Comparative Genomic Analysis Of Tailed Chicken And Rumpless Chicken

Chicken is one of the first domestic animals.In China,eggs and chicken are the main animal protein sources in life.It is second only to pork,and play a pivotal role in the national economy.Due to different economic,cultural and natural conditions,chicken breeds with different production performance,genetic characteristics and appearance characteristics have been formed.The diversity of appearance characteristics is mostly due to the difference of body bones and skins,which leads to phenotypic diversity among different domestic chicken strains.Piao chicken is a rumpless breed,lacks the coccyx and the tail feather,provides a good experimental material for the study of species differentiation and genetic diversity.The phenotypic difference of each breed is based on the difference of the genome and the transcriptional regulation.With the development of the next generation sequencing technology,it is possible to find the difference between rumpless chicken and tailed chicken at the genomics level.Therefore,we screened the regions with high degrees of fixation and specific candidate genes in the rumpless chicken genome by whole genome resequencing.Using the coccyx and skin of the chicken embryo as the model,we compared the dynamic changes of the gene expression regulation network in the developmental process of rumpless and tailed chicken.This will lay the foundation for the study of the genetic diversity of chickens.The results of the study are as follows:First,we obtained 8,371,409 high quality SNP loci through whole genome resequencing,of which 3,089,095 were not reported.By calculating the ZH_P value,we obtained 17 regions with high degrees of fixation and 298 candidate genes in rumpless chicken genome.KEGG pathway analysis and GO enrichment analysis showed that candidate genes were mainly related to neural development,cell growth,basal metabolism,growth and development and organogenesis,chemotaxis regulation,skin cell growth,cell proliferation,cytoskeleton rearrangement,vascular regeneration,bone development,and body development.Furthermore,the QTLs in candidate areas were found to be related to egg weight,carcass weight,peck feather,tibial value,spleen weight,body weight and growth.Second,RNA-Seq technology was used to sequence the coccyx transcriptome of rumpless chicken and tailed chicken at different embryonic development stages,and 2714 differentially expressed genes(DEGs)were found.A gene co-expression network(GCN)was constructed using the expression value of DEGs,in which 1777 unique genes of rumpless chicken network were related to 11 neurodevelopmental signaling pathways,437 unique genes in tailed chicken network were related to 4 immune system signaling pathways,821 common genes of two GCN were related to 7 basal metabolism regulation and cell signal transduction process.The results implied that there are differences in bone development,immune function and basal metabolism between rumpless and tailed chickens.KEGG pathway analysis showed that the expression patterns of those differential expression genes related to the insulin signaling pathway and the calcium signaling pathway were different between two chicken breeds,which indicated that the two breeds may have differences during the formation of bone matrix.A GCN was constructed for those 298 candidate genes in the first part of the paper,and 17 Hub genes were obtained by calculating the central values by scoring method.Among them,FGFBP1 gene was closely related to the development of central nervous system and the body weight of the chicken.P2RX7 gene was related to the growth of bone and lipoid,and ABCB9 gene was involved lipid metabolism and immune function.The three genes were differentially expressed in the coccyx of rumpless and tailed chickens.Third,26 chicken embryo skin transcriptomes were sequenced by RNA-Seq technique,including 18 skin transcriptomes of chicken embryonic development in time series,and 8 transcriptomes of the skin in tail feather of rumpless and tailed chicken.Then,5830 DEGs during the skins of the chicken embryonic development were obtained.The results showed that skin morphogenesis can be divided into 19 modules during the embryonic development,which correspond to different physiological functions.The back-skin transcriptome of tailed chicken and rumpless chicken had little difference.However,the GCN of rumpless chicken is more closely connected than the tailed chicken,and the specific genes of the two co-expression networks are involved in different signaling pathways respectively.The expression patterns of 298 candidate genes in the first part of the paper were quite different in the early and late stages of embryonic skin development,the earlier interaction was more complex than that in the later stage,including that semaphorin family members(SEMA3A,SEMA3E,SEMA5A,SEMA4B and SEMA3D).Conclusion:In this study,the comparative genomics method was used to find the difference between the rumpless chicken and the tailed chicken in the genome level and the gene co-expression network level,and we provided the candidate gene set related to the phenotypes of the rumpless chicken.This study will provide a theoretical evidence and data support for understanding the molecular genetic basis of different traits in rumpless chickens.Meanwhile,the research methods of developmental modules and co-expression networks in this study will also provide new ideas for the application of comparative genomics technology in livestock and poultry.