Identification of candidate genes affecting chronic subclinical mastitis in Norwegian Red cattle: combining genome‐wide association study, topologically associated domains and pathway enrichment analysis

Abstract

SummaryThe aim of this study was to identify genes associated with chronic subclinical mastitis (SCM) in Norwegian Red (NR) cattle. Twelve SCM traits defined based on fixed threshold for test‐day somatic cell count (SCC) were, together with lactation‐average somatic cell score (LSCS) used for association and pathway enrichment analyses. A GWAS was performed on 3795 genotyped NR bulls with 777K SNP data and phenotypic information from 7 300 847 test‐day SCC observations from 3 543 764 cows. At 5% chromosome‐wide significance level 36 unique SNP were detected to be associated with one or more of the traits. These SNPs were analysed for linked genes using genomic positions of topologically associated domains (TAD). For the SCM traits with SCC >50 000 and >100 000 cells/ml on two test‐days in a row and LSCS, the same top significant genes were identified – checkpoint clamp loader component (RAD17) and cyclin B1 (CCNB1). The SCM traits with SCC >250 000, 300 000, 350 000 or 400 000 cells/ml on two test‐days in a row and D400 (number of days before the first case with SCC >400 000 cells/ml) displayed similar top significant genes: acyl‐CoA thioesterase 2 and 4 (ACOT2; ACOT4). For the traits SCM200_3 (SCC >200 000 cells/ml on three test‐days in a row) and SCM150, SCM200 (SCC >150 000; 200 000 cells/ml on two test‐days in a row) a group of chemokine (C–X–C motif) ligand genes and the Fos proto‐oncogene, AP‐1 transcription factor subunit (FOS) gene, were identified. Further functional studies of these identified candidate genes are necessary to clarify their actual role in development of chronic SCM in NR cattle.

Expression analysis of candidate genes for chronic subclinical mastitis in Norwegian Red cattle

“…Interestingly, the FOS gene showed lower expression in the high GEBV for LSCS group, which may indicate that a lower basic expression level leads to a fewer number of cells moving from blood to the infected tissue. This corresponds to the previously reported association of the FOS gene with SCM traits, with SCC threshold above 150,000 to 400,000 cells/mL (Kirsanova et al, 2020). The association might be explained by higher expression of the FOS gene that leads to higher number of cells in milk.…”

“…The CXCL1 gene was observed to have a higher level of expression in the group of cows with high GEBV for LSCS, that is, cows with expected low probability to get high SCC level in milk in compared with cows with low GEBV for LSCS. This gene was found in association with a long-term SCM trait with SCC >200,000 cells/mL during a 3 test-day period (Table 2; Kirsanova et al, 2020) and reported previously as upregulated after infection of monocyte cells with mastitis-causing bacteria (Lewandowska-Sabat et al, 2012;Han, 2019). In PBMC, the main sources of CXCL1 are described to be monocytes and dendritic cells (Eberlein et al, 2010;Hussen et al, 2013).…”

“…Fourteen candidate genes [RAD17, ACOT2, ACOT4, FOS, CXCL1 (also known as GRO1), CXCL8 (also known as IL8), CCNB1, CDK7, TGFB3, SEL1L, STAT4, C6, GLI2, AP1, SLC18A2] presented in Table 2 and 3 were selected based on the results from a genome-wide association study of alternative chronic SCM traits (Kirsanova et al, 2020). The most frequent genes involved in several canonical pathways associated with several defined traits or unique genes were analyzed.…”

“…In a previous study (Kirsanova et al, 2019), we defined novel alternative chronic SCM traits for NR by analyzing genotype data from NR bulls with corresponding test day SCC records of their daughters. Moreover, genes associated with the novel defined traits were identified (Kirsanova et al, 2020). The aim of the present study was to perform further functional analysis of the identified genes.…”

Association of bovine CXCL8 polymorphism with clinical mastitis and fertility trait in Polish HF cattle

“…In cattle, identification of candidate genes that underlie complex traits such as susceptibility to clinical mastitis are the major goal of many genetic and biomedical studies, which provides mechanistic insights into host resistance in addition to improving the diagnosis and treatment of the disease. In a recent studies identification of candidate genes for clinical mastitis in Norwegian cattle were reported using the genome-wide association study (GWAS) approaches and transcriptome analysis [5][6]. In other trait-associated studies, candidate genes for clinical mastitis viz., bovine Toll-like receptor (TLR) and pro-inflammatory cytokine genes families including the chemokine CXCL8 were reported as potentially biomarkers associated the clinical mastitis in cattle [7][8][9].…”