Cattle are the most abundant and important livestock species found throughout the world. Long-term natural and artificial selection have played crucial roles in enabling cattle to adapt to diverse ecological environments and agricultural production systems across different regions. This has resulted in distinct phenotypes and unique adaptive abilities in different populations. By combining genomic variations and regulatory elements, we effectively found abundant variations in regulatory regions, further explaining the important functions of genetic variations in noncoding regions. On the basis of approximately 2000 short-read sequences and 300 long-read sequences, we found that there were highly differentiated genomic variations between indicine and taurine cattle. To further validate the function of noncoding region variations in the cattle genome, we utilized multiomics data and cell biology experiments. Additionally, we identified cis-regulatory element (CRE) information and constructed CRE collections at both the tissue and cellular levels. This research provides a scientific basis for the improvement of genetic resources in Chinese native cattle, which will be valuable in both theory and practice.

genetic variant,cis-regulatory element,cattle