# Genome-WideAnalysis of Copy Number Variations in Three Populations of Nanyang Cattle Using Whole-Genome Resequencing

## TL;DR

This study analyzes copy number variations in three breeds of Nanyang cattle to understand genetic diversity and traits important for breeding.

## Contribution

The study identifies genome-wide CNVs and their functional relevance to economic traits in Nanyang cattle.

## Key findings

- 97,564 CNVs were identified, merging into 10,349 CNV regions covering 1.48% of the genome.
- CNVR genes were enriched in organ development, immune regulation, and metabolism.
- 131 CNVRs overlapped with QTLs related to growth, carcass traits, and reproduction.

## Abstract

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.