| Lueyang black-bone chicken is a unique poultry breed which located at Shaanxi Province and has high economic value.There are three kinds of Lueyang black-bone chicken,which were black feather,white feather and hemp feather.More and more research concerned about Lueyang black-bone chickens with black feathers because of high ecnomic value,while white feathers and hemp feathers have almost disappeared for their less ecnomic value.Feather color,as an important trait of poultry,is an important indicator of consumer choice and affects the economic value of the product directly.Therefore,the protection of feather color diversity and to investigate the formation mechanism of Lueyang black-bone chicken is of great significance to the protection and industrial development of this breed.As an important local breed,the genetic resources of Lueyang black-bone chicken are well protected.However,the genetic structure of the population of different feather colors have not been systematically studied,and the genetic mechanism of the formation of black feathers and white feathers in the population has not been studied.This study intends to systematically analyze and evaluate the population genetic diversity and genetic structure through the re-sequencing of the genomes of Lueyang black-feathered chickens and white-feathered chickens,and provide genomic data for the protection of genetic resources of Lueyang black-feathered chickens.At the same time,candidate genes and SNPs related to the black and white feather color traits of Lueyang black-bone chickens were screened out,which providing new genetic markers and gene targets for the refined breeding of Lueyang black-bone chickens with different feather colors.The main experimental results obtained in this study as followings:1.In this study,a total of 20 DNA samples of Lueyang black-feathered chicken and white-feathered chicken were sequenced.Each sample was sequenced at a depth of 30× to ensure the accuracy of the sequencing data,and the reference genome used was at the chromosome level.The chicken genome has laid a good foundation for subsequent analysis.This study produced a total of 734.889 G Raw data,with an average of 36744.433 M Raw data for each sample,and a total of 723.276 G of clean data.A total of more than 6882530 SNPs were identified in 20 individuals.Among them,4801421 SNPs were identified in Lueyang black-feathered chickens,and more than 2081109 SNPs were identified in Lueyang white-feathered chickens.SNPs shared between the two populations there are 1130594.SNP statistics show that Lueyang black-feathered chickens and white-feathered chickens are quite different between groups.2.Principal component analysis and population genetic structure analysis show that Lueyang black-feathered chicken and white-feathered chicken can be clearly divided into two subgroups,which proves that the two subgroups have very obvious differences at the whole genome level.The groups of Lueyang black-feathered chickens and white-feathered chickens have minimal gene exchange.When the K value is equal to 3,4,and 5,Lueyang black-feathered chickens are divided into the corresponding number of subgroups as expected,but white-feathered chickens are still a group and the internal individuals are not separated.From this perspective,Lueyang black-feathered chickens have higher genetic diversity,while Lueyang white-feathered chickens have relatively low genetic diversity,which may because Lueyang white-feathered chickens have fewer sample collections,and there is a phenomenon of small population breeding.3.Selective analysis found that there were 33 chromosomes in the chicken species genome,and 12 chromosomes were found to have FST values higher than 0.3.The KEGG enrichment analysis of these regions found that these selected genes were enriched to match the feather color.The shape forms the related signal pathway Tgf-β signal pathway.Further analysis of these genes by pfam annotation revealed that these selected regions were annotated to the TYR gene that affects feather color traits,and the gene ID(ENSGALP00000046568,ENSGALP00000049491,ENSGALP00000068800,ENSGALP00000073653,ENSGALP00000068819,ENSGALP00000037901,ENSGALP00000069809 and ENSGALP00000056246)was identified.Candidate genes with FST values greater than 0.5 were identified as RVT＿1,and G-gamma,FA,FERM,Kelch,TGFb,Arf,FERM and other genes with average FST values greater than 0.3 were identified.These genes will be developed in Lueyang black-feathered chickens and white-feathered chickens can be used as a candidate gene in research. |
PDF Full Text Request