Y chromosome and mitochondria genetic diversity provide further insights into the introgression history of sheep

Abstract Background: Introgression is an important way to reveal the origin, domestication, and migration of domestic animals. Great progress has been made in the research on the introgression of domestic sheep from wild sheep over recent years. However, it is still difficult to explain some adaptations to the weather or environment of livestock species because of the complexity of the introgression events and domestication process. Here, we provide further insights into the introgression history of sheep by not only paternal genetic diversity but maternal inheritance based on the whole genome resequencing data of 412 rams worldwide and 396 complete mitogenomes of O.aries. Results: Analysis of paternal and maternal genetic diversity showed that 5 Y chromosome haplogroups and 7 mitochondrial haplogroups were identified, in which the lineage mtF and mtG were newly found and defined, making a foundation on further investigation to the introgression history of sheep and we speculated the lineage HY2 and mtC were introgressed from Iranian mouflons. We first revealed the mouflon sheep in the central and western Iran have higher introgression ratio into domestic sheep, the average rate reaching above 10%, indicating they were more likely to be the infiltrated ancestral contributors. In addition, the results of enrichment analysis on introgressive fragments showed that the gene flow of Iranian mouflon sheep into domestic sheep mainly enriches pathways such as protein binding, cell migration and other biological reaction process, providing supports for illustrating the climatic and environmental adaptions on domestic sheep. Interestingly, we found an infiltrated gene KYAT3 from Iranian mouflons may have an effect on the metabolism of Ethiopian local sheep. Conclusion: In this study, we analyzed the Y chromosome and mitochondrial haplotype diversity to identify clades that may influence infiltration in Iranian mouflons, calculated the percentage of infiltration of Iranian mouflons into the world’s domestic sheep and obtained some infiltration fragments adapted to the environment. These results will provide further insights into the introgression history of sheep.