A genome-wide scan for signatures of differential artificial selection in ten cattle breeds

BMC Genomics

Research Article

Martin Förster¹  Sophie Rothammer¹  Ivica Medugorac¹  Doris Seichter² 

[1] Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539, Munich, Germany;Tierzuchtforschung e.V. München, Senator-Gerauer-Straße 23, 85586, Grub, Germany;

关键词: Selection signature;    XP-EHH;    Cattle;    Artificial selection;    Adaptation;   

DOI  :  10.1186/1471-2164-14-908

 received in 2013-01-23, accepted in 2013-12-16,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSince the times of domestication, cattle have been continually shaped by the influence of humans. Relatively recent history, including breed formation and the still enduring enormous improvement of economically important traits, is expected to have left distinctive footprints of selection within the genome. The purpose of this study was to map genome-wide selection signatures in ten cattle breeds and thus improve the understanding of the genome response to strong artificial selection and support the identification of the underlying genetic variants of favoured phenotypes. We analysed 47,651 single nucleotide polymorphisms (SNP) using Cross Population Extended Haplotype Homozygosity (XP-EHH).ResultsWe set the significance thresholds using the maximum XP-EHH values of two essentially artificially unselected breeds and found up to 229 selection signatures per breed. Through a confirmation process we verified selection for three distinct phenotypes typical for one breed (polledness in Galloway, double muscling in Blanc-Bleu Belge and red coat colour in Red Holstein cattle). Moreover, we detected six genes strongly associated with known QTL for beef or dairy traits (TG, ABCG2, DGAT1, GH1, GHR and the Casein Cluster) within selection signatures of at least one breed. A literature search for genes lying in outstanding signatures revealed further promising candidate genes. However, in concordance with previous genome-wide studies, we also detected a substantial number of signatures without any yet known gene content.ConclusionsThese results show the power of XP-EHH analyses in cattle to discover promising candidate genes and raise the hope of identifying phenotypically important variants in the near future. The finding of plausible functional candidates in some short signatures supports this hope. For instance, MAP2K6 is the only annotated gene of two signatures detected in Galloway and Gelbvieh cattle and is already known to be associated with carcass weight, back fat thickness and marbling score in Korean beef cattle. Based on the confirmation process and literature search we deduce that XP-EHH is able to uncover numerous artificial selection targets in subpopulations of domesticated animals.

【 授权许可】

Unknown   
© Rothammer et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.