Imputation for sequencing variants preselected to a customized low-density chip

doi:10.1038/s41598-020-66523-7

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	Imputation for sequencing variants preselected to a customized low-density chip
	Liu, Aoxing 3,4,5; Lund, Mogens Sando 5; Boichard, Didier 2; Mao, Xiaowei 6,7; Karaman, Emre 5; Fritz, Sebastien 2,8; Aamand, Gert Pedersen 1; Wang, Yachun 3,4; Su, Guosheng 5
刊名	SCIENTIFIC REPORTS
	2020-06-12
卷号	10 期号:1 页码:9
ISSN号	2045-2322
DOI	10.1038/s41598-020-66523-7
英文摘要	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.
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关键词	DAIRY-CATTLE ; GENOMIC PREDICTIONS ; MARKER PANELS ; HOLSTEIN ; GENOTYPES ; RELIABILITY ; ASSOCIATION ; TRAITS
WOS研究方向	Science & Technology - Other Topics
语种	英语
出版者	NATURE PUBLISHING GROUP
WOS记录号	WOS:000543969200005
内容类型	期刊论文
源URL	[http://119.78.100.205/handle/311034/17669]
专题	古脊椎动物与古人类研究所_图书馆1
通讯作者	Wang, Yachun; Su, Guosheng
作者单位	1.Nord Cattle Genet Evaluat, DK-8200 Aarhus, Denmark 2.Univ Paris Saclay, GABI, INRA, AgroParisTech, F-78350 Jouy En Josas, France 3.China Agr Univ, Natl Engn Lab Anim Breeding, Coll Anim Sci & Technol, Beijing 100193, Peoples R China 4.China Agr Univ, MARA, Key Lab Anim Genet Breeding & Reprod, Beijing 100193, Peoples R China 5.Aarhus Univ, Ctr Quantitat Genet & Genom, DK-8830 Tjele, Denmark 6.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China 7.CAS Ctr Excellence Life & Paleoenvironm, Beijing 100044, Peoples R China 8.ALLICE, F-75012 Paris, France
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.