DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection
文献类型： 外文期刊
作者： Zheng, Weigang 1 ; Ma, Wenlong 3 ; Chen, Zhilong 3 ; Wang, Chao 1 ; Sun, Tao 3 ; Dong, Wenjun 1 ; Zhang, Wenjing 5 ; Zhang, Song 3 ; Tang, Zhonglin 3 ; Li, Kui 3 ; Zhao, Yunxiang 7 ; Liu, Yuwen 1 ;
作者机构： 1.Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan 430070, Peoples R China
2.Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Swine Genet & Breeding, Minist Agr & Rural Affairs, Wuhan 430070, Peoples R China
3.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Key Lab Livestock & Poultry Multiom MARA, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr, Shenzhen 518124, Peoples R China
4.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Res Ctr Anim Genome, Innovat Grp Pig Genome Design & Breeding, Shenzhen 518124, Peoples R China
5.South China Agr Univ, Natl Engn Res Ctr Breeding Swine Ind, State Key Lab Swine & Poultry Breeding Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Guangzhou 510642, Peoples R China
6.Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Foshan 528226, Peoples R China
7.Guangxi Univ, Coll Anim Sci & Technol, Guangxi Key Lab Anim Breeding Dis Control & Preven, Nanning 530004, Peoples R China
关键词： breeding models; genetic screening of embryos; genomic selection; genotype imputation; single cell genotype
期刊名称：ADVANCED SCIENCE （ 影响因子：14.1； 五年影响因子：15.6 ）
ISSN：
年卷期： 2025 年 12 卷 16 期
页码：
收录情况： SCI
摘要： Whole-genome sequencing is pivotal for elucidating the complex relationships between genotype and phenotype. However, its widespread application is hindered by the high sequencing depth and large sample sizes required, especially for genomic selection (GS) reliant on precise phenotype prediction from high-density genotype data. To address this, DPImpute (Dual-Phase Impute) is developed, an two-step imputation pipeline enabling accurate whole-genome SNP genotyping under ultra-low coverage whole-genome sequencing (ulcWGS) depths, small testing sample sizes, and limited reference populations. DPImpute achieved 98.06% SNP imputation accuracy with minimal testing samples (<= 10), reference samples (<= 100), and an ultra-low sequencing depth of 0.3X, surpassing the accuracy of existing imputation methods. Moreover, this high accuracy is maintained across multi-ancestry human populations. Remarkably, DPImpute demonstrated accurate SNP imputation from low-coverage sequencing data from single blood cells and single blastocyst cells, highlighting its potential in embryo GS. To enhance the accessibility of DPImpute, a user-friendly web server () is developed and a Docker container for seamless implementation. In summary, DPImpute can significantly expedite breeding programs through precise and cost-effective genotyping and serve as a valuable tool for diverse population genotyping, encompassing both human and animal studies.
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