Genomic Resequencing Reveals Genetic Diversity And Evolutionary Selection Patterns In Chickens

Since the domestication of the red jungle fowl（Gallus gallus）,domestic chickens（Gallus gallus domesticus）have been subject to the combined effects of natural and artificial selection.This has resulted in marked genetic diversity in a number of traits.which provide a unique material to illustrate how selection shapes patterns of genetic variation.In this study,6 Tibet chicken population and 8 Sichuan local chicken breeds,a total 78 domestic chickens were used for whole genome resequencing.Together with 5 red jungle fowls（RJFs）and 8 Xishuangbanna Game fowl resequencing data download online,through comparative population genomics and bioinformatics analysis,excavating important genes and regulation mechanisms related to genetic diversity,phenotypic traits and high altitude adaptation of chickens.The main results in this study showed that:1.Genetic diversity of the chickensIn total,in this study we generated～1.69 trillion bases of resequencing data,18.03-fold coverage for each individual,A total of 7.43 Mb of SNPs out of 8.53 Mb highly credible SNPs were already present in the chicken dbSNP database（known SNPs）,and1.10 Mb SNPs were assigned as novel ones,We identified 3.46–7.52 Mb SNPs for each breed/population.In the meanwhile,there were 1398 to 7977 SNPs specifically detected in a breed/population.Nucleotide variability（θπ）and polymorphism（θω）in each population were analyzed using the method of sequence diversity statistics.Results indicating,compared with Sichuan local chicken breeds,Tibetan chicken populations have relatively higher genetic diversity.Pearson correlation coefficient was used to calculate the relationship between GC content and number of SNPs/Indels.Results indicating,the number of SNPs and the GC level are positively correlated in the isochores of the chicken genome（r=0.73,p=0）.Meanwhile,the number of indels and the GC level in the isochores are negatively correlated in the whole chicken population and each chicken breed/population,shows that the mutation rate is highly dependent on the GC content of the genome.More than 80%of the InDels were 1–5 bp in length.About half of the InDels occurred in the intergenic regions.The neighbor-joining phylogenetic tree and principal component analysis（PCA）revealed the presence of at least three distinct clusters among the six geographically representative populations of Tibetan fowls.These distinct distribution patterns and expansion signatures suggested that the divergent Tibetan clades may have originated from different regions.Linkage disequilibrium（LD）analysis showed that other domestic chicken breeds had a faster LD decay rate than Tibetan chicken populations,as did RJFs,reflecting a relatively high level of inbreeding under artificial breeding programs.We then used Japanese quail（Coturnix japonica）as an outgroup to detect introgression between RJFs and 15 domestic chicken populations.Our population structure analyses indicate a recent history of mutual introgression between Tibetan chickens and other breeds,as well as between wild RJFs and domestic populations.More introgression from RJFs to Tibetan chickens were found compared to other chicken breeds.Through pairwise comparisons of the genome-wide variation between the wild fowls and phenotypically diverse domestic breeds.Strikingly,five genes（CH25H,PANK1,LIPA,SLC16A12 and IFIT5）in an 80-kb region（18.86–18.94 Mb）of chromosome 6 were under positive selection in at least five of the domestic populations,many genes in genomic regions with strong selective sweep signals are involved in growth,metabolism,immunity,behavior and reproduction and may potentially contribute causally to phenotypic changes during selective breeding.Collectively,LIPA,SLC16A12 and IFIT5may be the main candidate genes to meat yield and disease resistance in modern chickens.This potential candidate region on chromosome 6 containing LIPA,SLC16A12 and IFIT5could be considered as the mainly selected genes to chicken domestication.2.Selection of the important genes related to chicken phenotypic traitsFurther analysis found that genes related to chicken phenotypic traits（feathers,skin color,growth,reproduction and aggression）in the genome area were under strong selective sweep signals.We observed 204 unique selected genes in a 20.7-Mb region on the chromosomes of Jinyang silky fowls,with the highest F_ST–window occurring at 10.02–10.38 Mb(F_ST=0.69,zF_ST=7.68,p<0.001).It should be noted that PDSS2 is a gene previously established as the causal gene for the silky-feather phenotype.In addition,in this study,we found a SNP located in the coding region of PDSS2 that is specific for this breed,and the function of this mutation has not been reported yet.We detected the strongest selective sweep located in the upstream non-coding region of the SMPD3 gene,reaching a zF_STT score of 9.67(F_ST=0.70,p<0.001)in Muchuan black-boned fowl;SMPD3 controls postnatal growth and development.The represented genes encoding myofibrillar proteins（MYH1E,MYH1C and MYPN）also had high zF_STT scores.These genes are found to be associated with growth,consistent with the fact that the chicken breed has the greatest body weight at 180 days of age among all the included breeds.Tianfu black-boned fowls and Pengxian yellow fowl lay the greatest number of eggs at 300 days of age.We found that KIF18A was under selection in both breeds.By comparing black-boned chickens with non-black-boned domestic fowls,we found that the genes,such as EDN3(F_ST=0.153,zF_ST=5.23,p<0.001)and TUBB1(F_ST=0.156,zF_ST=5.33,p<0.001)showed high differentiation peaks.Among the Xishuangbanna game fowl,many genes related to muscle development and cardiovascular activity,such as FGF14,VCL,MYH11 and SYNE1were found to be altered in the game breed.A network of the proteins encoded by these genes shows their involvement in pathways that are probably responsible for aggressiveness.3.High altitude adaptation of the Tibetan chickenTo determine whether the Tibetan chicken has been subject to natural selective pressure for high altitude adaptation,we explored the genomic landscape of population differentiation to identify genes that potentially control high altitude specific adaptive traits present in Tibetan chickens.We screened the individual sequence data for the presence of mutations that showed a marked allele frequency difference between Tibetan chickens and other domestic chickens（p<0.001）.Eleven SNPs located in coding regions were found to have extreme differences in allele frequencies between Tibetan chickens and other domestic chickens,and three genes,namely,PKD2L1,EVI5 and ZDHHC9,consisted of nonsynonymous mutations.We measured genome-wide variations and the frequency spectrum separately in Tibetan and lowland chickens.We discovered five genes under selection in all Tibetan chickens（TRIT1,HPCAL4,NT5C1A,LOC419677,and HEYL）in a small region（40kb）of chromosome 23.A total of 127 candidate genes with selection signals were identified using sliding-window analysis;those genes were involved in 25categories which mainly involved in energy metabolism,body size maintenance and digestion,which could be related the chilly climate of the highlands,the high body temperature characteristic of birds,and adaption to available food sources.