Abstract
Mastitis is an inflammation-driven disease of the bovine mammary gland that occurs in response to physical damage or infection and is one of the most costly production-related diseases in the dairy industry worldwide. We performed a genome-wide association study (GWAS) to identify genetic loci associated with somatic cell score (SCS), an indicator trait of mammary gland inflammation. A total of 702 Holstein-Friesian bulls were genotyped for 777,962 single nucleotide polymorphisms (SNPs) and associated with SCS phenotypes. The SCS phenotypes were expressed as daughter yield deviations (DYD) based on a large number of progeny performance records. A total of 138 SNPs on 15 different chromosomes reached genome-wide significance (corrected p-value ≤ 0.05) for association with SCS (after correction for multiple testing). We defined 28 distinct QTL regions and a number of candidate genes located in these QTL regions were identified. The most significant association (p-value = 1.70 × 10−7) was observed on chromosome 6. This QTL had no known genes annotated within it, however, the Ensembl Genome Browser predicted the presence of a small non-coding RNA (a Y RNA gene) in this genomic region. This Y RNA gene was 99% identical to human RNY4. Y RNAs are a rare type of non-coding RNA that were originally discovered due to their association with the autoimmune disease, systemic lupus erythematosus. Examining small-RNA sequencing (RNAseq) data being generated by us in multiple different mastitis-pathogen challenged cell-types has revealed that this Y RNA is expressed (but not differentially expressed) in these cells. Other QTL regions identified in this study also encoded strong candidate genes for mastitis susceptibility. A QTL region on chromosome 13, for example, was found to contain a cluster of β-defensin genes, a gene family with known roles in innate immunity. Due to the increased SNP density, this study also refined the boundaries for several known QTL for SCS and mastitis.
Highlights
Mastitis is an inflammatory disease of the bovine mammary gland that occurs in response to physical damage or infection with pathogenic microorganisms such as Escherichia coli, Streptococcus uberis, and Staphylococcus aureus (Schukken et al, 2011)
These quantitative trait locus (QTL) regions were cross-referenced to known QTLs for somatic cell score (SCS) / somatic cell count (SCC) and Clinical mastitis (CM) in the cattle QTL database as of May 2013 and 11 QTLs fell within previously identified QTL regions; this left 17 remaining novel QTL regions
The QTL regions identified using the high-density chip were more strongly associated with SCS and the boundaries of the QTL regions were more precise than those identified in our previous SCS genome-wide association study (GWAS) in a similar population of animals using the lower-density Illumina BovineSNP50 BeadChip (Meredith et al, 2012)
Summary
Mastitis is an inflammatory disease of the bovine mammary gland that occurs in response to physical damage or infection with pathogenic microorganisms such as Escherichia coli, Streptococcus uberis, and Staphylococcus aureus (Schukken et al, 2011). Upon infection of the mammary gland, macrophages and epithelial cells release cytokines which cause polymorphonuclear neutrophils (PMNs), monocytes, and other leukocytes to migrate from the blood to the site of infection in the mammary tissue (Paape et al, 2003). This influx of leukocytes results in an increased level of what is commonly termed “somatic cells” in the milk. Clinical mastitis (CM) is common in dairy herds and is estimated to occur in 20–40% of cows in a dairy herd annually (Heringstad et al, 2000).
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