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Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle

We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed...

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Detalles Bibliográficos
Autores principales: Ogawa, Shinichiro, Taniguchi, Yukio, Watanabe, Toshio, Iwaisaki, Hiroaki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859149/
https://www.ncbi.nlm.nih.gov/pubmed/36672767
http://dx.doi.org/10.3390/genes14010024
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author Ogawa, Shinichiro
Taniguchi, Yukio
Watanabe, Toshio
Iwaisaki, Hiroaki
author_facet Ogawa, Shinichiro
Taniguchi, Yukio
Watanabe, Toshio
Iwaisaki, Hiroaki
author_sort Ogawa, Shinichiro
collection PubMed
description We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results.
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spelling pubmed-98591492023-01-21 Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle Ogawa, Shinichiro Taniguchi, Yukio Watanabe, Toshio Iwaisaki, Hiroaki Genes (Basel) Article We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results. MDPI 2022-12-22 /pmc/articles/PMC9859149/ /pubmed/36672767 http://dx.doi.org/10.3390/genes14010024 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ogawa, Shinichiro
Taniguchi, Yukio
Watanabe, Toshio
Iwaisaki, Hiroaki
Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle
title Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle
title_full Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle
title_fullStr Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle
title_full_unstemmed Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle
title_short Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle
title_sort fitting genomic prediction models with different marker effects among prefectures to carcass traits in japanese black cattle
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859149/
https://www.ncbi.nlm.nih.gov/pubmed/36672767
http://dx.doi.org/10.3390/genes14010024
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