly designed and 461 previously reported primer sets, respectively. In addition, a strawberry genetic linkage map covering a total genetic distance of 1504.7 cM and consisting of 759 loci on 35 linkage groups was constructed. The linkage groups were assigned to corresponding chromosomes using the informative SSR-based markers and a BLAST search to the diploid strawberry genome, Fragaria vesca ver. 2.0.a1. Furthermore, the genome-wide HRM markers were applied to analyze the homozygosity of the inbred strawberry line ‘Wongyo 3115’, which showed a homozygosity of 96.6%. This marker and map information will be useful for future genomic and genetic research of the octoploid strawberry.
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Acknowledgements
This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through the Export Promotion Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (Grant Number: 315047-3).
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YRL performed all experiments and wrote manuscript. JK and SYL provided a strawberry inbred line and performed heterozygosity analysis. JL contributed to the concept of the study and experiment design, analyzed all data, and revised manuscript.
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Lee, Y.R., Kim, J., Lee, S.Y. et al. Diallelic SNP marker development and genetic linkage map construction in octoploid strawberry (Fragaria × ananassa) through next-generation resequencing and high-resolution melting analysis. Hortic. Environ. Biotechnol. 61, 371–383 (2020). https://doi.org/10.1007/s13580-019-00223-8
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DOI: https://doi.org/10.1007/s13580-019-00223-8