Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips
The accuracy of genomic estimated breeding values (GEBV) was evaluated for sixteen meat quality traits in a Berkshire population (n = 1,191) that was collected from Dasan breeding farm, Namwon, Korea. The animals were genotyped with the Illumina porcine 62 K single nucleotide polymorphism (SNP) bead...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2014-11-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-27-11-1540.pdf |
| _version_ | 1828528139849957376 |
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| author | S. Baby K.-E. Hyeong Y.-M. Lee J.-H. Jung D.-Y. Oh K.-C. Nam T. H. Kim H.-K. Lee J.-J. Kim |
| author_facet | S. Baby K.-E. Hyeong Y.-M. Lee J.-H. Jung D.-Y. Oh K.-C. Nam T. H. Kim H.-K. Lee J.-J. Kim |
| author_sort | S. Baby |
| collection | DOAJ |
| description | The accuracy of genomic estimated breeding values (GEBV) was evaluated for sixteen meat quality traits in a Berkshire population (n = 1,191) that was collected from Dasan breeding farm, Namwon, Korea. The animals were genotyped with the Illumina porcine 62 K single nucleotide polymorphism (SNP) bead chips, in which a set of 36,605 SNPs were available after quality control tests. Two methods were applied to evaluate GEBV accuracies, i.e. genome based linear unbiased prediction method (GBLUP) and Bayes B, using ASREML 3.0 and Gensel 4.0 software, respectively. The traits composed different sets of training (both genotypes and phenotypes) and testing (genotypes only) data. Under the GBLUP model, the GEBV accuracies for the training data ranged from 0.42±0.08 for collagen to 0.75±0.02 for water holding capacity with an average of 0.65±0.04 across all the traits. Under the Bayes B model, the GEBV accuracy ranged from 0.10±0.14 for National Pork Producers Council (NPCC) marbling score to 0.76±0.04 for drip loss, with an average of 0.49±0.10. For the testing samples, the GEBV accuracy had an average of 0.46±0.10 under the GBLUP model, ranging from 0.20±0.18 for protein to 0.65±0.06 for drip loss. Under the Bayes B model, the GEBV accuracy ranged from 0.04±0.09 for NPCC marbling score to 0.72±0.05 for drip loss with an average of 0.38±0.13. The GEBV accuracy increased with the size of the training data and heritability. In general, the GEBV accuracies under the Bayes B model were lower than under the GBLUP model, especially when the training sample size was small. Our results suggest that a much greater training sample size is needed to get better GEBV accuracies for the testing samples. |
| first_indexed | 2024-12-11T21:49:09Z |
| format | Article |
| id | doaj.art-c8d153c4cf57404381e05c85295a4aa6 |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-11T21:49:09Z |
| publishDate | 2014-11-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-c8d153c4cf57404381e05c85295a4aa62022-12-22T00:49:32ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172014-11-0127111540154710.5713/ajas.2014.1437122959Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism ChipsS. BabyK.-E. HyeongY.-M. LeeJ.-H. Jung0D.-Y. Oh1K.-C. Nam2T. H. Kim3H.-K. Lee4J.-J. Kim Dasan Pig Breeding Co., Namwon 590-831, .Korea Gyeongbuk Livestock Research Institute, Yeungju 750-780, .Korea Department of Animal Science and Technology, Sunchon National University, Suncheon 540-950, .Korea Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon 441-706, .Korea Genomic Informatics Center, Hankyong National University, Anseong 456-649, .KoreaThe accuracy of genomic estimated breeding values (GEBV) was evaluated for sixteen meat quality traits in a Berkshire population (n = 1,191) that was collected from Dasan breeding farm, Namwon, Korea. The animals were genotyped with the Illumina porcine 62 K single nucleotide polymorphism (SNP) bead chips, in which a set of 36,605 SNPs were available after quality control tests. Two methods were applied to evaluate GEBV accuracies, i.e. genome based linear unbiased prediction method (GBLUP) and Bayes B, using ASREML 3.0 and Gensel 4.0 software, respectively. The traits composed different sets of training (both genotypes and phenotypes) and testing (genotypes only) data. Under the GBLUP model, the GEBV accuracies for the training data ranged from 0.42±0.08 for collagen to 0.75±0.02 for water holding capacity with an average of 0.65±0.04 across all the traits. Under the Bayes B model, the GEBV accuracy ranged from 0.10±0.14 for National Pork Producers Council (NPCC) marbling score to 0.76±0.04 for drip loss, with an average of 0.49±0.10. For the testing samples, the GEBV accuracy had an average of 0.46±0.10 under the GBLUP model, ranging from 0.20±0.18 for protein to 0.65±0.06 for drip loss. Under the Bayes B model, the GEBV accuracy ranged from 0.04±0.09 for NPCC marbling score to 0.72±0.05 for drip loss with an average of 0.38±0.13. The GEBV accuracy increased with the size of the training data and heritability. In general, the GEBV accuracies under the Bayes B model were lower than under the GBLUP model, especially when the training sample size was small. Our results suggest that a much greater training sample size is needed to get better GEBV accuracies for the testing samples.http://www.ajas.info/upload/pdf/ajas-27-11-1540.pdfBerkshireGenomic Estimated Breeding Values [GEBV]Meat QualityGenome Based Linear Unbiased Prediction Method [GBLUP]Bayes B |
| spellingShingle | S. Baby K.-E. Hyeong Y.-M. Lee J.-H. Jung D.-Y. Oh K.-C. Nam T. H. Kim H.-K. Lee J.-J. Kim Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips Asian-Australasian Journal of Animal Sciences Berkshire Genomic Estimated Breeding Values [GEBV] Meat Quality Genome Based Linear Unbiased Prediction Method [GBLUP] Bayes B |
| title | Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips |
| title_full | Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips |
| title_fullStr | Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips |
| title_full_unstemmed | Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips |
| title_short | Evaluation of Genome Based Estimated Breeding Values for Meat Quality in a Berkshire Population Using High Density Single Nucleotide Polymorphism Chips |
| title_sort | evaluation of genome based estimated breeding values for meat quality in a berkshire population using high density single nucleotide polymorphism chips |
| topic | Berkshire Genomic Estimated Breeding Values [GEBV] Meat Quality Genome Based Linear Unbiased Prediction Method [GBLUP] Bayes B |
| url | http://www.ajas.info/upload/pdf/ajas-27-11-1540.pdf |
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