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Title: Estimation of Genomic Inbreeding Coefficients Using BovineSNP50 genotypes from U.S. Jersey Cattle

Author
item Kim, Eui-Soo
item Van Tassell, Curtis - Curt
item Sonstegard, Tad

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/31/2009
Publication Date: 1/9/2010
Citation: Kim, E., Van Tassell, C.P., Sonstegard, T.S. 2010. Estimation of Genomic Inbreeding Coefficients Using BovineSNP50 genotypes from U.S. Jersey Cattle. Plant and Animal Genome Conference Proceedings.

Interpretive Summary:

Technical Abstract: In dairy cattle, inbreeding coefficients have been estimated from pedigree information; however, recent advances in genotyping technology allow the calculation of inbreeding based on molecular pedigree information. Because strong selection and recurrent inbreeding have decreased genetic variation, the frequency of founder haplotypes should have increased rapidly in specific genomic regions. Using homozygous haplotypes from a founding individual, we attempted to estimate a genome-wide inbreeding coefficient based on haplotype homozygosity. First, a simulation was performed to obtain the distribution of homozygous genomic fragment sizes that most accurately reflect inbreeding. In a case of inbreeding loops occurring within 7 generations, intact homozygous genomic regions greater than 1.0-1.5 Mb represented over 90% of true inbreeding coefficients. Next, genomic inbreeding coefficients for U.S. Jersey cattle (N=1,569 genotyped animals) were estimated. The correlation coefficient (r) between pedigree and haplotype-based inbreeding coefficients was ~0.7. The distribution of intact homozygous haplotypes in the founder generation was related to genome-wide inbreeding pattern in current generations with over 10 strong signatures of homozygosity across the genome. The approach used in this study is applicable for detecting genomic region under strong positive selection and analysis of inbreeding depression in livestock and wild life species.