The Evolutionary Characteristics Of INDEL Variation During Dog Domestication Revealed By Genome-scaledpopulation Analysis

As man’s closest companion,dog is the most widely distributed domestic animal in the world,which is famous as a hotspot model organism of the long-term evolutionary experiments research.Using modern molecular biological technology.scientists have revealed that dog was domesticated from the gray wolf.The domestic history,demographic dynamics,and the genetic mechanisms underlying specific phenotypes have been largely explored,based on the mitochondrial DNA,molecular markers of Y chromosome and genome-wide SNPs(single-nucleotide polymorphism).However,as the second most common type of polymorphism,the variation of insertion and deletion(INDEL),which is an important resource of molecular markers in studies of human,plant and other model biological organisms,is rarely analyzed in canines.The domesticated dogs experienced extreme behavioral transformation in a short time scale and formed diverse breeds with tremendous diversity of morphology.Still,the evolutionary characteristics of INDEL during dog domestication remains largely unknown,as previous studies mainly focused on the variation pattern of single-nucleotide polymorphisms in population genomic that may relate to phenotypic changes.Here,we gathered a dataset of 381 canine individuals,including 336 dogs,40 gray wolves,and 5 outgroups(including 3 Coyotes,1 Goalden Jackal and 1 Lycalopex Culpaeus),to explore the INDELs that evolved rapidly during the process of dog domestication,probably due to artificial selection.These rapidly evolved INDELs were rich in UTR regions,possessed high GC content and showed bias of 10-50 bp length variation,with more significant differentiation between dog and wolf.Noticeably,these rapidly evolved INDELs expressed preferentially in brain region and were overrepresented in categories related to neural system.Collectively,these results suggested a rapid evolution of INDELs that may influence biology function of genes involved in neural systems during dog domestication,which may account for the behavioral transformation of dog occurred in primary domestication.Among these genes with rapidly evolved INDEls,two of them(NOCT and MBP)are highly involved in neural system and therefore deserve more notification.NOCT(Nocturnin),a deadenylase,also known as CCRAN4L,is a circadian-regulated gene performing biological rhythm transcription.Noct-nockout mice exhibited delayed embryonic development.We found that one INDEL mutation in the downstream region of this gene,showed the strongest differentiation signal across chromosome 19.Subsequently,another 2 bp deletion homozygotes were found in all dog sequenced by 3730,while no homozygote was observed in gray wolf.With a combination of outgroups,we further confirmed that this deletion occurred recently and got fixed rapidly in dogs during the domestication.The dual-luciferase reporter experiiment showed that this deletion caused the decreased expression,consistent with a lower expression of NOCT in dog compared with wolf detected,which might delay the development process of dog,specially the appearance of "fear-aggressive"response.We further constructed brain conditional knockout(CKO)transgenic mice.Differences on anxiety,exploration and cognition between wild mice and CKO mice will be detected in future.The other gene MBP.myelin basic protein,the second most abundant protein in myelin of central nervous system,encodes two major families of proteins:the classical MBP constituents of myelin and the Golli-MBPs.Oligodendrocyte and myelin sheath defects are associated with higher brain function and diseases such as schizophrenia.MBP+/-mice exhibited increased cognitive ability.Besides,through Whole-genome analysis of INDEL,it is found that MBP,expressed in brain bias,is a highly differentiated gene with the largest expression difference between domestic dogs and gray wolves.Next we plan to do the dual-luciferase reporter to detect the molecular function of the highly differentiated INDFEL of-MBP,and further construct transgenic and MBP knock-out mice to explore the effect of the change of expression on behavior,especially fear response.In this paper,we investigated the genetic and evolutionary characteristics of INDEL during dog domestication and found some rapidly evolved INDEL that may related to the behavioral transformation,which is the prerequisite of dog domestication,it provide not only new insight into our understanding of dog domestication history,but also clues on the molecular mechanism of canine and human co-diseases.At the same time,it can help researchers study the evolutionary mechanism of other domestic animals with a new perspective.