How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: linkage disequilibrium based variant filtering
The results indicate that identifying erroneous variants due to subgenome similarity can be effectively achieved without extensive genotyping of mapping populations. By implementing the LD-based filtering method, the phasing accuracy improved which improves the tracability of important alleles in the germplasm, paving the way for better understanding of trait associations in F. x ananassa.
Authors
- Richard G. F. Visser (ORCID: https://orcid.org/0000-0002-0213-4016)
- Johan Willemsen
- Dominic G. Hildebrand
- Chris Maliepaard (ORCID: https://orcid.org/0000-0002-7319-5270)
- Tim Koorevaar (ORCID: https://orcid.org/0000-0002-2122-2652)
- Paul Arens (ORCID: https://orcid.org/0000-0003-2118-389X)
Institutions
- Graduate School Experimental Plant Sciences (NL)
- Institute for Animal Husbandry (RS)
- Wageningen University & Research (NL)
Publication Details
- Journal
- BMC Genomics
- Published
- 2024-11-28
- DOI
- https://doi.org/10.1186/s12864-024-10987-8
- Citations
- 2
- Primary Topic
- Berry genetics and cultivation research
- Type
- article
- Field-Weighted Citation Impact
- 1.20