Contrasting Patterns Of Genetic Variability Of X Chromosome In Domestic Sheep And Its Wild Relatives

The domestic sheep(Ovis aries)is among the most important livestock species,which provides animal products such us meat,milk and fine wool.During the process of domestication,the morphology,behaviour,and genetics of the sheep were reshaped.And the selection and subsequent breed formation has likely left detectable signatures within the genome of modern sheep.The unique inheritance pattern of the X chromosome exposes it in a way that is different from that of the autosomes,so the elucidation of these signatures of selection on X chromosome is of interest from the perspective of evolutionary biology.Genetic diversity benefits populations coping with diverse range of environmental conditions and provides the basis for improving economically important traits in accordance with consumer demand.However,the genetic diversity in livestock is declining worldwide.We investigate this question by studying a large dataset of BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep.Our study illustrates population structure and genetic diversity on sheep X chromosome and allows the deciphering of ecolutionary history of population.At the same time,in order to protect the genetic resources of domestic animals,we selected the world’s sheep populations as the research object,and put forward some suggestions on how to protect this species through analyzing their genetic diversity.Analysing the whole-genome sequences,we identified a substantially reduced X-to-autosome(X/A)diversity ratio(-0.6)compared to the expected value under a neutral model(0.75).Particularly,a large X-linked segment(43.05-79.25 Mb)was found to exhibit extremely low diversity,which is likely to be consered caused by the high density of coding genes.The results show that higher nucleotide diversity on the autosomes and a flat diversity gradient in X-linked segments,which could be explained by that the function of increasing distance from the nearest genes leading to a decreased X/A diversity ratio,what is contrasting to that in primates and other model animals.Our results also suggest that there were many reasons for low X-chromosome diversity in sheep species,including accelerated genetic drift,reduced directional selection on X chromosome,as well as sex-biased demographic events.The patterns of X-linked and X/A diversity are distinct between Near Eastern and non-Near Eastern sheep populations,which could be caused by multiple migrations,selection and admixture during the domestic sheep’s recent post domestication demographic expansion,coupled with natural selection for adaptation to new environments.We also document important novel genes involved in abnormal behavioral phenotypes,metabolism and immunity,under selection on the sheep X-chromosome.We also apply the 50K BeadChip array data to analysis genomic diversity of domestic sheep.Particularly,we for the first time quantified the contribution of each breed to the whole genomic diversity(within-breed,between-breed and total)and by combining the result of heterozygosity,effective population size,runs of homozygosity and inbreeding coefficient to consider the priority protection order of the breed.Meanwhile,cattle were added to verify whether the conservation strategy is suitable for other livestock species.We find that livestock in developed regions maintained high levels of genomic diversity,in contrast to those lived in other types of economically developed regions.And the developed regions can make the sustainable utilization of animal genetic resources more efficient by maintaining the balance between wthin-and between-breed genetic diversity.Therefore,we give priority to the breeds in the developed regions in order to protect the genomic diversity resources of livestock and animals.