Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds  

作　　者：Michael N.Romanov Alexandra S.Abdelmanova Vladimir I.Fisinin Elena A.Gladyr Natalia A.Volkova Olga A.Koshkina Andrey N.Rodionov Anastasia N.Vetokh Igor V.Gusev Dmitry V.Anshakov Olga I.Stanishevskaya Arsen V.Dotsev Darren K.Griffin Natalia A.Zinovieva 

机构地区：[1]L.K.Ernst Federal Research Centre for Animal Husbandry,Dubrovitsy,Podolsk,Moscow Region,Russia [2]School of Biosciences,University of Kent,Canterbury,UK [3]Federal State Budget Scientific Institution Federal Research Centre“All-Russian Poultry Research and Technological Institute”of the Russian Academy of Sciences,Sergiev Posad,Moscow Region,Russia [4]Breeding and Genetic Centre“Zagorsk Experimental Breeding Farm”–Branch of the Federal Research Centre“All-Russian Poultry Research and Technological Institute”of the Russian Academy of Sciences,Sergiev Posad,Moscow Region,Russia [5]Russian Research Institute of Farm Animal Genetics and Breeding–Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry,St.Petersburg,Russia

出　　处：《Journal of Animal Science and Biotechnology》2023年第3期887-907,共21页畜牧与生物技术杂志（英文版）

基　　金：supported by the Russian Science Foundation within the Project No.21-66-00007;support of the Russian Ministry of Science and Higher Education。

摘　　要：Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

关 键 词：ACCLIMATION Adaptation Chicken breeds Cold tolerance Divergent selection Genetic diversity Genomewide scan Phenotypic traits Selective sweeps 

分 类 号：S831.2[农业科学—畜牧学]