Study On Cold And Hot Adaptation And Construction Of Multi-omics Database For Domestic Chicken

After domestication,chickens migrated around the world with human activities and adapted to different agro-ecological regions under the combined action of natural selection and artificial selection.Domestic chickens are fed in large quantities and distributed in a wide range,which is a good model for studying temperature adaptability.The rapid development of high-throughput sequencing technology has provided new and broad perspectives for humans to study the complex traits of domestic chickens,but the explosive growth of data has not been effectively collated,categorized and analyzed.In the study,we analyzed the cold adaptation and heat adaptation of chickens,and constructed a chicken multi-omics comprehensive database.The main research results are as follows:1.The Chantecler chicken,a unique Canadian indigenous breed,is well adapted to extremely cold environments.However,its genetic characteristics have not been well studied.Here,we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens,which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding.Based on a genome-wide scan,we identified two vital candidate regions containing candidate genes ME3,DDIAS,PRSS23,PRCP,FAM181 B and ZNF536,which are related to cold adaptation.Besides,we found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions,such as northern China.Our study indicated that specialized commercial chickens in the early 20 th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time.These findings enrich our understanding of the adaptive potential of commercial species.2.To investigate the hot adaptation of local chickens,we performed genomic analyses on three indigenous chicken groups from Indonesia,India,and Saudi Arabia and their combination.The results showed that indigenous chickens of northern China had a remote relationship with the three chicken groups,while Saudi Arabian indigenous chickens harbor a closer relationship with Indian indigenous chickens.The reliable candidate genes identified by the genome-wide selection scanning analysis are all unique candidate genes of each population.These genes are related to nerve regulation,vascular function,immune function,lipid metabolism,kidney development and function,and then participate in the adaptation process in the thermal environment.Although a common hot adaptation gene was successfully identified in this study,it could not be verified by other analyses.Our results suggest that the thermal adaptation of chickens is not caused by a single genetic variation,but is the result of parallel evolution of different local species under similar selection pressures.Our study provides a reasonable explanation for the rapid adaptation of chickens to diverse tropical climate and offers practical values for poultry breeding.3.Multiple omics data can provide a stereoscopic perspective for exploring potential causal variation,genes,and potential genetic mechanisms of complex traits.However,for many non-mammal species,including chickens,the integration and reuse of these resources is poor,which greatly limit genetic research and breeding processes for the species.So,we construct a comprehensive chicken database(Galbase,http://animal.nwsuaf.edu.cn/Chicken Var),which integrated 928 re-sequenced genomes,429 transcriptomes,118 epigenomes,14519 QTL entries and 6692 associations,and detected 21.67 million SNPs,2.71 million In Dels and 476,689 cis-regulatory elements.Galbase allows users to retrieve genomic variations in geographical maps,gene expression profiling in heatmaps,and epigenomic signals in peak patterns,and provides modules for batch annotation of genes,regions,and loci based on multi-omics data.Galbase also provides convenient tools,including UCSC Genome Browser,Wash U Epigenome Browser,BLAT,BLAST,and Lift Over,to facilitate the search,visualization,and analysis of sequence features.All these options make Galbase a useful resource for identifying genetic variations that lead to complex traits in chickens.Galbase grants a new approach for the research communities to conduct in-depth functional genomic studies of chickens.In conclusion,in the study,we analyzed cold and hot adaptability of chickens at the genome-wide level which lay a molecular basis for breed improvement and new breed breeding of chicken.At the same time,we constructed a chicken multi-omics comprehensive database which provide a convenient platform for analysis molecular mechanisms of complex traits in chickens.