Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows
Open Access
- 11 August 2011
- journal article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 12 (1), 408
- https://doi.org/10.1186/1471-2164-12-408
Abstract
Background: Genome-wide association analysis is a powerful tool for annotating phenotypic effects on the genome and knowledge of genes and chromosomal regions associated with dairy phenotypes is useful for genome and gene-based selection. Here, we report results of a genome-wide analysis of predicted transmitting ability (PTA) of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows. Results: Genome-wide association analysis identified a number of candidate genes and chromosome regions associated with 31 dairy traits in contemporary U.S. Holstein cows. Highly significant genes and chromosome regions include: BTA13's GNAS region for milk, fat and protein yields; BTA7's INSR region and BTAX's LOC520057 and GRIA3 for daughter pregnancy rate, somatic cell score and productive life; BTA2's LRP1B for somatic cell score; BTA14's DGAT1-NIBP region for fat percentage; BTA1's FKBP2 for protein yields and percentage, BTA26's MGMT and BTA6's PDGFRA for protein percentage; BTA18's 53.9-58.7 Mb region for service-sire and daughter calving ease and service-sire stillbirth; BTA18's PGLYRP1-IGFL1 region for a large number of traits; BTA18's LOC787057 for service-sire stillbirth and daughter calving ease; BTA15's CD82, BTA23's DST and the MOCS1-LRFN2 region for daughter stillbirth; and BTAX's LOC520057 and GRIA3 for daughter pregnancy rate. For body conformation traits, BTA11, BTAX, BTA10, BTA5, and BTA26 had the largest concentrations of SNP effects, and PHKA2 of BTAX and REN of BTA16 had the most significant effects for body size traits. For body shape traits, BTAX, BTA19 and BTA3 were most significant. Udder traits were affected by BTA16, BTA22, BTAX, BTA2, BTA10, BTA11, BTA20, BTA22 and BTA25, teat traits were affected by BTA6, BTA7, BTA9, BTA16, BTA11, BTA26 and BTA17, and feet/legs traits were affected by BTA11, BTA13, BTA18, BTA20, and BTA26. Conclusions: Genome-wide association analysis identified a number of genes and chromosome regions associated with 31 production, health, reproduction and body conformation traits in contemporary Holstein cows. The results provide useful information for annotating phenotypic effects on the dairy genome and for building consensus of dairy QTL effects.Keywords
This publication has 25 references indexed in Scilit:
- A genome-wide association study for milk production traits in Danish Jersey cattle using a 50K single nucleotide polymorphism chip1Journal of Animal Science, 2010
- Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham Heart Study dataBMC Medical Genetics, 2010
- Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and CanadaJournal of Dairy Science, 2009
- Development and Characterization of a High Density SNP Genotyping Assay for CattlePLOS ONE, 2009
- Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle BreedsScience, 2009
- A whole-genome assembly of the domestic cow, Bos taurusGenome Biology, 2009
- Efficient Methods to Compute Genomic PredictionsJournal of Dairy Science, 2008
- Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studiesBMC Bioinformatics, 2008
- A Whole-Genome Scan to Map Quantitative Trait Loci for Conformation and Functional Traits in Canadian Holstein BullsJournal of Dairy Science, 2008
- Ten novel mutations in the molybdenum cofactor genes MOCS1 and MOCS2 and in vitro characterization of a MOCS2 mutation that abolishes the binding ability of molybdopterin synthaseHuman Genetics, 2005