Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle
Abstract Background Within 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 gen...
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| Format: | Article |
| Language: | English |
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BMC
2017-12-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4390-2 |
| _version_ | 1811302917739642880 |
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| author | Mirjam Frischknecht Hubert Pausch Beat Bapst Heidi Signer-Hasler Christine Flury Dorian Garrick Christian Stricker Ruedi Fries Birgit Gredler-Grandl |
| author_facet | Mirjam Frischknecht Hubert Pausch Beat Bapst Heidi Signer-Hasler Christine Flury Dorian Garrick Christian Stricker Ruedi Fries Birgit Gredler-Grandl |
| author_sort | Mirjam Frischknecht |
| collection | DOAJ |
| description | Abstract Background Within 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. Results In 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. Conclusions Our 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. |
| first_indexed | 2024-04-13T07:37:52Z |
| format | Article |
| id | doaj.art-6001e8ec268c4e3fa8399158794e818b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T07:37:52Z |
| publishDate | 2017-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6001e8ec268c4e3fa8399158794e818b2022-12-22T02:56:03ZengBMCBMC Genomics1471-21642017-12-0118111010.1186/s12864-017-4390-2Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattleMirjam Frischknecht0Hubert Pausch1Beat Bapst2Heidi Signer-Hasler3Christine Flury4Dorian Garrick5Christian Stricker6Ruedi Fries7Birgit Gredler-Grandl8Qualitas AGChair of Animal Breeding, Technische Universität MünchenQualitas AGBern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFLBern University of Applied Sciences, School of Agricultural, Forest and Food Sciences HAFLInstitute of Veterinary, Animal & Biomedical Sciences, Massey Universityagn Genetics GmbHChair of Animal Breeding, Technische Universität MünchenQualitas AGAbstract Background Within 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. Results In 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. Conclusions Our 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.http://link.springer.com/article/10.1186/s12864-017-4390-2Whole genome sequencingImputationAccuracyGenome-wide association studyQTL discoveryMilk traits |
| spellingShingle | Mirjam Frischknecht Hubert Pausch Beat Bapst Heidi Signer-Hasler Christine Flury Dorian Garrick Christian Stricker Ruedi Fries Birgit Gredler-Grandl Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle BMC Genomics Whole genome sequencing Imputation Accuracy Genome-wide association study QTL discovery Milk traits |
| title | Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle |
| title_full | Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle |
| title_fullStr | Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle |
| title_full_unstemmed | Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle |
| title_short | Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle |
| title_sort | highly accurate sequence imputation enables precise qtl mapping in brown swiss cattle |
| topic | Whole genome sequencing Imputation Accuracy Genome-wide association study QTL discovery Milk traits |
| url | http://link.springer.com/article/10.1186/s12864-017-4390-2 |
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