A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure

Francesco Tiezzi; Kristen L Parker-Gaddis; John B Cole; John S Clay; Christian Maltecca

doi:10.1371/journal.pone.0114919

A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure

PLoS One. 2015 Feb 6;10(2):e0114919. doi: 10.1371/journal.pone.0114919. eCollection 2015.

Authors

Francesco Tiezzi¹, Kristen L Parker-Gaddis², John B Cole³, John S Clay⁴, Christian Maltecca¹

Affiliations

¹ Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States of America.
² Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States of America; Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, United States of America.
³ Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, United States of America.
⁴ Dairy Records Management Systems, Raleigh, NC, 27603, United States of America.

Abstract

Clinical mastitis (CM) is one of the health disorders with large impacts on dairy farming profitability and animal welfare. The objective of this study was to perform a genome-wide association study (GWAS) for CM in first-lactation Holstein. Producer-recorded mastitis event information for 103,585 first-lactation cows were used, together with genotype information on 1,361 bulls from the Illumina BovineSNP50 BeadChip. Single-step genomic-BLUP methodology was used to incorporate genomic data into a threshold-liability model. Association analysis confirmed that CM follows a highly polygenic mode of inheritance. However, 10-adjacent-SNP windows showed that regions on chromosomes 2, 14 and 20 have impacts on genetic variation for CM. Some of the genes located on chromosome 14 (LY6K, LY6D, LYNX1, LYPD2, SLURP1, PSCA) are part of the lymphocyte-antigen-6 complex (LY6) known for its neutrophil regulation function linked to the major histocompatibility complex. Other genes on chromosome 2 were also involved in regulating immune response (IFIH1, LY75, and DPP4), or are themselves regulated in the presence of specific pathogens (ITGB6, NR4A2). Other genes annotated on chromosome 20 are involved in mammary gland metabolism (GHR, OXCT1), antibody production and phagocytosis of bacterial cells (C6, C7, C9, C1QTNF3), tumor suppression (DAB2), involution of mammary epithelium (OSMR) and cytokine regulation (PRLR). DAVID enrichment analysis revealed 5 KEGG pathways. The JAK-STAT signaling pathway (cell proliferation and apoptosis) and the 'Cytokine-cytokine receptor interaction' (cytokine and interleukines response to infectious agents) are co-regulated and linked to the 'ABC transporters' pathway also found here. Gene network analysis performed using GeneMania revealed a co-expression network where 665 interactions existed among 145 of the genes reported above. Clinical mastitis is a complex trait and the different genes regulating immune response are known to be pathogen-specific. Despite the lack of information in this study, candidate QTL for CM were identified in the US Holstein population.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cattle
Chromosomes, Mammalian / genetics*
Female
Genome-Wide Association Study*
Mastitis, Bovine / genetics*
Polymorphism, Single Nucleotide*
Quantitative Trait Loci*
United States

Grants and funding

This project was supported by project 2010-1714 from Select Sires — The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.