The Yunling cattle breed, a three-breed crossbreed, which comprises 50% Brahman cattle, 25% Murray Grey cattle and 25% Yunnan Yellow cattle, has several advantageous traits, including rapid growth, superior meat quality, ability to improve tolerance in hot and humid climates, tick resistance and rough feed. It can be rightfully stated that Yunling cattle serve as vital genetic repositories of the local Yunnan cattle. Gaining insights into the genetic information of Yunling cattle plays a significant role in the formulation of sound breeding strategies for this breed, safeguarding genetic resources and mitigating the risks associated with inbreeding depression. In this study, we constructed the Yunling cattle standard reference genome and aligned the whole genomes of 129 Yunling cattle individuals to the constructed reference genome to estimate the current genetic status of Yunling cattle in Yunnan Province, China. The average alignment rate and the average percentage of properly paired are both 99.72%. The average nucleotide diversity in Yunling cattle is 0.000166, which indicates a lower level of diversity. Population structure analysis classified Yunling cattle into two subgroups. Inbreeding analysis revealed that inbreeding events did occur in the Yunling cattle, which may have contributed to the low genetic diversity observed. This study presents a comprehensive assessment of the genetic structure and diversity among the Yunling cattle and provides a theoretical foundation for the preservation and exploitation of these precious germplasm resources.

Copy number variation (CNV) serves as a crucial contributor to genetic diversity, exerting a profound influence on phenotypic diversity, traits of economic significance, and the evolutionary trajectory of livestock species. This study aimed to dissect the genome-wide CNV landscape of the Nanyang cattle line (Nanyang, Pinnan, and Xianan cattle) to identify functionally relevant CNVs associated with key economic traits and breed differentiation. In this study, 27 resequencing datasets were utilized to analyze the genome-wide distribution of CNVs in three breeds of Nanyang cattle (Nanyang cattle, Pinnan cattle, and Xianan cattle) based on the latest reference genome ARS-UCD2.0. This study identified a total of 97,564 CNVs, and after merging CNVs with overlapping genomic positions, we obtained 10,349 CNV regions (CNVRs), accounting for 1.48% of the reference genome. Functional enrichment analysis showed that CNVR genes were mainly involved in organ development, neural regulation, immune regulation, and metabolism. In addition, 131 CNVRs overlapped with 81 quantitative trait loci (QTLs), such as growth and carcass QTL, multiple birth QTL, tenderness score QTL, and antal follicle number QTL. Additionally, AOX1, KRT72, and ZBTB7C were found to overlap with body weight QTLs. Furthermore, a selective sweep analysis of CNVR revealed that numerous genes (KIF26A, SPINT4, OR5W1, etc.) exhibited divergent copy numbers between breeds. Conclusively, this study facilitates comprehension of the genetic characteristics of the Nanyang cattle line at the CNV level and furnishes valuable information for the advancement of the Nanyang cattle line breeding system.