Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study
As optimization methods to identify the best animals for dense genotyping to construct a reference population for genotype imputation, the MCA and MCG methods, which use the pedigree-based additive genetic relationship matrix (<b>A</b> matrix) and the genomic relationship matrix (<b&g...
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MDPI AG
2023-02-01
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author | Shinichiro Ogawa Atsushi Zoda Rino Kagawa Rui Obinata |
author_facet | Shinichiro Ogawa Atsushi Zoda Rino Kagawa Rui Obinata |
author_sort | Shinichiro Ogawa |
collection | DOAJ |
description | As optimization methods to identify the best animals for dense genotyping to construct a reference population for genotype imputation, the MCA and MCG methods, which use the pedigree-based additive genetic relationship matrix (<b>A</b> matrix) and the genomic relationship matrix (<b>G</b> matrix), respectively, have been proposed. We assessed the performance of MCA and MCG methods using 575 Japanese Black cows. Pedigree data were provided to trace back up to five generations to construct the <b>A</b> matrix with changing the pedigree depth from 1 to 5 (five MCA methods). Genotype information on 36,426 single-nucleotide polymorphisms was used to calculate the <b>G</b> matrix based on VanRaden’s methods 1 and 2 (two MCG methods). The MCG always selected one cow per iteration, while MCA sometimes selected multiple cows. The number of commonly selected cows between the MCA and MCG methods was generally lower than that between different MCA methods or between different MCG methods. For the studied population, MCG appeared to be more reasonable than MCA in selecting cows as a reference population for higher-density genotype imputation to perform genomic prediction and a genome-wide association study. |
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last_indexed | 2024-03-11T09:16:10Z |
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spelling | doaj.art-921c1ef3aff5459dae8e84fcae0d802b2023-11-16T18:39:26ZengMDPI AGAnimals2076-26152023-02-0113463810.3390/ani13040638Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case StudyShinichiro Ogawa0Atsushi Zoda1Rino Kagawa2Rui Obinata3Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, JapanResearch and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, JapanResearch and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, JapanResearch and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, JapanAs optimization methods to identify the best animals for dense genotyping to construct a reference population for genotype imputation, the MCA and MCG methods, which use the pedigree-based additive genetic relationship matrix (<b>A</b> matrix) and the genomic relationship matrix (<b>G</b> matrix), respectively, have been proposed. We assessed the performance of MCA and MCG methods using 575 Japanese Black cows. Pedigree data were provided to trace back up to five generations to construct the <b>A</b> matrix with changing the pedigree depth from 1 to 5 (five MCA methods). Genotype information on 36,426 single-nucleotide polymorphisms was used to calculate the <b>G</b> matrix based on VanRaden’s methods 1 and 2 (two MCG methods). The MCG always selected one cow per iteration, while MCA sometimes selected multiple cows. The number of commonly selected cows between the MCA and MCG methods was generally lower than that between different MCA methods or between different MCG methods. For the studied population, MCG appeared to be more reasonable than MCA in selecting cows as a reference population for higher-density genotype imputation to perform genomic prediction and a genome-wide association study.https://www.mdpi.com/2076-2615/13/4/638high-density genotypingimputationJapanese Black cattlepedigreereference populationsingle-nucleotide polymorphism |
spellingShingle | Shinichiro Ogawa Atsushi Zoda Rino Kagawa Rui Obinata Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study Animals high-density genotyping imputation Japanese Black cattle pedigree reference population single-nucleotide polymorphism |
title | Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study |
title_full | Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study |
title_fullStr | Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study |
title_full_unstemmed | Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study |
title_short | Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study |
title_sort | comparing methods to select candidates for re genotyping to impute higher density genotype data in a japanese black cattle population a case study |
topic | high-density genotyping imputation Japanese Black cattle pedigree reference population single-nucleotide polymorphism |
url | https://www.mdpi.com/2076-2615/13/4/638 |
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