Population Genetic Analysis And Uncovering Of Candidate Gene Related To Black Color Of Lueyang And Zhenping Black-bone Chicken

Lueyang black-bone chicken（LBC）and Zhenping black-bone chicken（ZBC）are indigenous populations in Shaanxi Province,China.Due to their black-colored trait and distinctive taste,they are highly favored by consumers.However,the genetic diversity of LBC and ZBC have not been systematically evaluated,and their genetic relationship with other Chinese local chickens is not well understood.The genetic mechanism of black-colored trait is also rarely reported.In this study,we performed whole genome re-sequencing of 20 LBC and 20 ZBC.Combined with published data,a dataset of 150chickens from 12 breeds（populations）was obtained.Genomic-level analysis based on this dataset revealed the genetic diversity,population structure,and selection signals of LBC and ZBC.Furthermore,a support vector machine model was constructed to discriminate LBC.The main results are as follows:1.The inbreeding coefficients of LBC and ZBC were 0.0341 and 0.0432,respectively.And the observed heterozygosity was 0.3009 and 0.3005,respectively.And LBC and ZBC also had rapid decay of linkage disequilibrium,indicating rich genetic diversity.Neighbor-joining tree,principal component analysis and ancestry component analysis revealed that there were differences in the population structure of chickens in different regions of China.Populations that are geographically close often shared similar ancestral components and exhibit close genetic relationships.The genetic distance between LBC and ZBC is the shortest,showing a mixture of genetic components of northern and southern domestic chickens.2.With Bian and Dagu chicken as reference populations,XP-EHH and F_ST were performed to detect selection signals.The EDN3 gene was identified as a candidate gene for the black-colored trait in LBC and ZBC.Immune-related genes such as Bcl11a,USP34,and TLR2 were also detected,which is consistent with their characteristics of long-term free-range breeding and strong stress resistance.3.Based on Bayesian parameter tuning and five-fold cross-validation,a support vector machine model for identifying LBC was constructed.When the number of input feature SNP is greater than or equal to 19,the model effect is the best.This model can effectively distinguish LBC from other chicken breeds.This study systematically evaluated the genetic diversity and population structure of LBC and ZBC at the whole-genome level,identified potential candidate genes for the black-colored trait,and constructed a machine learning model to identify LBC.These findings hold significant reference value for the protection of germplasm resources and breeding of LBC and ZBC.