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 

机构地区：[1]Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry.Pushkin,St.Petersburg,196601,Russia [2]School of Biosciences,University of Kent,Canterbury,CT27NJ,UK [3]L.K.Ernst Federal Research Center for Animal Husbandry,Dubrovitsy,Podolsk,Moscow Oblast,142132,Russia

出　　处：《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》2024年第4期324-340,共17页浙江大学学报（英文版）B辑（生物医学与生物技术）

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)。

摘　　要：The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These 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 out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An 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 breeds.Such 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 breeding.In 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.

关 键 词：Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry PHYLOGENY Demographic history 

分 类 号：S831.2[农业科学—畜牧学]