Progress 01/01/08 to 08/31/10
Outputs
Progress Report Objectives (from AD-416) Identify genome signatures of artificial selection by genotyping and analyzing at least 48,000 SNPs covering all the 29 bovine autosomes and the X-chromosome on 1008 cows from the control line, selection line, and the mixed and elite contemporary Holstein lines. Then to identify those SNP markers associated with daughter pregnancy rate, somatic cell Scores, productive life, and milk production traits by genome-wide association analysis of additive and non-additive effects. Approach (from AD-416) The two objectives of detecting signatures of selection and genome-wide association between SNP markers and economically important dairy traits will be achieved by genotyping and analyzing at least 48,000 SNPs on 1008 Holsteins cows from four lines. These four lines were chosen and defined to maximize general genome differences and genetic differences for economically important traits among Holstein cows in this study. This report serves to document research conducted under funding proposal (2008-35205-18846) from the USDA NRI-CGP 43.1 Animal Genome. Award money (~$67,000) is a sub-contract to the Beltsville Area made available in March, 2008 that terminates on Aug. 31, 2010. The objectives of this grant proposal were to; 1) identify genome signatures of artificial selection by genotyping and analyzing at least 40,000 SNPs covering all chromosome on 1,008 cows from a selection line (selected for higher milk production), a control line (no selection since 1964), and elite contemporary Holstein lines and 2) identify those SNP markers associated with daughter pregnancy rate, somatic cell scores, productive life, and milk production traits by genome-wide association analysis of additive and non-additive effects. Both objectives were exceeded. For the first time, this project unveiled genome-wide changes in allele frequencies that estimated about 22% of the Holstein genome was affected by the 40 years of artificial selection. Four manuscripts are in preparation detailing genome regions relevant to the phenotypes of the contemporary Holstein cattle. Some analyses to best determine how to detect signature of selections in Holstein are ongoing. Monitoring activities associated with this project included email correspondence, annual updates presented to CSREES-NRI NPS in conjunction with Plant and Animal Genome Conferences and submission to CSREES-NRI of an annual progress report. This research continues to support two objectives of its related in-house project: 1) to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches (obj. #2) and 2) to characterize conserved genome elements and identify functional genetic variation (obj. #3).
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) Identify genome signatures of artificial selection by genotyping and analyzing at least 48,000 SNPs covering all the 29 bovine autosomes and the X-chromosome on 1008 cows from the control line, selection line, and the mixed and elite contemporary Holstein lines. Then to identify those SNP markers associated with daughter pregnancy rate, somatic cell Scores, productive life, and milk production traits by genome-wide association analysis of additive and non-additive effects. Approach (from AD-416) The two objectives of detecting signatures of selection and genome-wide association between SNP markers and economically important dairy traits will be achieved by genotyping and analyzing at least 48,000 SNPs on 1008 Holsteins cows from four lines. These four lines were chosen and defined to maximize general genome differences and genetic differences for economically important traits among Holstein cows in this study. Significant Activities that Support Special Target Populations The project will identify general and specific genome changes due to 40 years of artificial selection in Holstein cattle using a novel approach that combines unique Holstein genetic resources, unique experimental design, and the latest SNP genotyping platform for cattle. The objectives of this project have been exceeded. Sample size (2450 cattle) has more than doubled in part due to a resource contribution from Holstein Association USA. All the cattle have been genotyped and analyzed. For the first time, this project unveiled genome-wide changes in allele frequencies due to artificial selection. We estimated that about 30% of the Holstein genome was affected by the 40 years of artificial selection. This finding allows identifying genome regions relevant to the phenotypes of the contemporary Holstein cattle. Preliminary results of SNP sets associated with dairy traits were obtained. Of the 31 SNPs with the most significant effects on both milk and daughter pregnancy rate, 29 had opposite effects on these traits providing strong evidence for the antagonistic effects between fertility and production. This research continues to support two objectives of its related in-house project. The first is to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches (objective #2). The second is to characterize conserved genome elements and identify functional genetic variation (objective #3).
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