Detection of genome-wide structural variations in the Shanghai Holstein cattle population using next-generation sequencing.

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases and suffers from hot weather and long-term humidity in Shanghai, where the main centre for providing Holstein semen for farms distributed throughout China is located. Our objective was to determine the genetic mechanisms influencing important economic traits, especially diseases that heavily impact the yield and quality of milk and reproduction.

Methods: In our study, we detected the structural variations of 1092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify CNVs. Furthermore, we annotated these structural variations using different bioinformatics tools, such as Gene Ontology, Cattle QTL database and Ingenuity Pathway Analysis.

Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease, reproduction. In addition, the enrichment results based on the Cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle.

Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein experience.