ArticlePloS one2017
Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.G3 (Bethesda, Md.) · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- Haplotype analysis incorporating ancestral origins identified novel genetic loci associated with chicken body weight using an advanced intercross line.Genetics, selection, evolution : GSE · 2024Article
- A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of goldenEvolutionary applications · 2023Article
- Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA.BMC genomics · 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
- Article
- 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
- Genome-wide association study for the primary feather color trait in a native Chinese duck.Frontiers in genetics · 2023Article
- Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing.BMC genomics · 2022Article
- High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits inFrontiers in plant science · 2022Article
- Genome‑wide association study and genomic prediction for growth traits in yellow-plumage chicken using genotyping-by-sequencing.Genetics, selection, evolution : GSE · 2021Article
- In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Animals : an open access journal from MDPI · 2021Article
- Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?Molecular genetics and genomics : MGG · 2021Article
- Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka FHeredity · 2021Article
- Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits.Communications biology · 2020Article
- Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats.G3 (Bethesda, Md.) · 2020Article
- High-Throughput Sequencing With the Preselection of Markers Is a Good Alternative to SNP Chips for Genomic Prediction in Broilers.Frontiers in genetics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-density single nucleotide polymorphism (SNP) markers are crucial to improve the resolution and accuracy of genome-wide association study (GWAS) and genomic selection (GS). Numerous approaches, including whole genome sequencing, genome sampling sequencing, and SNP chips are able to discover or genotype markers at different densities and costs. Achieving an optimal balance between sequencing resolution and budgets, especially in large-scale population genetics research, constitutes a major challenge. Here, we performed improved double-enzyme digestion genotyping by sequencing (ddGBS) on chicken. We evaluated eight double-enzyme digestion combinations, and EcoR I- Mse I was chosen as the optimal combination for the chicken genome. We firstly proposed that two parameters, optimal read-count point (ORP) and saturated read-count point (SRP), could be utilized to determine the optimal sequencing volume. A total of 291,772 high-density SNPs from 824 animals were identified. By validation using the SNP chip, we found that the consistency between ddGBS data and the SNP chip is over 99%. The approach that we developed in chickens, which is high-quality, high-density, cost-effective (300 K, $30/sample), and time-saving (within 48 h), will have broad applications in animal breeding programs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.