Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle.

Shadi Nayeri,Paul Stothard,Stephen P Miller,Mohammed K Abo-Ismail,Stephen S Moore,Flavio Schenkel,Natalie May,Mehdi Sargolzaei

doi:10.1186/s12863-016-0386-1

Shadi Nayeri, Paul Stothard + Show 6 more

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https://doi.org/10.1186/s12863-016-0386-1

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Abstract

BackgroundGenome-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.ResultSeveral 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0386-1) contains supplementary material, which is available to authorized users.

Highlights

Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype
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
The deviations from expectations observed for milk, fat, protein and fat deviations appear to be due largely to the strong effect of the DGAT1 gene and the many single nucleotide polymorphisms (SNP) in linkage disequilibrium that show some degree of association with it

Summary

Introduction

Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. Milk production and fertility are two economically important traits affecting profitability in dairy cattle. These traits are polygenic, affected by many genes and variants, each with small effects on the observed phenotype [1]. Important genomic associations for fertility traits were found in previous GWAS studies, including significant QTLs for calving to first service interval [15,16,17], days open [18], cow non-return rate [15, 19], heifer nonreturn rate [20], daughter pregnancy rate [12, 21], age at puberty [22] and interval from first service to last service for cows and heifers [15]

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