Whole-genome Resequencing And Hi-C Technology Reveals The High And Low Temperature Selection Signatures Of Chicken Domestication

Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and potential influences of climate change on long-term population dynamics.The chicken is a significative species to study local genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties in multiple environments.Yet,few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments.Here we generated whole genome resequencing and characterized 3D genome architectures with Hi-C technique of chickens from different environmental temperature areas to obtain advantageous genomic adaptions to tropical and frigid environments in poultry,which provides a valuable resource for selective breeding of chickens and other domestic animals.To investigate population genetic structure of chicken domestication,here we generated whole genome resequencing of 119 domesticated chickens in China including Wenchang chicken(WCC),Green-shell chicken(GSC),TBC(Tibetan chicken)and Lindian chicken(LDC),and download resequenced data of 7 additional chickens including Red jungle fowl(RJF),Yunnan native chicken(YNC),Taiwan chicken(TWC)and Beijing-You chicken(BJY)from NCBI database.Results:(1)We uncovered >11.6 million high quality SNPs of which 16.45% were newly detected variants in chickens.(2)Analyses of population history showed RJF,as the ancestor of the domestic chicken,was in the root of the tree and clustered together with TBC and YNJ.WCC branched off earlier than LDC with an evident genetic admixture in WCC and LDC,suggesting their closer genetic relationship.Then we detected genomic regions that have been subject to selection with the data of whole genome resequencing of 119 domesticated chickens,to investigate the tropical and frigid selection signatures of chicken domestication.Results:(1)Further comparative genomic analyses among those 119 individuals in contrasting environments identified a set of novel candidate genes in five pathways related to glycometabolism and energy metabolism that were potentially involved in adaptation to tropical environments.We identified that SLC33A1 and TSHR genes showed stronger signature for positive selection in the WCC genome,and a set of loci with allele frequencies appeared strongly associated with tropical environment adaptation,which were further supported in ~3,000 African chicken local ecotype populations as well as some other indigenous chicken breeds in China.(2)We identified signature of selection including several genes in cardiac muscle contraction and oxidative phosphorylation pathways that were putatively associated with cardiac mitochondria responses to frigid environments.NADH:ubiquinone oxidoreductase subunit S4(NDUFS4)gene was found stronger signature for positive selection in the LDC genome,and the SNPs with marked allele frequency differences showed a highly significant relationship with frigid environment adaptation.Another experiment was designed to reveal 3D organization of chicken genome and demonstrate evolutionary conservation to extreme environments.Here we characterized 3D genome architectures with Hi-C technique for chicken hepatocytes by comparing LDC hepatocytes with WCC hepatocytes.Results:(1)Alignment of the obtained sequences to the chicken reference genome resulted in an average of ~263 million paired-end reads mapped for each individual,among which an average of ~207 million are intra-chromosomal reads.After data analysis,we acquired a typical plaid-pattern chromatin interaction heatmaps at 40-kb resolution for each sample.(2)We then determined the compartment types of the genome at 1M resolution in hepatocytes,and found the Compartments representing transcriptional activity were highly conserved,with approximately 5% Compartments occurring conversion.We called TADs from Hi-C interaction matrices at 40-kb resolution and identified 396,386 TADs in LDC and WCC hepatocytes,respectively,and there was no statistically difference in the number or size of TADs.(3)KEGG pathway analysis with genes located in the 5% genomic regions was performed and suggested the pathway enrichment analysis showed these genes were strongly associated with extreme environment adaption-related pathways,including Tight junction,Notch signaling pathway,Vascular smooth muscle contraction,RIG-I-like receptor signaling pathway and Glycosphingolipid biosynthesis pathways.In conclusion,whole genome resequencing and HI-C sequencing analysis revealed that Notch signaling pathway,vascular smooth muscle contraction and Glycosphingolipid biosynthesis were involved in the response to tropical and frigid environment in chickens,in which,SLC331A1,TSHR and NDUFS4,were considered as the selection footprint of chicken acclimation to extreme environment.The combined strategy of whole genome resequencing and HI-C sequencing provided more comprehensive information to elucidate the genetic selection characteristics of chicken acclimation to tropical and frigid environment systematically.