The objectives of this study were (1) to estimate the genetic diversity in Hanwoo breeding population, (2) to estimate the effective population size by looking at the linkage disequilibrium between SNP markers, (3) to estimate genetic parameters for carcass traits using relationship matrix comprisin...
The objectives of this study were (1) to estimate the genetic diversity in Hanwoo breeding population, (2) to estimate the effective population size by looking at the linkage disequilibrium between SNP markers, (3) to estimate genetic parameters for carcass traits using relationship matrix comprising all the animals that are genotyped with Illumina Bovine SNP 50K (or 777K also called HD) Beadchip or not genotyped, and (4) to optimize the Hanwoo breeding program when genomic selection is applied. Records of a total of 2,674 animals for carcass traits and genomic information of 1,004 heads of those animals were collected by the Hanwoo Improvement Center of National Agricultural Cooperatives Federation from 2005 to 2012. After eliminating SNPs with missing partial genotypes (over 10%), monomorphic SNPs, those with minor allele frequency (<5%) or with uncertain chromosome locations, and those located on sex chromosomes, there were 32,026 SNPs retained for this study. Genetic parameters for carcass traits were also estimated. A brief summary of the obtained estimates are as follows. The ranges of expected heterozygosity and inbreeding coefficients distributed on different chromosomes were 0.35 to 0.37 and -0.01 to 0.00, respectively. In general, current Hanwoo breeding population with its small population size can lose their genetic variability due to genetic drift, and rapid increase in inbreeding. The inbreeding coefficient(FIS) in the studied Hanwoo population was not high which can be explained by their genome-wide average homozygosity(Ho) which was similar to the expected theoretical homozygosity(He) by Hardy-Weinberg. The effective population size (Ne) in current population was estimated to be 144 heads while that of Hanwoo population in 5-10th generations earlier was 1,262 heads. The effective population size decreased at a rate of 10.1% between 5th to 10th ancestral generations but the rate became faster(18.4%) for recent five generations. The most probable reason for accelerated decreasing rate of Ne in Hanwoo could be the intensive use of a few prominent sires since the artificial insemination technic was introduced in Korea. In this current situation, the selection of various proven bulls and improvement in mating system considering genetic diversities are mostly needed to sustain the current Ne size or to increase in future generations. In addition, the genetic parameters for carcass traits were estimated using genomic information from combined relationships among genotyped and non-genotyped animals (usually termed as H matrix). The heritabilities of eye muscle area (EMA), backfat thickness (BF), marbling score (MS) were 0.46, 0.60, and 0.63, respectively. A higher accuracy in breeding value (up to 6%) was obtained from combined relationship when compared with traditional pedigree based relationships. For Hanwoo, the benefits for breeding system could come from the higher accuracy of breeding values, selection intensity, genetic standard deviation and generation intervals. The economic efficiency in this study was estimated through genetic gains and economic value for selection traits in Hanwoo. The resulted economic value of a bull selection using EBV and GEBV were 203,358 won/generation and 225,563 won/generation, respectively.
The objectives of this study were (1) to estimate the genetic diversity in Hanwoo breeding population, (2) to estimate the effective population size by looking at the linkage disequilibrium between SNP markers, (3) to estimate genetic parameters for carcass traits using relationship matrix comprising all the animals that are genotyped with Illumina Bovine SNP 50K (or 777K also called HD) Beadchip or not genotyped, and (4) to optimize the Hanwoo breeding program when genomic selection is applied. Records of a total of 2,674 animals for carcass traits and genomic information of 1,004 heads of those animals were collected by the Hanwoo Improvement Center of National Agricultural Cooperatives Federation from 2005 to 2012. After eliminating SNPs with missing partial genotypes (over 10%), monomorphic SNPs, those with minor allele frequency (<5%) or with uncertain chromosome locations, and those located on sex chromosomes, there were 32,026 SNPs retained for this study. Genetic parameters for carcass traits were also estimated. A brief summary of the obtained estimates are as follows. The ranges of expected heterozygosity and inbreeding coefficients distributed on different chromosomes were 0.35 to 0.37 and -0.01 to 0.00, respectively. In general, current Hanwoo breeding population with its small population size can lose their genetic variability due to genetic drift, and rapid increase in inbreeding. The inbreeding coefficient(FIS) in the studied Hanwoo population was not high which can be explained by their genome-wide average homozygosity(Ho) which was similar to the expected theoretical homozygosity(He) by Hardy-Weinberg. The effective population size (Ne) in current population was estimated to be 144 heads while that of Hanwoo population in 5-10th generations earlier was 1,262 heads. The effective population size decreased at a rate of 10.1% between 5th to 10th ancestral generations but the rate became faster(18.4%) for recent five generations. The most probable reason for accelerated decreasing rate of Ne in Hanwoo could be the intensive use of a few prominent sires since the artificial insemination technic was introduced in Korea. In this current situation, the selection of various proven bulls and improvement in mating system considering genetic diversities are mostly needed to sustain the current Ne size or to increase in future generations. In addition, the genetic parameters for carcass traits were estimated using genomic information from combined relationships among genotyped and non-genotyped animals (usually termed as H matrix). The heritabilities of eye muscle area (EMA), backfat thickness (BF), marbling score (MS) were 0.46, 0.60, and 0.63, respectively. A higher accuracy in breeding value (up to 6%) was obtained from combined relationship when compared with traditional pedigree based relationships. For Hanwoo, the benefits for breeding system could come from the higher accuracy of breeding values, selection intensity, genetic standard deviation and generation intervals. The economic efficiency in this study was estimated through genetic gains and economic value for selection traits in Hanwoo. The resulted economic value of a bull selection using EBV and GEBV were 203,358 won/generation and 225,563 won/generation, respectively.
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