Biology Faculty Articles
Document Type
Article
Publication Date
6-1-2016
Publication Title
G3
Keywords
Felis catus, Illumina 63K SNP array, Genetic map, Recombination, Domestic cat
ISSN
2160-1836
Volume
6
Issue/No.
6
First Page
1607
Last Page
1616
Abstract
High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catusv8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.
Additional Comments
Morris Animal Foundation/Cat Health Network grant #s: D12FE019, D12FE502, D12FE-501, D12FE507, D12FE560; Winn Feline Foundation grant #: W11-041; University of California-Davis grant #: 2010-09-F; NIH National Human Genome Research Institute grant #: 5U54HG00307907; National Robotics Initiative grant #s: 2009-35205-05209, 20008-04049; Russian Ministry of Science mega-grant #: 11.G34.31.0068
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
NSUWorks Citation
Li, Gang; LaDeana W. Hillier; Robert A. Grahn; Aleksey V. Zimin; Victor A. David; Marilyn Menotti-Raymond; Rondo Middleton; Steven S. Hannah; Sher L. Hendrickson; Alexey Makunin; Stephen J. O'Brien; Patrick Minx; Richard K. Wilson; Leslie A. Lyons; Wesley C. Warren; and William J. Murphy. 2016. "A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination." G3 6, (6): 1607-1616. doi:g3.116.028746v1.
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
DOI
g3.116.028746v1
Comments
© 2016 Li et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.