KMS Institute of Vertebrate Paleontology and Paleoanthropology
| Imputation for sequencing variants preselected to a customized low-density chip | |
| Liu, Aoxing1,2,3; Lund, Mogens Sando1; Boichard, Didier4; Mao, Xiaowei5,6; Karaman, Emre1; Fritz, Sebastien4,7; Aamand, Gert Pedersen8; Wang, Yachun2,3; Su, Guosheng1 | |
| 2020-06-12 | |
| 发表期刊 | SCIENTIFIC REPORTS
 |
| ISSN | 2045-2322 |
| 卷号 | 10期号:1页码:9 |
| 摘要 | The sequencing variants preselected from association analyses and bioinformatics analyses could improve genomic prediction. In this study, the imputation of sequencing SNPs preselected from major dairy breeds in Denmark-Finland-Sweden (DFS) and France (FRA) was investigated for both contemporary animals and old bulls in Danish Jersey. For contemporary animals, a two-step imputation which first imputed to 54 K and then to 54 K + DFS + FRA SNPs achieved highest accuracy. Correlations between observed and imputed genotypes were 91.6% for DFS SNPs and 87.6% for FRA SNPs, while concordance rates were 96.6% for DFS SNPs and 93.5% for FRA SNPs. The SNPs with lower minor allele frequency (MAF) tended to have lower correlations but higher concordance rates. For old bulls, imputation for DFS and FRA SNPs were relatively accurate even for bulls without progenies (correlations higher than 97.2% and concordance rates higher than 98.4%). For contemporary animals, given limited imputation accuracy of preselected sequencing SNPs especially for SNPs with low MAF, it would be a good strategy to directly genotype preselected sequencing SNPs with a customized SNP chip. For old bulls, given high imputation accuracy for preselected sequencing SNPs with all MAF ranges, it would be unnecessary to re-genotype preselected sequencing SNPs. |
| DOI | 10.1038/s41598-020-66523-7 |
| 关键词[WOS] | DAIRY-CATTLE ; GENOMIC PREDICTIONS ; MARKER PANELS ; HOLSTEIN ; GENOTYPES ; RELIABILITY ; ASSOCIATION ; TRAITS |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助项目 | VikingGenetics (Randers, Denmark) ; Nordic Cattle Genetic Evaluation (Aarhus, Denmark) ; Danish Council of Strategic Research (Aarhus, Denmark) ; China Scholarship Council (CSC) ; Program for Changjiang Scholar and Innovation Research Team in University[IRT_15R62] |
| WOS研究方向 | Science & Technology - Other Topics |
| WOS类目 | Multidisciplinary Sciences |
| WOS记录号 | WOS:000543969200005 |
| 出版者 | NATURE PUBLISHING GROUP |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://119.78.100.205/handle/311034/17670 |
| 专题 | 中科院古脊椎所（2000年以后） |
| 通讯作者 | Wang, Yachun; Su, Guosheng |
| 作者单位 | 1.Aarhus Univ, Ctr Quantitat Genet & Genom, DK-8830 Tjele, Denmark 2.China Agr Univ, MARA, Key Lab Anim Genet Breeding & Reprod, Beijing 100193, Peoples R China 3.China Agr Univ, Natl Engn Lab Anim Breeding, Coll Anim Sci & Technol, Beijing 100193, Peoples R China 4.Univ Paris Saclay, GABI, INRA, AgroParisTech, F-78350 Jouy En Josas, France 5.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China 6.CAS Ctr Excellence Life & Paleoenvironm, Beijing 100044, Peoples R China 7.ALLICE, F-75012 Paris, France 8.Nord Cattle Genet Evaluat, DK-8200 Aarhus, Denmark |
| 推荐引用方式 GB/T 7714 | Liu, Aoxing,Lund, Mogens Sando,Boichard, Didier,et al. Imputation for sequencing variants preselected to a customized low-density chip[J]. SCIENTIFIC REPORTS,2020,10(1):9. |
| APA | Liu, Aoxing.,Lund, Mogens Sando.,Boichard, Didier.,Mao, Xiaowei.,Karaman, Emre.,...&Su, Guosheng.(2020).Imputation for sequencing variants preselected to a customized low-density chip.SCIENTIFIC REPORTS,10(1),9. |
| MLA | Liu, Aoxing,et al."Imputation for sequencing variants preselected to a customized low-density chip".SCIENTIFIC REPORTS 10.1(2020):9. |
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