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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Análise de Associação por Todo o Genoma para Identificar Locos Relacionados ao Lucro Líquido, à Vida Produtiva e ao Escore de Células Somáticas na raça Jersey1

Authors
item Silva, Marcos -
item Vanraden, Paul
item Van Tassell, Curtis
item Sonstegard, Tad
item Matukumalli, Lakshmi -
item Schroeder, Steven
item Kim, Eui-Soo
item Wiggans, George

Submitted to: Brazilian Animal Science Society
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 15, 2009
Publication Date: July 17, 2009
Citation: Silva, M., Van Raden, P.M., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Kim, E., Wiggans, G.R. 2009. Análise de Associação por Todo o Genoma para Identificar Locos Relacionados ao Lucro Líquido, à Vida Produtiva e ao Escore de Células Somáticas na raça Jersey1. Brazilian Animal Science Society.

Interpretive Summary: A genome scan was conducted in the US Jersey population to identify QTL affecting net merit, productive life, and somatic cell score. Data used at this study were traditional genetic evaluations computed from DHI records by Animal Improvement Programs Laboratory, USDA/EUA. DNA has been acquired for 2,380 animals from Jersey breed and genetic evaluations released in Feb/2009 (http://greenbook.usjersey.com/) for 2,081 animals were used for the whole-genome association. Genotyping was performed using Illumina’s BovineSNP50 BeadChip with approximately 54,000 SNPs. For GWA study, any SNP with low call rate (<99%), departure from Hardy-Weinberg equilibrium (exact test p<0.01), and minor allele frequency below 5 percent, were excluded from the final analysis (30,342 markers retained). Bonferroni corrected level of 0.01 were used. For all traits, significant SNPs were found on many chromosomes, especially on BTAs 3, 4, 5, 6, 10, 12, 23, and 25. Most parts of the significant SNPs were located in similar positions on the chromosomes for all traits. Some of them localized within a single linkage disequilibrium (LD) block. Results suggest that marker solutions from genomic evaluations may be useful for identifying chromosomal regions that merit further study.

Technical Abstract: A genome scan was conducted in the US Jersey population to identify QTL affecting net merit, productive life, and somatic cell score. Data used at this study were DHI records from the national database of the Animal Improvement Programs Laboratory, USDA (Beltsville, MD). DNA was acquired for 2,380 animals from Jersey breed and genetic evaluations released in Feb/2009 (http://greenbook.usjersey.com/) from 2,081 animals was used for the whole-genome association. Genotyping was performed using Illumina’s BovineSNP50 BeadChip with approximately 54,000 SNPs. For GWA analysis, any SNP with low call rate (<99%), departure from Hardy-Weinberg equilibrium (exact test p<0.01), and minor allele frequency below 5 percent, were excluded from the final analysis (30,342 markers retained). Bonferroni corrected level of 0.01 were used. For all traits, significant SNPs were found on many chromosomes, especially on BTAs 3, 4, 5, 6, 10, 12, 23, and 25. For the most part of the significant SNPs were located in similar positions on the chromosomes for all traits. Some were localized within a single linkage disequilibrium (LD) block. Results suggest that marker solutions from genomic evaluations may be useful for identifying chromosomal regions that merit further study.

Last Modified: 9/1/2014
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