Detailed analysis of inbreeding in Tibetan sheep populations based on genome re-sequencing

This study investigates runs of homozygosity (ROH) in 11 Tibetan sheep using resequencing technology. The goal is to assess the inbreeding status and the timing of inbreeding events in Tibetan sheep. The study aims to deepen our understanding of the genomic diversity of Tibetan sheep by integrating analyses of gene flow and genetic diversity. The goal is to provide a theoretical foundation for conserving of genetic diversity and the optimizing genetic breeding strategies for Tibetan sheep.

Sequencing data were obtained from 220 Tibetan sheep representing 11 different breeds across the provinces of Gansu, Qinghai, and the Tibet Autonomous Region. The size and distribution of genomic ROH fragments in these 11 Tibetan sheep populations were analyzed.

In 11 Tibetan sheep populations, 85% of the ROH were ranged from 0.5 Mb to 1 Mb in length. Only five populations (Kecai sheep, Ganjia sheep [GJ], Qiaoke sheep [QK], Tianjun white sheep [WT], and Tibetan Gangba black sheep) exhibited ROH segments longer than 3 Mb, although these instances were fairly rare. Chromosome length affects the number and size of ROH in the genome. Tibetan sheep have longer chromosomes 1, 2, and 3, leading to a higher occurrence of ROH. The FROH values were high for Tao sheep, GJ, and QK populations, while the lowest for Zhashijia sheep. Tibetan sheep populations harbor individuals with high inbreeding (FROH>0.2), but overall inbreeding levels are low, primarily from earlier generations. The expected heterozygosity in the Tibetan sheep genome exceeds the observed heterozygosity, indirectly confirming the occurrence of inbreeding in Tibetan sheep populations. Gene flow is evident in various Tibetan sheep populations, particularly between Huoerba sheep and WT.

The current breeding strategy for Tibetan sheep has room for improvement; therefore, breeding management and genetic diversity conservation should be prioritized in future programs.