# Genomic Analysis of Indel and SV Reveals Functional and Adaptive Signatures in Hubei Indigenous Cattle Breeds

## TL;DR

This study explores genetic variations in Hubei cattle breeds, revealing insights into traits like meat quality and disease resistance through indels and structural variants.

## Contribution

The study provides a comprehensive analysis of indel and SVs in Hubei cattle, highlighting their functional and adaptive significance.

## Key findings

- Over 5 million indels were identified, many in non-coding regions linked to key traits.
- Transposable elements significantly contributed to structural differences in the cattle genome.
- A notable insertion in the NOTCH2 gene was validated, suggesting a role in bone remodeling and adaptation.

## Abstract

Understanding genetic variation in cattle is essential for taking advantage of economically important traits such as meat quality, reproduction, and disease resistance. While most studies have focused on single nucleotide polymorphisms (SNPs), this study investigated small indel and structural variants (SVs) across five native cattle breeds from Hubei, China. Whole-genome sequencing of 98 individuals identified over 5 million insertions and deletions, many of which were located in non-coding regions but were still associated with key traits. Several variants, particularly in immune gene-rich regions, were linked to health and meat quality. Our analysis also revealed that transposable elements and simple repeats significantly contributed to these structural differences. A notable insertion in the NOTCH2 gene, which plays a role in bone remodeling by promoting osteoclast maturation and enhancing their metabolic activity, was validated using PCR. These findings enhance our understanding of structural variation and offer valuable resources for the genetic improvement of Chinese indigenous cattle breeds.

The genetic diversity of cattle plays a crucial role in adapting to environmental challenges and enhancing production traits. While research has predominantly focused on single nucleotide polymorphisms (SNPs), small indel and structural variants (SVs) also significantly contribute to genetic variation. This study investigates the distribution and functional impact of insertions and deletions in five Hubei indigenous cattle breeds. A total of 3,208,816 deletions and 2,082,604 insertions were identified, with the majority found in intergenic and intronic regions. Hotspot regions enriched in immune-related genes were identified, underscoring the role of these variants in disease resistance and environmental adaptation. Our analysis revealed a strong influence of transposable elements (TEs), particularly LINEs and SINEs, on genomic rearrangements. The variants were also found to overlap with economically important traits, such as meat quality, reproduction, and immune response. Population structure analysis revealed genetic differentiation among the breeds, with Wuling cattle showing the highest differentiation. Notably, the NOTCH2 gene was identified as a candidate for regional adaptation due to its significant differentiation across populations. These findings provide valuable genomic resources for enhancing breeding programs, aiming at improving the productivity and resilience of indigenous cattle breeds in China.