ArticleScientific reports2016
High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Genome-Wide Association Analysis of Hippocampal Neuroplasticity as an Indicator of Stress Responsiveness in Laying Hens (Gallus gallus domesticus).Animal genetics · 2026Article
- Breed classification of Lao People's Democratic Republic (Lao PDR) and Thai native chickens using synchrotron radiation-based Fourier transform infrared spectroscopy and genotyping by sequencing.Poultry science · 2026Article
- Genome-wide comparative analysis of variability and population structure between autochthonous Turkish chicken breeds and commercial hybrid lines.Poultry science · 2025Article
- A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.G3 (Bethesda, Md.) · 2025Article
- Omics in mini-livestock: a genomic perspective on the future of sustainable food systems.Frontiers in genetics · 2025Review
- A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations.bioRxiv : the preprint server for biology · 2024Article
- Article
- An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets.Epigenetics · 2023Article
- 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
- Trait Analysis in Domestic Rabbits (Animals : an open access journal from MDPI · 2022Article
- GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.STAR protocols · 2022Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens.Genetics, selection, evolution : GSE · 2021Article
- Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing.Molecular genetics and genomics : MGG · 2021Article
- In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Animals : an open access journal from MDPI · 2021Article
- Article
- Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Genes · 2021Article
- Insights into the Mitochondrial and Nuclear Genome Diversity of Two High Yielding Strains of Laying Hens.Animals : an open access journal from MDPI · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chicken genotyping is becoming common practice in conventional animal breeding improvement. Despite the power of high-throughput methods for genotyping, their high cost limits large scale use in animal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and cost-effective genotyping by sequence approach developed in plants, for its application in chickens. Here we describe the successful genotyping of a large number of chickens (462) using CornellGBS approach. Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifying individual animals, and then sequenced on Illumina platform. After filtering parameters were applied, 134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 had a minimum taxon call rate of 90% and were considered 'unique tags'. Interestingly, 20.7% of these unique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs were concordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes. The application of CornellGBS in chickens showed high performance to infer SNPs, particularly in exonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample) and powerful alternative to current genotyping methods, which has the potential to improve whole-genome selection (WGS), and genome-wide association studies (GWAS) in chicken production.
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