Genomic and transcriptomic analysis reveals the genetic diversity and adaptive signatures of Maduo sheep

The alpine grassland ecosystem is characterized by high-altitude, hypoxia, harsh cold and strong radiation conditions, and the unique growth performance and stress resistance of indigenous domestic animals. Maduo sheep, a newly discovered Tibetan sheep breed living in the source area of the Yellow River, is famous for its high-quality wool and meat production. However, its genome and genetic features still need to be deciphered. The genomes of 12 Maduo sheep were sequenced on a genome-wide scale and compared with those of 6 other Tibetan sheep breeds. Population structure analyses revealed that Maduo sheep were distinctly separated from other Tibetan sheep breeds with a higher genetic diversity. Strong selective signatures were detected by the FST and XP-CLR results, identifying MREG, RXFP2 and SYNDIG1 in Maduo sheep. To explore the molecular regulation of Maduo sheep adaptability to the high-altitude environment, the muscle tissues of 3 Tibetan sheep populations living at different altitudes (1500 m, 2500 m and 4200 m) were sampled for RNA sequencing. We found 132, 269 and 149 specific transcripts from 1500 m, 2500 m and 4200 m groups respectively. A total of 327 differentially expressed transcripts were found in both 2500 m vs. 1500 m and 4200 m vs. 1500 m comparisons, which were closely related to stem cell differentiation, p38-MAPK cascade, skeletal system morphogenesis, etc. On the other hand, 122 differentially expressed transcripts were found in both 4200 m vs. 1500 m and 4200 m vs. 2500 m comparisons, which should be responsible for adaptive immune response, cytoskeleton, apoptotic regulation and so on. This study provides important genomic insights into the genetic resources of Maduo sheep and could be helpful for understanding the mechanisms of hypoxic adaptability. •A unique Tibetan sheep resource, Maduo sheep, was identified by genome sequencing.•The genetic diversity of Maduo sheep was interpreted through comparing with other Tibetan sheep breeds.•Genes related with plateau adaptability were screened by genetic signature selection and expression level.