Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle.
Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine the positions of genomic regions affecting milk production, milk components and fertility traits in Canadian Holstein cattle, and to use these positions to identify genes and pathways that may influence these traits.



Several QTL regions were detected for milk production (MILK), fat production (FAT), protein production (PROT) and fat and protein deviation (FATD, PROTD respectively). The identified QTL regions for production traits (including milk production) support previous findings and some overlap with genes with known relevant biological functions identified in earlier studies such as DGAT1 and CPSF1. A significant region on chromosome 21 overlapping with the gene FAM181A and not previous linked to fertility in dairy cattle was identified for the calving to first service interval and days open. A functional enrichment analysis of the GWAS results yielded GO terms consistent with the specific phenotypes tested, for example GO terms GO:0007595 (lactation) and GO:0043627 (response to estrogen) for milk production (MILK), GO:0051057 (positive regulation of small GTPase mediated signal transduction) for fat production (FAT), GO:0040019 (positive regulation of embryonic development) for first service to calving interval (CTFS) and GO:0043268 (positive regulation of potassium ion transport) for days open (DO). In other cases the connection between the enriched GO terms and the traits were less clear, for example GO:0003279 (cardiac septum development) for FAT and GO:0030903 (notochord development) for DO trait.



The chromosomal regions and enriched pathways identified in this study confirm several previous findings and highlight new regions and pathways that may contribute to variation in production or fertility traits in dairy cattle.
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
Shadi
S
Nayeri
Department of Animal Bioscience, Centre for the Genetic Improvement of Livestock, University of Guelph, Ontario, Canada.|The Semex Alliance, Guelph, Canada.
Mehdi
M
Sargolzaei
Department of Animal Bioscience, Centre for the Genetic Improvement of Livestock, University of Guelph, Ontario, Canada.|Department of Animal and Poultry Production, Damanhour University, Damanhour, Egypt.
Mohammed K
MK
Abo-Ismail
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
Natalie
N
May
Department of Animal Bioscience, Centre for the Genetic Improvement of Livestock, University of Guelph, Ontario, Canada.|Invermay Agricultural Centre, AgResearch Limited, Mosgiel, New Zealand.
Stephen P
SP
Miller
Department of Animal Bioscience, Centre for the Genetic Improvement of Livestock, University of Guelph, Ontario, Canada.
Flavio
F
Schenkel
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.|Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, Queensland, Australia.
Stephen S
SS
Moore
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada. stothard@ualberta.ca.
Paul
P
Stothard
D000273:Adipose Tissue / Q000166:cytology; D000818:Animals; D002417:Cattle; D003612:Dairying; D005260:Female; D005298:Fertility / Q000235:genetics*; D055106:Genome-Wide Association Study; D008892:Milk / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide
Female fertility and milk production; Functional analysis; Genome-wide association analysis; Holstein cattle