Abstract: H. bulbosum WGS contigs, which were not included in the high-density genetic maps at first instance were included into these frameworks by applying an approach that anchors markers into genetic bins of a framework map as described earlier (Mascher et al., 2013a). To do so, a nearest-neighbor search was performed to find the set of framework markers with minimal Hamming distance to a given SNP. SNPs were placed into the framework map using the program canchor as published (Mascher et al., 2013a). Subsequently, SNP markers were filtered using the R statistical environment (R Core Team, 2012) in order to keep only H. bulbosum contigs where the major chromosome is supported by >= 95 % of framework map markers and the standard deviation of cM positions was at maximum 3.
License: CC0 1.0 Universal (Creative Commons Public Domain Dedication)
DOI: 10.5447/ipk/2017/15
Content: 0 Directories 1 Files (302.9 KB)
| CONTRIBUTOR: |
Martin Mascher,
Axel Himmelbach,
Federica Bini,
Jochen Kumlehn,
Nils Stein
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| CREATOR: |
Neele Wendler
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| PUBLISHER: | e!DAL - Plant Genomics and Phenomics Research Data Repository (PGP), IPK Gatersleben, Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany |
| SIZE: | 302.9 KB |
| SUBJECT: | De novoassembly of Hordeum bulbosum, Framework genetic map integration |