2023
A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes
Zhu F, Yin Z, Zhao Q, Sun Y, Jie Y, Smith J, Yang Y, Burt D, Hincke M, Zhang Z, Yuan M, Kaufman J, Sun C, Li J, Shao L, Yang N, Hou Z. A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Communications Biology 2023, 6: 1233. PMID: 38057566, PMCID: PMC10700341, DOI: 10.1038/s42003-023-05619-y.Peer-Reviewed Original ResearchConceptsGenome assemblyReference genomeChromosome-level reference genomeChromosome-level genome assemblyGenetic variation mapResponse to pathogen challengeComplex genetic regionWhole-genome methylationImmunologically important genesDifferentially regulated genesPan-genomeGenome sequenceGenetic regionsGenomic studiesImportant genesOvocleidin-17Pathogen challengeSilky chickenGenetic foundationImmune genesGenomeFunctional validationGenesFibromelanosisSilky
2004
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
Ka-Shu Wong G, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier L, Yang S, Warren W, Wilson R, Brandström M, Ellegren H, Crooijmans R, van der Poel J, Bovenhuis H, Groenen M, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young J, Rogers S, Walker B, van Hateren A, Kaufman J, Bumstead N, Lamont S, Zhou H, Hocking P, Morrice D, de Koning D, Law A, Bartley N, Burt D, Hunt H, Cheng H, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi M, Andersson B, Webber C, Ponting C, Overton I, Boardman P, Tang H, Hubbard S, Wilson S, Yu J, Wang J, Yang H. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 2004, 432: 717-722. PMID: 15592405, PMCID: PMC2263125, DOI: 10.1038/nature03156.Peer-Reviewed Original ResearchConceptsSingle-nucleotide polymorphismsGenetic variation mapRed jungle fowlJungle fowlWild ancestorDomesticated linesMean nucleotide diversityDomestic chicken breedsChicken breedsNucleotide diversityChicken genomeAdaptive allelesDomestic breedsVariant sitesDomestic animalsVariation mapsBreedingFowlChickenAncestorPolymorphismGenomeKilobasesAllelesDomestication
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