Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices
Abstract: The objective of this work was to evaluate the effects of genomic information on the genetic evaluation of hip height in Brahman cattle using different matrices built from genomic and pedigree data. Hip height measurements from 1,695 animals, genotyped with high-density SNP chip or imputed from 50 K high-density SNP chip, were used. The numerator relationship matrix (NRM) was compared with the H matrix, which incorporated the NRM and genomic relationship (G) matrix simultaneously. The genotypes were used to estimate three versions of G: observed allele frequency (HGOF), average minor allele frequency (HGMF), and frequency of 0.5 for all markers (HG50). For matrix comparisons, animal data were either used in full or divided into calibration (80% older animals) and validation (20% younger animals) datasets. The accuracy values for the NRM, HGOF, and HG50 were 0.776, 0.813, and 0.594, respectively. The NRM and HGOF showed similar minor variances for diagonal and off-diagonal elements, as well as for estimated breeding values. The use of genomic information resulted in relationship estimates similar to those obtained based on pedigree; however, HGOF is the best option for estimating the genomic relationship matrix and results in a higher prediction accuracy. The ranking of the top 20% animals was very similar for all matrices, but the ranking within them varies depending on the method used.
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Embrapa Secretaria de Pesquisa e Desenvolvimento
2018
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oai:scielo:S0100-204X20180006007172018-08-27Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matricesFarah,Michel MarquesFortes,Marina Rufino SalinasKelly,MatthewPorto-Neto,Laercio RibeiroMeira,Camila TangariCarreño,Luis Orlando DuitamaFonseca,Ricardo daMoore,Stephen Stewart Bos indicus beef cattle genomics rare alleles Abstract: The objective of this work was to evaluate the effects of genomic information on the genetic evaluation of hip height in Brahman cattle using different matrices built from genomic and pedigree data. Hip height measurements from 1,695 animals, genotyped with high-density SNP chip or imputed from 50 K high-density SNP chip, were used. The numerator relationship matrix (NRM) was compared with the H matrix, which incorporated the NRM and genomic relationship (G) matrix simultaneously. The genotypes were used to estimate three versions of G: observed allele frequency (HGOF), average minor allele frequency (HGMF), and frequency of 0.5 for all markers (HG50). For matrix comparisons, animal data were either used in full or divided into calibration (80% older animals) and validation (20% younger animals) datasets. The accuracy values for the NRM, HGOF, and HG50 were 0.776, 0.813, and 0.594, respectively. The NRM and HGOF showed similar minor variances for diagonal and off-diagonal elements, as well as for estimated breeding values. The use of genomic information resulted in relationship estimates similar to those obtained based on pedigree; however, HGOF is the best option for estimating the genomic relationship matrix and results in a higher prediction accuracy. The ranking of the top 20% animals was very similar for all matrices, but the ranking within them varies depending on the method used.info:eu-repo/semantics/openAccessEmbrapa Secretaria de Pesquisa e DesenvolvimentoPesquisa Agropecuária BrasileiraPesquisa Agropecuária Brasileira v.53 n.6 20182018-06-01info:eu-repo/semantics/articletext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2018000600717en10.1590/s0100-204x2018000600008 |
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Farah,Michel Marques Fortes,Marina Rufino Salinas Kelly,Matthew Porto-Neto,Laercio Ribeiro Meira,Camila Tangari Carreño,Luis Orlando Duitama Fonseca,Ricardo da Moore,Stephen Stewart |
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Farah,Michel Marques Fortes,Marina Rufino Salinas Kelly,Matthew Porto-Neto,Laercio Ribeiro Meira,Camila Tangari Carreño,Luis Orlando Duitama Fonseca,Ricardo da Moore,Stephen Stewart Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices |
author_facet |
Farah,Michel Marques Fortes,Marina Rufino Salinas Kelly,Matthew Porto-Neto,Laercio Ribeiro Meira,Camila Tangari Carreño,Luis Orlando Duitama Fonseca,Ricardo da Moore,Stephen Stewart |
author_sort |
Farah,Michel Marques |
title |
Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices |
title_short |
Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices |
title_full |
Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices |
title_fullStr |
Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices |
title_full_unstemmed |
Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices |
title_sort |
accuracy of genomic selection predictions for hip height in brahman cattle using different relationship matrices |
description |
Abstract: The objective of this work was to evaluate the effects of genomic information on the genetic evaluation of hip height in Brahman cattle using different matrices built from genomic and pedigree data. Hip height measurements from 1,695 animals, genotyped with high-density SNP chip or imputed from 50 K high-density SNP chip, were used. The numerator relationship matrix (NRM) was compared with the H matrix, which incorporated the NRM and genomic relationship (G) matrix simultaneously. The genotypes were used to estimate three versions of G: observed allele frequency (HGOF), average minor allele frequency (HGMF), and frequency of 0.5 for all markers (HG50). For matrix comparisons, animal data were either used in full or divided into calibration (80% older animals) and validation (20% younger animals) datasets. The accuracy values for the NRM, HGOF, and HG50 were 0.776, 0.813, and 0.594, respectively. The NRM and HGOF showed similar minor variances for diagonal and off-diagonal elements, as well as for estimated breeding values. The use of genomic information resulted in relationship estimates similar to those obtained based on pedigree; however, HGOF is the best option for estimating the genomic relationship matrix and results in a higher prediction accuracy. The ranking of the top 20% animals was very similar for all matrices, but the ranking within them varies depending on the method used. |
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Embrapa Secretaria de Pesquisa e Desenvolvimento |
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2018 |
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http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2018000600717 |
work_keys_str_mv |
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