ArticleAsian-Australasian journal of animal sciences2019
Detection of genome-wide structural variations in the Shanghai Holstein cattle population using next-generation sequencing.
Article in Asian-Australasian journal of animal sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 5 citations in OpenAlex.
- Transcriptome-derived variants in milk reveal host response signatures to subclinical intramammary infection in Holstein cattle.Journal of animal science and biotechnology · 2026Article
- Novel genotyping assay for a 212-kb deletion from theJournal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Molecular detection and association of 12.1 kb deletion within the high mobility AT-hook 2 gene in the Netherlands dwarf rabbit (Analytical science advances · 2024Article
- Article
- Somatic cell score: gene polymorphisms and other effects in Holstein and Simmental cows.Animal bioscience · 2022Article
- Genetic parameters and genome-wide association for milk production traits and somatic cell score in different lactation stages of Shanghai Holstein population.Frontiers in genetics · 2022Article
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
objectiveThe Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction.
methodsIn our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA).
resultsThe 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 and 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.
conclusionStructural 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 cattle experience.
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