RESEARCH ARTICLE
Rare Variants in Transcript and Potential Regulatory Regions Explain a Small Percentage of the Missing Heritability of Complex Traits in Cattle Oscar Gonzalez-Recio1,2*, Hans D. Daetwyler1,2,3, Iona M. MacLeod1,2,4, Jennie E. Pryce1,2,3, Phil J. Bowman1,2, Ben J. Hayes1,2,3, Michael E. Goddard1,4 1 Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, 3083, Australia, 2 Dairy Futures Cooperative Research Centre, Bundoora, Victoria, 3083, Australia, 3 School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia, 4 Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria, 3010, Australia *
[email protected] OPEN ACCESS Citation: Gonzalez-Recio O, Daetwyler HD, MacLeod IM, Pryce JE, Bowman PJ, Hayes BJ, et al. (2015) Rare Variants in Transcript and Potential Regulatory Regions Explain a Small Percentage of the Missing Heritability of Complex Traits in Cattle. PLoS ONE 10(12): e0143945. doi:10.1371/journal. pone.0143945 Editor: Marinus F.W. te Pas, Wageningen UR Livestock Research, NETHERLANDS Received: August 26, 2015 Accepted: November 11, 2015 Published: December 7, 2015 Copyright: © 2015 Gonzalez-Recio et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Variants annotations were obtained from www.1000bullgenomes.com/ (see Daetwyler et al., 2014 in Nature Genetics). Phenotypes are owned by the Australian Dairy Herd Improvement Scheme (ADHIS) www.adhis.com.au. Their public availability is out of control of the authors, and confidential restrictions may apply. Please contact General Manager Daniel Abernethy (
[email protected]) for data requests.
Abstract The proportion of genetic variation in complex traits explained by rare variants is a key question for genomic prediction, and for identifying the basis of “missing heritability”–the proportion of additive genetic variation not captured by common variants on SNP arrays. Sequence variants in transcript and regulatory regions from 429 sequenced animals were used to impute high density SNP genotypes of 3311 Holstein sires to sequence. There were 675,062 common variants (MAF>0.05), 102,549 uncommon variants (0.01
