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.
Highlights
Holstein cows are famous for having the highest milk yield in the world; much attention has shifted to the breeding of Holstein cattle for many years [1]
We used the cn.MOPS algorithm to detect copy-number variants (CNVs), which are defined as unbalanced structural variants that change the number of base pairs in the genome. cn.MOPS is proposed to increase statistical power and decrease computational burden based on a multiple samples approach. cn.MOPS proposed a data processing pipeline using a mixture of Poisson models to reduce the false discovery rate (FDR) in CNV detection
This is the first time nextgeneration sequencing (NGS) methods have been used to detect CNVs in a large Shanghai Holstein population with low coverage, and it can be expected that a larger number of CNVs www.ajas.info 329 across genomes can be identified with this technique compared to the Bovine SNP50K Beadchip
Summary
Holstein cows are famous for having the highest milk yield in the world; much attention has shifted to the breeding of Holstein cattle for many years [1]. Chinese Holstein is the main dairy cattle breed in China, and the semen of their bulls are used in approximately 20% of the whole country. It is important to conduct studies to improve the breeding value of bulls in Shanghai to further enhance the performance of Holstein cows in China. The Holstein breed is categorized as a heat-sensitive cattle breed that originated in Europe. High environmental temperatures have a negative influence on the performance of Chinese Holstein cattle, especially in Shanghai [2,3]. The living environment of Shanghai Holstein www.ajas.info
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