Whole-genome resequencing and genetic diversity of five indigenous cattle breeds from China

China's abundant indigenous yellow cattle resources are of great significance for studying environmental adaptability evolution, genetic resource conservation, and breeding improvement. The majority of the cattle population consists of indigenous breeds. Understanding the genetic architecture of these cattle breeds is essential for effective management and conservation efforts. In this study, we collected DNA samples from five local cattle breeds (n = 56) and obtained whole-genome sequencing (WGS) data for 10 Jinchuan (JC) yak samples from the NCBI database as the outgroup. Whole-genome resequencing generated approximately 2.3 TB of paired-end data, achieving an average depth of 13X and a depth range of 9.75X to 39.03X across the 66 samples. The sequencing data were pre-processed and mapped to the cattle reference genome (ARS-UCD1.2) with an alignment rate of 99.5%. Finally, the variant calling process produced approximately 31 million high-quality SNPs. These data enhance our understanding of cattle genetic architecture, enabling the discovery of functional variants and evolutionary insights to inform breeding strategies for climate-resilient and sustainable cattle production.