Abstract
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.
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Data availability
The raw sequencing data generated in this study have been deposited in both the NCBI Sequence Read Archive under BioProject accession PRJNA1369724 (SRA: SRP655464)21 and the China National GeneBank DataBase (CNGBdb) under accession number CNP000755222. The final variant sets (including SNPs, InDels, SVs, and CNVs) are available in the Figshare repository23.
Code availability
Data analyses were primarily performed using standard bioinformatics tools within a Linux operating system environment. Detailed information regarding software versions and parameter settings is available at: https://github.com/triple-y/WGS-Chinese-yellow-cattle.
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Acknowledgements
This work was supported by the Sichuan Province Science and Technology Planning Project (2021YFYZ0001), the “5 + 1” Special Project for Breakthroughs in Cutting-Edge Agricultural Technologies (5 + 1QYGG003), the Sichuan Beef Cattle Innovation Team Project (SCCXTD-2025-13), the Sichuan Fiscal Operations Special Program (SASA2025CZYX003), the Basic Research Projects of Scientific Research Institutes (SASA202505), and the Sichuan Province Science and Technology Support Project (2024ZYD0283).
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W.W. and J.Y. conceived and designed the study. W.W. were involved in the review and writing process, L.L., Y.C., X.M., Y.A., J.G., D.F., X.D., X.C., F.H., Y.S., C.W., Z.Y., M.F. performed experiments and analyzed data. W.W. and J.Y. supervised the project and acquired funding. All authors made critical contributions to the manuscript drafts.
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Wang, W., Li, L., Chen, Y. et al. Whole-genome resequencing and genetic diversity of five indigenous cattle breeds from China. Sci Data (2026). https://doi.org/10.1038/s41597-026-06610-y
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DOI: https://doi.org/10.1038/s41597-026-06610-y
