A Genome-wide Association Study for Somatic Cell Score Using the Illumina High-Density Bovine BeadChip Identifies Several Novel QTL Potentially Related to Mastitis Susceptibility

Frontiers in Genetics

Francis eKearney¹  David eLynn²  Donagh eBerry²  Emma eFinlay²  Dan eBradley³  Brian eMeredith⁴  Alan eFahey⁴ 

[1] Irish Cattle Breeding Federation;Teagasc;Trinity College Dublin;University College Dublin;

关键词: Mastitis;    GWAS;    SNP;    somatic cell score;    Holstein-Friesian;   

DOI  :  10.3389/fgene.2013.00229

来源: DOAJ

【 摘 要 】

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 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 x 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.

【 授权许可】

Unknown