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Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation

In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM)...

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Autores principales: Gershoni, Moran, Shirak, Andrey, Ben-Meir, Yehoshav, Shabtay, Ariel, Cohen-Zinder, Miri, Seroussi, Eyal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048120/
https://www.ncbi.nlm.nih.gov/pubmed/36980820
http://dx.doi.org/10.3390/genes14030547
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author Gershoni, Moran
Shirak, Andrey
Ben-Meir, Yehoshav
Shabtay, Ariel
Cohen-Zinder, Miri
Seroussi, Eyal
author_facet Gershoni, Moran
Shirak, Andrey
Ben-Meir, Yehoshav
Shabtay, Ariel
Cohen-Zinder, Miri
Seroussi, Eyal
author_sort Gershoni, Moran
collection PubMed
description In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM) methods (n = 114 cows), for mutations in the FABP4 gene that had been suggested to have a large effect on RFI. Combining the whole genome sequence (n = 19 bulls) and the cows’ BovineHD BeadChip allowed imputing genotypes for these mutations that were verified by Sanger sequencing, whereas, an error rate of 11.6% and 10.7% were encountered for HRM and TaqMan, respectively. We show that this error rate seriously affected the linkage-disequilibrium analysis that supported this gene candidacy over other BTA14 gene candidates. Thus, imputation produced superior genotypes and should also be regarded as a method of choice to validate the reliability of the genotypes obtained by other methodologies that are prone to genotyping errors due to technical conditions. These results support the view that RFI is a complex trait and that searching for the causative sequence variation underlying cattle RFI should await the development of statistical methods suitable to handle additive and epistatic interactions.
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spelling pubmed-100481202023-03-29 Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation Gershoni, Moran Shirak, Andrey Ben-Meir, Yehoshav Shabtay, Ariel Cohen-Zinder, Miri Seroussi, Eyal Genes (Basel) Article In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM) methods (n = 114 cows), for mutations in the FABP4 gene that had been suggested to have a large effect on RFI. Combining the whole genome sequence (n = 19 bulls) and the cows’ BovineHD BeadChip allowed imputing genotypes for these mutations that were verified by Sanger sequencing, whereas, an error rate of 11.6% and 10.7% were encountered for HRM and TaqMan, respectively. We show that this error rate seriously affected the linkage-disequilibrium analysis that supported this gene candidacy over other BTA14 gene candidates. Thus, imputation produced superior genotypes and should also be regarded as a method of choice to validate the reliability of the genotypes obtained by other methodologies that are prone to genotyping errors due to technical conditions. These results support the view that RFI is a complex trait and that searching for the causative sequence variation underlying cattle RFI should await the development of statistical methods suitable to handle additive and epistatic interactions. MDPI 2023-02-22 /pmc/articles/PMC10048120/ /pubmed/36980820 http://dx.doi.org/10.3390/genes14030547 Text en © 2023 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
Gershoni, Moran
Shirak, Andrey
Ben-Meir, Yehoshav
Shabtay, Ariel
Cohen-Zinder, Miri
Seroussi, Eyal
Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
title Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
title_full Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
title_fullStr Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
title_full_unstemmed Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
title_short Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
title_sort re-evaluation of genotyping methodologies in cattle: the proficiency of imputation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048120/
https://www.ncbi.nlm.nih.gov/pubmed/36980820
http://dx.doi.org/10.3390/genes14030547
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