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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Assessment of inbreeding depression in Nellore cows (Bos indicus) through high-density SNP genotypes

Authors
item Zavarez, Ludmilla -
item Utsunomiya, Yuri -
item Sonstegard, Tad
item Garcia, Jose -

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: April 15, 2014
Publication Date: April 23, 2014
Citation: Zavarez, L.B., Utsunomiya, Y.T., Sonstegard, T.S., Garcia, J.F. 2014. Assessment of inbreeding depression in Nellore cows (Bos indicus) through high-density SNP genotypes. BARC Poster Day, Poster 59, pp. 71.

Technical Abstract: Inbreeding has been incriminated as a cause of decrease in reproductive performance in cattle. This negative correlation is known as ‘inbreeding depression’, and evidence supporting this hypothesis was generated from association studies between reproductive traits and estimates of inbreeding coefficients (F). Traditionally, inbreeding coefficients are calculated from pedigree data (FPED), but this source of information is susceptible to errors and is often incomplete. The use of high density SNP genotypes to scan individual genomes for contiguous homozygous chromosome fragments has been proposed as a proxy for the identification of genome-wide identical by descent haplotypes (i.e., autozygous chromosome fragments). We applied a Runs of Homozygosity (ROH) method to estimate genomic inbreeding coefficients in 1278 Nellore cows (Bos indicus) genotyped for over 777,000 SNPs, and assessed their association birth weight, pre-weaning gain, post-weaning gain, navel, muscling, precocity and conformation at weaning and at yearling, gestation length and age at first calving. We identified ROH using the algorithm implemented in SVS 7 and F_ROH was calculated based on ROH of different minimum lengths (> 1, > 2, > 4, > 8 or > 16 Mb). Chromosome segments presenting ROH for a minimum of 60 individuals (approximately 5% of the samples) were declared common ROH. In order to assess the putative effect of inbreeding levels on performance, all phenotypic traits were regressed against the measures of inbreeding via ordinary least squares. In order to evaluate phenotypic differences among individuals according to their homozygous state in common ROH regions, t-tests were applied to investigate phenotypic mean difference. Over 600 animals presented homozygous fragments larger than 16 Mb, indicating recent inbreeding. This may be due to increased use of artificial insemination and dissemination of the germplasm of one important bull implicated in transmitting offspring with early puberty. ROH was detected in 76 genomic regions, and this included detection of an extended ROH region on chromosome 14 (fragment from 22.4 Mb to 27.5 Mb), which contains PLAG1. This gene has a known variant affecting birth weight and scrotal circumference in all cattle, and overlaps perfectly with the strong linkage disequilibrium in this region.

Last Modified: 12/22/2014
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