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Applications and efficiencies of the first cat 63K DNA array

Gandolfi, Barbara, Alhaddad, Hasan, Abdi, Mona, Bach, Leslie H., Creighton, Erica K., Davis, Brian W., Decker, Jared E., Dodman, Nicholas H., Grahn, Jennifer C., Grahn, Robert A. , Haase, Bianca, Haggstrom, Jens, Hamilton, Michael J., Helps, Christopher R., Kurushima, Jennifer D., Lohi, Hannes, Longeri, Maria, Malik, Richard, Meurs, Kathryn M., Montague, Michael J., Mullikin, James C., Murphy, William J., Nilson, Sara M., Pedersen, Niels C., Peterson, Carlyn B., Rusbridge, Clare, Saif, Rashid, Shelton, Diane G., Warren, Wesley C., Wasim, Muhammad and Lyons, Leslie A. (2018) Applications and efficiencies of the first cat 63K DNA array Scientific Reports, 8 (1), 7024. pp. 1-15.

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Abstract

The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infnium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efciency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confrmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under diferent modes of inheritance, selection and population sizes. The efcient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Veterinary Medicine
Authors :
NameEmailORCID
Gandolfi, Barbara
Alhaddad, Hasan
Abdi, Mona
Bach, Leslie H.
Creighton, Erica K.
Davis, Brian W.
Decker, Jared E.
Dodman, Nicholas H.
Grahn, Jennifer C.
Grahn, Robert A.
Haase, Bianca
Haggstrom, Jens
Hamilton, Michael J.
Helps, Christopher R.
Kurushima, Jennifer D.
Lohi, Hannes
Longeri, Maria
Malik, Richard
Meurs, Kathryn M.
Montague, Michael J.
Mullikin, James C.
Murphy, William J.
Nilson, Sara M.
Pedersen, Niels C.
Peterson, Carlyn B.
Rusbridge, Clarec.rusbridge@surrey.ac.uk
Saif, Rashid
Shelton, Diane G.
Warren, Wesley C.
Wasim, Muhammad
Lyons, Leslie A.
Date : 4 May 2018
DOI : 10.1038/s41598-018-25438-0
Copyright Disclaimer : © The Author(s) 2018. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Te images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Depositing User : Melanie Hughes
Date Deposited : 08 May 2018 14:12
Last Modified : 16 Jan 2019 19:09
URI: http://epubs.surrey.ac.uk/id/eprint/846371

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