Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

作     者：Natalia V.DEMENTIEVA Yuri S.SHCHERBAKOV Olga I.STANISHEVSKAYA Anatoly B.VAKHRAMEEV Tatiana A.LARKINA Artem P.DYSIN Olga A.NIKOLAEVA Anna E.RYABOVA Anastasiia I.AZOVTSEVA Olga V.MITROFANOVA Grigoriy K.PEGLIVANYAN Natalia R.REINBACH Darren K.GRIFFIN Michael N.ROMANOV Natalia V.DEMENTIEVA;Yuri S.SHCHERBAKOV;Olga I.STANISHEVSKAYA;Anatoly B.VAKHRAMEEV;Tatiana A.LARKINA;Artem P.DYSIN;Olga A.NIKOLAEVA;Anna E.RYABOVA;Anastasiia I.AZOVTSEVA;Olga V.MITROFANOVA;Grigoriy K.PEGLIVANYAN;Natalia R.REINBACH;Darren K.GRIFFIN;Michael N.ROMANOV

作者机构：Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry.PushkinSt.Petersburg196601Russia School of BiosciencesUniversity of KentCanterburyCT27NJUK L.K.Ernst Federal Research Center for Animal HusbandryDubrovitsyPodolskMoscow Oblast142132Russia 

出 版 物：《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 (浙江大学学报（英文版）B辑（生物医学与生物技术）)

年 卷 期：2024年第25卷第4期

页      面：324-340页

核心收录：

学科分类：0905[农学-畜牧学] 09[农学] 090501[农学-动物遗传育种与繁殖] 

基　　金：supported by the Ministry of Science and Higher Education of the Russian Federation(No.075-152021-1037 Internal No.15.BRK.21.0001) 

主　　题：Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry Phylogeny Demographic history 

摘      要：The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse *** study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 *** populations represent a significant sample of the world s chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried *** included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population *** also included assessment of linkage disequilibrium and construction of phylogenetic *** multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each *** overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous *** a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry *** general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.