Genomic Diversity and Selection Signatures for Zaosheng Cattle

Abstract Zaosheng cattle have a long history, closely related to Qinchuan cattle. This cattle breed is still under developing phase from a drought type to a beef breed. Followed by years of improvement, Zaosheng cattle have shown certain germline characteristics and genetic potential. Here, we used whole genome sequencing data from 19 Zaosheng cattle and 91 published genomes to understand its genetic diversity, population structure, and environmentally adapted performance. We provide a comprehensive overview of the sequence variation in the Zaosheng cattle genome to explore the genetic changes in Zaosheng cattle due to environmental adaptation. The findings of this study demonstrate that the genetic composition of Zaosheng cattle was primarily derived from Chinese and East Asian indicine cattle, where, Zaosheng and Qinchuan cattle were found to be genetically closest. Through ancestral fragment inference and selective sweep, we identified several genes linked to lipid metabolism, immune regulation, fertility and meat quality across the mosaic genome of Zaosheng cattle showing an excess of taurine or indicine ancestry. In summary, this study supplies essential genetic insights into the genome diversity within Zaosheng cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.