| Introgression,the thransfer of genetic material between domestic animals/plants and their wild relatives,is an important source of genetic variations along with standing variation and denovo mutation.Genetic variations introduced through introgression may affect phenotypes,facilitating rapid adaptation of plants and animals to changing environments during domestication and migration,also known as adaptive introgression.The frequency of adaptive introgressions can be elevated under natural and artificial selection,furthermore play an important role in domestication,population differentiation and phenotypic variations of plants and animals.At present,there is still a lack of systematic research on genetic introgression in domestic animals,and the specific proportion of infiltration,the function of introgressed fragments and the relationship between introgression and domestication are very little known.Sheep was one of the most important domestic animals,which direct ancestor was the wild mouflons in Southeastern Anatolia.In addition,there are many types of wild sheep in nature,including snow sheep,bighorn,thinhorn,argali,urial and so on.In this study,through collecting and newly sequencing 1403 genome sequencing data,including 1334 samples representing 171 domestic sheep breeds worldwide and 69 samples from their wild relatives,we systematic analyzed of the introgressed region from various wild relatives into different domestic sheep populations.Moreover,combined with the domestication selected signals and genomic association analysis(GWAS),we investigated the functional importance of introgressed region,and explore their contributions to genetic diversity,their influence on domestication and morphology.The main results are as follows:1.Genetic structure and common gene flow among Ovis speciesGenome-wide population structure analysis revealed that the most closely wild relatives to domestic sheep were European mouflon,secondly is mouflon sampled from Iran.Domestic sheep can be divided into Europe,America,Middle East,East Asia,Africa and Oceania six groups according to geographical distribution:The analysis of gene introgression from different wild relatives into domestic sheep showed that the average introgressed proportions of Asian mouflon,urial,argali,bighorn and thinhorn sheep were 7.43%,1.03%,0.19%,0.03% and 0.01%,respectively.The introgression ratio of different geographical domestic populations showed significant differences.Highest introgression ratio was from Iran mouflon into domestic sheep,especially in Middle East population,indicating that a major introgression event probably occurred between direct ancestor of domestic sheep and Iran mouflon around the domestication center.These introgressed fragment spread worldwide after domestication.Subsequently,the continuous gene flow between domestic sheep and their sympatric wild relatives resulted in higher introgression percentage between them,which lead to the different introgression ratio among various populations of domestication sheep.2.Introgression and morphological variaions in domestic sheepThere exist about 1400 sheep breeds worldwide,and they differ in a series of morphological phenotypes.In this study,introgressed fragments were identified in several genes associated with appearance.There is an introgressed fragment within RXFP2 gene,which is related to horn morphology.Three major and multiple low-frequency haplotypes were identified in domestic sheep within this region.The three major haplotypes were strongly associated with three horn statu,both sex carry horns,males have well-developed horns,females are polled and both sexes are polled.Hornless haplotypes have been existed in mouflon sheep(heterozygosity),which were contrary to previous studies that hornless phenotypes were derived from mutations.There was a 30 kb introgressed fragment located in MSRB3,which was proved to be significantly correlated with ear width through genomewide association analysis(GWAS)of the F2 hybrids between East Friensian and Hu sheep.There were also three main haplotypes in the introgressed region.One of them was introgressed from argali and univerally existed in Diqing sheep,Oula sheep and Dorper sheep.Another haplotype mainly presented in waggir sheep and duolang sheep with typical large droop ears.The third haplotype was identical to the reference genome and had the lowest frequency in domestic sheep.The RXFP2 and MSRB3 introgression analysis above demonstrated that the introgression increased the haplotype diversity of domestic sheep.Natural and artificial selection collectively caused differences in haplotype frequency among domestic sheep breeds.The combination of different haplotypes in numerous haploblocks may play an important role in the formation of the morphology diversity among domestic breeds.3.The characteristics of introgression and the similarities and differences in introgression between animals and plantsIn both plants and animals,genetic introgression introduced new haplotypes,which increased the genetic diversity.And the frequency of numerous introgressed fragments changed significantly during domestication and artificial breeding precess,which may play important role in the formation of breeds.These results suggest that introgression can be an important selection model.In addition,here are differences between plants and animals in introgression,mainly reflected in the source and the length of introgresssed fragments.In conclusion,this study analyzed population structure,stimated the introgression in domestic sheep from wild relatives,investigate the important function of introgressions using large-scale resequencing data.Analysis of important functional introgressions under selection revealed the role of introgression in the domestication and improvement processes,demonstrating that introgression has great effect on phenotypic variations.This study provides insights into the domestication,migration,and phenotypic diversity of sheep,and provides a new perspective for understanding the evolution of species. |
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