Co-Authors:
Cohen-Zinder, M., Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Rm. 1608, 1206 W. Gregory Dr, Urbana, IL 61801, United States
Donthu, R., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Larkin, D.M., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Kumar, C.G., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Rodriguez-Zas, S.L., Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Rm. 1608, 1206 W. Gregory Dr, Urbana, IL 61801, United States, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Andropolis, K.E., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Oliveira, R., Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Lewin, H.A., Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Rm. 1608, 1206 W. Gregory Dr, Urbana, IL 61801, United States, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
Abstract:
The goal of this study was to identify candidate genes and DNA polymorphisms for quantitative trait loci (QTL) affecting milk yield (MY), fat yield (FY), and protein yield (PY) previously mapped to bovine chromosome 3 (BTA3). To accomplish this, 373 half-siblings sired by three bulls previously shown to be segregating for lactation trait QTL, and 263 additional sires in the U.S. Dairy Bull DNA Repository (DBDR) were genotyped for 2,500 SNPs within a 16.3 Mbp QTL critical region on BTA3. Targeted resequencing of ̃1.8 Mbp within the QTL critical region of one of the QTL heterozygous sires identified additional polymorphisms useful for association studies. Twentythree single nucleotide polymorphisms (SNPs) within a fine-mapped region were associated with effects on breeding values for MY, FY, or PY in DBDR sires, of which five SNPs were in strong linkage disequilibrium in the population. This multisite haplotype included SNPs located within exons or promoters of four tightly linked genes: RAP1A, ADORA3, OVGP1, and C3H1orf88. An SNP within RAP1A showed strong evidence of a recent selective sweep based on integrated haplotype score and was also associated with breeding value for PY. Because of its known function in alveolar lumen formation in the mammary gland, RAP1A is thus a strong candidate gene for QTL effects on lactation traits. Our results provide a detailed assessment of a QTL region that will be a useful guide for complex traits analysis in humans and other noninbred species. © 2011 the American Physiological Society.
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