Genetic Diversity And Selection Signatures In Chinese Native Game Chickens Based On Whole Genome Sequencing

China is rich in poultry genetic resources,among which the fighting cock,as a unique local breed,its characteristics differ greatly from those of other domestic chicken breeds.Compared with other domestic chicken breeds.Game chickens are tall,with strong muscles,strong fighting and aggressiveness,strong disease resistance,and fast metabolism.The morphogenesis of tissues and organs is different from other chicken breeds.At present,there are 6 local breeds of game chickens in China,namely Turpan game chickens(Xinjiang),Xishuangbanna game chickens(Yunnan),Luxi game chickens(Shandong),Anhui Beidou game chickens(Anhui),Henan game chickens(Henan)and Zhangzhou game chickens(Fujian).In this study,whole-genome resequencing data of 6 Chinese fighting cock breeds,1commercial broiler breed,1 commercial laying hen breed and wild red jungle fowl were obtained from the whole genome resequencing data of 152 chickens.The analysis yielded the following main results:(1)Heterozygosity(Ho),expected heterozygosity(He),allele frequency(MAF),nucleotide diversity(π)and inbreeding coefficient(FROH)were observed by analyzing the genomes of game chickens,wild red jungle fowls and commercial breed chickens),found that the genetic diversity of fighting cock breeds and wild red jungle fowls was higher than that of commercial breeds,among which fighting cock breeds had a low level of inbreeding;Xishuangbanna game chickens had the highest genetic diversity and had high conservation potential;commercial breeds had the highest genetic diversity.The level was the lowest,and the proportion of long ROH was higher than that of game chickens and wild red jungle chickens,indicating that there was a certain degree of inbreeding in recent generations of commercial breeds.Using principal component analysis and phylogenetic tree to analyze the genetic structure of the population,the study found that the genetic distance between the fighting cock population and the wild red jungle fowl and commercial breeds is far,the clustering is obvious,and the genetic distance between the six fighting cock breeds is relatively close.The genetic distances between the game chickens,the Henan game chickens and the Anhui Bei game chickens are more similar.The results of the ancestral component analysis also verifies the conclusion that the genetic structures of the six game chickens are similar in the principal component analysis and the phylogenetic tree analysis.Fighting cock is more similar to the ancestor of the Anhui Beidou cock.(2)The genetic comparison of the fighting cock population with wild red jungle fowl,commercial laying hens,and commercial broiler chickens was carried out respectively,and the comparison among the fighting cock populations was found.,it was found that the genes in the selected regions were mainly related to the nervous system(EPHA4,CAMK2 D,CLSTN2,ARHGAP39,ROBO2,GLRA2,GRIK2,CNTNAP2,GRID2,IL1RAPL1,WNT1,CDH8,etc.),skeletal development(VWC2,CPZ,WNT1),muscle development(TMEM8c,LOC101748756,PDGFC,LOC101748756),immunity(IL18,ALK,GPR65,UBAC2),metabolism(SLC16A9,SLC11A2,DGKB),reproduction(PLCL2),growth(IGF1R)and other traits.Further study on the specific genes selected by different breeds of game chickens shows that the genes related to bone development in Luxi game chickens are specifically selected,the genes related to nerve development in Zhangzhou game chickens are specifically selected,and the specific genes selected by Henan game chickens and Xishuangbanna game chickens are all related to muscle development,which indicates that the cultivation emphasis of different game chickens breeds may be different in the process of artificial selection.This study systematically analyzed the genetic diversity of Chinese game chickens at the genome-wide level,and found that the game chickens population differs significantly from other chicken breeds at the molecular level and is strongly selected for functional genes in the nervous system.The results of this study provide a molecular genetic basis for analyzing the unique characteristics of game chickens,and lay the genetic foundation for the conservation and genetic improvement of game chickens in China.This is consistent with the behavior,physical appearance and other characteristics of game chickens.