ArticleBMC biology2023
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.
Article in BMC biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 35 citations in OpenAlex.
- Multi-omics integration and artificial intelligence for the conservation and utilization of local chicken genetic resources.Poultry science · 2026Review
- Long-read low-pass sequencing enhances variant detection in a peanut MAGIC population.G3 (Bethesda, Md.) · 2026Article
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Revealing the Shared Genetic Basis of Thermal Adaptation and Abdominal Adiposity in Wenchang Chicken Using Whole-Genome Structural Variation Analysis.Animals : an open access journal from MDPI · 2026Article
- Large-Scale Genomics Reveals Three-Source Ancestry and Layered Adaptation to High Altitude in Tibetan Chickens.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.bioRxiv : the preprint server for biology · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- Advancements in Animal Breeding: From Mendelian Genetics to Machine Learning.International journal of molecular sciences · 2025Review
- High-quality phased genome assemblies of line-bred Korean Hanwoo cattle.Scientific data · 2025Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Article
- Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.Journal of animal science and biotechnology · 2025Article
- LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals.Genomics, proteomics & bioinformatics · 2025Article
- Exploration of gene presence/absence variations inOpen biology · 2025Article
- Application of Omics in Donkey Meat Research: A Review.Animals : an open access journal from MDPI · 2025Review
Corrections and comments
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Authors and funding
22 authors at 13 institutions in 7 countries.
Funding
Abstract
backgroundThe red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.
methodsWe present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines.
resultsWe demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference.
conclusionsWe expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.
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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.