Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle

BMC Genomics

Research Article

Heidi Signer-Hasler¹  Christine Flury¹  Ruedi Fries²  Hubert Pausch³  Dorian Garrick⁴  Birgit Gredler-Grandl⁵  Beat Bapst⁵  Mirjam Frischknecht⁶  Christian Stricker⁷ 

[1]Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, 3052, Zollikofen, Switzerland

[2]Chair of Animal Breeding, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany

[3]Chair of Animal Breeding, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany

[4]Agriculture Victoria, AgriBio, Centre for AgriBioscience, 3083, Bundoora, VIC, Australia

[5]ETH Zurich, Tannenstrasse 1, 8092, Zurich, Switzerland

[6]Institute of Veterinary, Animal & Biomedical Sciences, Massey University, 4442, Palmerston North, New Zealand

[7]Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland

[8]Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland

[9]Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFL, Länggasse 85, 3052, Zollikofen, Switzerland

[10]agn Genetics GmbH, 8b Börtjistrasse, 7260, Davos, Switzerland

关键词: Whole genome sequencing;    Imputation;    Accuracy;    Genome-wide association study;    QTL discovery;    Milk traits;    Brown Swiss;    Dairy cattle;   

DOI  :  10.1186/s12864-017-4390-2

 received in 2017-03-14, accepted in 2017-12-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundWithin the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required.ResultsIn this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study.ConclusionsOur study demonstrates that whole-genome sequence information can be imputed at high accuracy in cattle populations. Using imputed sequence variant genotypes in genome-wide association studies may facilitate causal variant detection.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

Fig. 1