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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.

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows