journal article·2025-04Open access

DPImpute: A Genotype Imputation Framework for Ultra‐Low Coverage Whole‐Genome Sequencing and its Application in Genomic Selection

Weigang Zheng, Wenlong Ma, Zhilong Chen, Chao Wang, Tao Sun, Wenjun Dong, Wenjing Zhang, Song Zhang, Zhonglin Tang, Kui Li, Yunxiang Zhao, Yuwen Liu

Advanced Science· Volume 12· Issue 16

Abstract

Abstract 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 (https://agdb.ecenr.com/DPImpute/home) 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.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Genetic and phenotypic traits in livestock · Genetic Mapping and Diversity in Plants and Animals · Genetic Associations and Epidemiology

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs College of Animal Science and Technology Huazhong Agricultural University Wuhan 430070 China

Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture Key Laboratory of Livestock and Poultry Multi‐Omics of MARA Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518124 China

Innovation Group of Pig Genome Design and Breeding Research Centre for Animal Genome Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518124 China

State Key Laboratory of Swine and Poultry Breeding Industry National Engineering Research Center for Breeding Swine Industry Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding College of Animal Science South China Agricultural University Guangzhou 510642 China

Kunpeng Institute of Modern Agriculture at Foshan Chinese Academy of Agricultural Sciences Foshan 528226 China

Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology Guangxi University Nanning 530004 China

Funding

National Natural Science Foundation of China · National Key Research and Development Program of China

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