4.7 Article

The construction of a haplotype reference panel using extremely low coverage whole genome sequences and its application in genome-wide association studies and genomic prediction in Duroc pigs

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biology

Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy

Ruifei Yang et al.

Summary: This study presents a Tn5-based low-coverage sequencing method for obtaining a large number of whole-genome single-nucleotide polymorphisms in Duroc boars, leading to the identification of 14 quantitative trait loci for important agricultural traits in pigs. These findings provide insights into the genetic architecture of these traits and offer guidance for genetic improvement strategies in agricultural breeding.

GIGASCIENCE (2021)

Article Biochemistry & Molecular Biology

Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation

Wenqian Yang et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Agriculture, Dairy & Animal Science

Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling

Roger Ros-Freixedes et al.

GENETICS SELECTION EVOLUTION (2020)

Article Agriculture, Dairy & Animal Science

Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations

Roger Ros-Freixedes et al.

GENETICS SELECTION EVOLUTION (2020)

Article Agriculture, Dairy & Animal Science

Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle

Zexi Cai et al.

GENETICS SELECTION EVOLUTION (2020)

Article Biochemical Research Methods

Gimpute: an efficient genetic data imputation pipeline

Junfang Chen et al.

BIOINFORMATICS (2019)

Article Biochemical Research Methods

Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data

Ryan J. Eller et al.

BMC BIOINFORMATICS (2019)

Article Agriculture, Dairy & Animal Science

Genome-Wide Association Study for Reproductive Traits in a Duroc Pig Population

Zhe Zhang et al.

ANIMALS (2019)

Article Biochemical Research Methods

Very low-depth whole-genome sequencing in complex trait association studies

S. Arthur Gilly et al.

BIOINFORMATICS (2019)

Review Genetics & Heredity

Harnessing genomic information for livestock improvement

Michel Georges et al.

NATURE REVIEWS GENETICS (2019)

Article Agriculture, Dairy & Animal Science

Using imputed whole-genome sequence data to improve the accuracy of genomic prediction for parasite resistance in Australian sheep

Mohammad Al Kalaldeh et al.

GENETICS SELECTION EVOLUTION (2019)

Article Agriculture, Dairy & Animal Science

Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies

Sanne van den Berg et al.

GENETICS SELECTION EVOLUTION (2019)

Article Agriculture, Dairy & Animal Science

Using imputation-based whole-genome sequencing data to improve the accuracy of genomic prediction for combined populations in pigs

Hailiang Song et al.

GENETICS SELECTION EVOLUTION (2019)

Article Agriculture, Dairy & Animal Science

Genomic prediction based on selected variants from imputed whole-genome sequence data in Australian sheep populations

Nasir Moghaddar et al.

GENETICS SELECTION EVOLUTION (2019)

Article Agriculture, Dairy & Animal Science

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach

Yanjun Zan et al.

GENETICS SELECTION EVOLUTION (2019)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Agriculture, Dairy & Animal Science

Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Shaopan Ye et al.

JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY (2018)

Article Genetics & Heredity

A One-Penny Imputed Genome from Next-Generation Reference Panels

Brian L. Browning et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Article Agriculture, Dairy & Animal Science

Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees

Andrew Whalen et al.

GENETICS SELECTION EVOLUTION (2018)

Article Agriculture, Dairy & Animal Science

Assessment of the performance of hidden Markov models for imputation in animal breeding

Andrew Whalen et al.

GENETICS SELECTION EVOLUTION (2018)

Article Genetics & Heredity

Concepts, estimation and interpretation of SNP-based heritability

Jian Yang et al.

NATURE GENETICS (2017)

Article Agriculture, Dairy & Animal Science

Incorporation of causative quantitative trait nucleotides in single-step GBLUP

Breno O. Fragomeni et al.

GENETICS SELECTION EVOLUTION (2017)

Review Genetics & Heredity

10 Years of GWAS Discovery: Biology, Function, and Translation

Peter M. Visscher et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2017)

Article Agriculture, Dairy & Animal Science

Accuracy of genomic prediction using imputed whole-genome sequence data in white layers

M. Heidaritabar et al.

JOURNAL OF ANIMAL BREEDING AND GENETICS (2016)

Article Genetics & Heredity

Rapid genotype imputation from sequence without reference panels

Robert W. Davies et al.

NATURE GENETICS (2016)

Article Genetics & Heredity

A reference panel of 64,976 haplotypes for genotype imputation

Shane McCarthy et al.

NATURE GENETICS (2016)

Article Genetics & Heredity

Next-generation genotype imputation service and methods

Sayantan Das et al.

NATURE GENETICS (2016)

Review Genetics & Heredity

Developing and evaluating polygenic risk prediction models for stratified disease prevention

Nilanjan Chatterjee et al.

NATURE REVIEWS GENETICS (2016)

Article Multidisciplinary Sciences

Comparing performance of modern genotype imputation methods in different ethnicities

Nab Raj Roshyara et al.

SCIENTIFIC REPORTS (2016)

Article Agriculture, Dairy & Animal Science

Within- and across-breed genomic prediction using whole-genome sequence and single nucleotide polymorphism panels

Oscar O. M. Iheshiulor et al.

GENETICS SELECTION EVOLUTION (2016)

Article Biotechnology & Applied Microbiology

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations

Reuben J. Pengelly et al.

BMC GENOMICS (2015)

Article Agriculture, Dairy & Animal Science

Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction

R. F. Brondum et al.

JOURNAL OF DAIRY SCIENCE (2015)

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Article Agriculture, Dairy & Animal Science

Genomic prediction using imputed whole-genome sequence data in Holstein Friesian cattle

Rianne van Binsbergen et al.

GENETICS SELECTION EVOLUTION (2015)

Review Plant Sciences

Natural Variations and Genome-Wide Association Studies in Crop Plants

Xuehui Huang et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 65 (2014)

Article Biotechnology & Applied Microbiology

Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle

Rasmus Froberg Brondum et al.

BMC GENOMICS (2014)

Article Biotechnology & Applied Microbiology

A new approach for efficient genotype imputation using information from relatives

Mehdi Sargolzaei et al.

BMC GENOMICS (2014)

Article Genetics & Heredity

Genome-Wide Regression and Prediction with the BGLR Statistical Package

Paulino Perez et al.

GENETICS (2014)

Letter Biochemical Research Methods

Improved whole-chromosome phasing for disease and population genetic studies

Olivier Delaneau et al.

NATURE METHODS (2013)

Article Genetics & Heredity

Genome-wide efficient mixed-model analysis for association studies

Xiang Zhou et al.

NATURE GENETICS (2012)

Article Agriculture, Dairy & Animal Science

A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation

John M. Hickey et al.

GENETICS SELECTION EVOLUTION (2012)

Article Genetics & Heredity

GCTA: A Tool for Genome-wide Complex Trait Analysis

Jian Yang et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2011)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Genetics & Heredity

Genotype-Imputation Accuracy across Worldwide Human Populations

Lucy Huang et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Review Genetics & Heredity

Mapping genes for complex traits in domestic animals and their use in breeding programmes

Michael E. Goddard et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances

Thomas LaFramboise

NUCLEIC ACIDS RESEARCH (2009)

Article Genetics & Heredity

A new multipoint method for genome-wide association studies by imputation of genotypes

Jonathan Marchini et al.

NATURE GENETICS (2007)

Article Agriculture, Dairy & Animal Science

Strategy for applying genome-wide selection in dairy cattle

L. R. Schaeffer

JOURNAL OF ANIMAL BREEDING AND GENETICS (2006)