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Genome-wide association study in Chinese Holstein cows reveal two candidate genes for somatic cell score as an indicator for mastitis susceptibility.

ABSTRACT: Bovine mastitis is a typical inflammatory disease causing seriously economic loss. Genome-wide association study (GWAS) can be a powerful method to promote marker assistant selection of this kind of complex disease. The present study aimed to analyze and identify single nucleotide polymorphisms (SNPs) and candidate genes that associated with mastitis susceptibility traits in Chinese Holstein.Forty eight SNPs were identified significantly associated with mastitis resistance traits in Chinese Holstein cows, which are mainly located on the BTA 14. A total of 41 significant SNPs were linked to 31 annotated bovine genes. Gene Ontology and pathway enrichment revealed 5 genes involved in 32 pathways, in which, TRAPPC9 and ARHGAP39 genes participate cell differentiation and developmental pathway together. The six common genome-wide significant SNPs are found located within TRAPPC9 and flanking ARHGAP39 genes.Our data identified the six SNPs significantly associated with SCS EBVs, which suggest that their linked two genes (TRAPPC9 and ARHGAP39) are novel candidate genes of mastitis susceptibility in Holsteins.

SUBMITTER: Wang X

PROVIDER: S-EPMC4570044 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genome-wide association study in Chinese Holstein cows reveal two candidate genes for somatic cell score as an indicator for mastitis susceptibility.

Wang Xiao X Ma Peipei P Liu Jianfeng J Zhang Qin Q Zhang Yuan Y Ding Xiangdong X Jiang Li L Wang Yachun Y Zhang Yi Y Sun Dongxiao D Zhang Shengli S Su Guosheng G Yu Ying Y

BMC genetics 20150915

<h4>Backgrounds</h4>Bovine mastitis is a typical inflammatory disease causing seriously economic loss. Genome-wide association study (GWAS) can be a powerful method to promote marker assistant selection of this kind of complex disease. The present study aimed to analyze and identify single nucleotide polymorphisms (SNPs) and candidate genes that associated with mastitis susceptibility traits in Chinese Holstein.<h4>Results</h4>Forty eight SNPs were identified significantly associated with mastit ...[more]

PMID: 26370837

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Project description:Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) following experimentally induced S. aureus mastitis, and to explore the potential gene regulatory mechanisms affected by DNA methylation during S. aureus mastitis. DNA was extracted from S. aureus-positive (n = 3) and S. aureus-negative (n = 3) mammary gland quarters and subjected to methylation-dependent restriction-site associated DNA sequencing (Methyl-RAD Seq). Results showed that CmCGG/CmCWGG DNA methylation sites were unevenly distributed and concentrated on chromosomes 5, 11, and 19, and within intergenic regions and intron regions of genes. Compared with healthy control quarters, 9,181 significantly differentially methylated (DM) CmCGG sites and 1,790 DM CmCWGG sites were found in the S. aureus-positive quarters (P < 0.05, |log2FC| > 1). Furthermore, 363 CmCGG differently methylated genes (DMGs) and 301 CmCWGG DMGs (adjusted P < 0.05, |log2FC| > 1) were identified. Gene ontology and KEGG enrichment analysis indicated that CmCGG DMGs are involved in immune response pathways, while the CmCWGG DMGs were mainly enriched in gene ontology terms related to metabolism. The mRNAs of 526 differentially methylated CmCGG genes and 124 differentially methylated CmCWGG genes were also significantly differentially expressed (RNA-Seq data) in the same samples, herein denoted differentially methylated and expressed genes (DMEGs) (P < 0.05). Functional enrichment analysis of DMEGs revealed roles related to biological processes, especially the regulation of immune response to diseases. CmCGG DMEGs like IL6R, TNF, BTK, IL1R2, and TNFSF8 enriched in several immune-related GO terms and pathways indicated their important roles in host immune response and their potential as candidate genes for S. aureus mastitis. These results suggest potential regulatory roles for DNA methylation in bovine mammary gland processes during S. aureus mastitis and serves as a reference for future epigenetic regulation and mechanistic studies.

Dataset Information

Genome-wide association study in Chinese Holstein cows reveal two candidate genes for somatic cell score as an indicator for mastitis susceptibility.

Publications

Genome-wide association study in Chinese Holstein cows reveal two candidate genes for somatic cell score as an indicator for mastitis susceptibility.

Similar Datasets

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