Population Structure And Genetic Introgression From Wild Relatives In Worldwide Goat Populations

As one of the earliest domesticated livestock,goats(Capra hircus)have undergone great changes in their behavior,physiology and morphology compared with their wild counterparts during the long-term domestication process.Gene flow and introgression between domestic animals and their wild relatives is an important process that has strong implications for domestication.Combining archaeological studies with ancient and modern genomic analysis,research on the origin and domestication of goats has made some progress.However,the possible genetic contribution of other closely related Capra species to goats during goat domestication is still unclear.In this study,we sequenced 101 modern Capra genomes,including 88 domestic goats,one bezoar(C.aegagrus),one Alpine ibex(C.ibex),three Siberian ibexes(C.sibirica),three Markhors(C.falconeri),one West Caucasian tur(C.caucasica)and four Nubian ibex × domestic goat hybrids(C.nubiana × C.hircus).Together with the publicly available genomic resources for modern goat and bezoar genomes,as well as ancient genomes,we compiled a worldwide collection of 164 modern domestic goats,51 ancient genomes throughout the Near East,four hybrids and 33 modern wild goats including 24 bezoars and nine individuals of four ibex species.This study has detailed investigated the whole genome variation in Capra species.The results as follows:1.By comparing the genome-wide variation,the worldwide domestic goats fell into four geographic subgroups: East Asia(EAS),Southwest Asia-South Asia(SWA-SAS),Africa(AFR)and Europe(EUR).Moreover,the sampled bezoars are structured and cluster corresponding to their geographic origin from the Zagros,Alborz and Azerbaijan regions.2.We found the divergence times among Asian,African and European goat populations predated the archaeologically estimated domestication time by a large margin.In addition,the three bezoar populations have significantly different levels of allele sharing with different goat populations.These results support the hypothesis of the multiple origins of goat domestication or post-domestication recruitment from different local bezoar populations.A study based on ancient DNA showed that mitochondrial variation of Neolithic goats was strongly structured but with weak population structuring in the later post-Neolithic and until now.However,by Ychromosome haplotype analyses,we found a clear geographic differentiation between comtinents from Neolithic Age to present.These results indicate more female movement during goat domestication.3.Using whole-genome sequencing,we discovered that the West Caucasica tur,Alpine ibex,markhor and Siberian ibex have different levels of allele sharing with domestic goats,with all populations showing the greatest sharing with the West Caucasian tur,indicating that gene flow between these species.We identified a total of 112 putative introgressed regions containing 81 protein-coding genes in domestic goats.The KEGG pathway enrichment analysis showed some genes are enrichend in immune system.4.We found that a region with nearly fixed introgressed haplotype in domestic goats contains one intact gene,Mucin 6(MUC6).The comparison of the introgressed MUC6 haplotype with the wild Capra species revealved the it was introgressed from a West Caucasian tur-like species.The results of transcriptome sequencing,qPCR and immunohistochemistry confirmed that MUC6 is specifically expressed in the abomasum and duodenum of goat.Combining with the putative biological functions of MUC6 gene,we speculate that the introgressed MUC6 haplotype helped the managed herds to adapt to the captive management.In addition,we developed CNVcaller,a software used for detecting copy number variations(CNVs)based on large-scale genome resequencing data of animals and plants.As most animal and plant reference genomes are of poor quality compared with human,and the extant softwares used for detecting CNVs are designed and optimized using human reference genome,these factors will challenge the efficiency and robustness of current human-oriented CNV detection methods.Thus,considering the large population resequencing data and the quality of non-human reference genomes,we developed CNVcaller,a read-depth method for discoving CNVs.Based on simulated and actual data,we showed that CNVcaller achieved the higher efficiency,accuracy and sensitivity when compared with the popular programs: CNVnator and Genome STRiP.