ArticlePloS one2013
Genotyping by genome reducing and sequencing for outbred animals.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis.Animals : an open access journal from MDPI · 2023Article
- Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens.BMC genomics · 2023Article
- 3D-GBS: a universal genotyping-by-sequencing approach for genomic selection and other high-throughput low-cost applications in species with small to medium-sized genomes.Plant methods · 2023Article
- Article
- PHARP: a pig haplotype reference panel for genotype imputation.Scientific reports · 2022Article
- Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits.BMC genomics · 2021Review
- Article
- Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation.BMC genomics · 2021Article
- Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data.Frontiers in genetics · 2021Article
- Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats.G3 (Bethesda, Md.) · 2020Article
- Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs.Evolutionary applications · 2020Article
- Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs.Asian-Australasian journal of animal sciences · 2020Article
- Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing.Frontiers in genetics · 2020Article
- Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed.Frontiers in genetics · 2020Article
- NanoGBS: A Miniaturized Procedure for GBS Library Preparation.Frontiers in genetics · 2020Article
- Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix).Scientific reports · 2019Article
- Detection of genome-wide structural variations in the Shanghai Holstein cattle population using next-generation sequencing.Asian-Australasian journal of animal sciences · 2019Article
- Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data.Frontiers in genetics · 2019Article
- Exploring the Structure of Haplotype Blocks and Genetic Diversity in Chinese Indigenous Pig Populations for Conservation Purpose.Evolutionary bioinformatics online · 2019Article
- Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.
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