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 (<i>n</i> = 192 cows) to those obtained using the TaqMan and high-resolu...
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MDPI AG
2023-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/3/547 |
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| author | Moran Gershoni Andrey Shirak Yehoshav Ben-Meir Ariel Shabtay Miri Cohen-Zinder Eyal Seroussi |
| author_facet | Moran Gershoni Andrey Shirak Yehoshav Ben-Meir Ariel Shabtay Miri Cohen-Zinder Eyal Seroussi |
| author_sort | Moran Gershoni |
| collection | DOAJ |
| 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 (<i>n</i> = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM) methods (<i>n</i> = 114 cows), for mutations in the <i>FABP4</i> gene that had been suggested to have a large effect on RFI. Combining the whole genome sequence (<i>n</i> = 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. |
| first_indexed | 2024-03-11T06:30:06Z |
| format | Article |
| id | doaj.art-7b97bd8f4c9b4e969fb2601c9ac2e8ed |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T06:30:06Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-7b97bd8f4c9b4e969fb2601c9ac2e8ed2023-11-17T11:16:06ZengMDPI AGGenes2073-44252023-02-0114354710.3390/genes14030547Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of ImputationMoran Gershoni0Andrey Shirak1Yehoshav Ben-Meir2Ariel Shabtay3Miri Cohen-Zinder4Eyal Seroussi5Institute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, IsraelInstitute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, IsraelInstitute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, IsraelBeef Cattle Section, Newe-Ya’ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 30095, IsraelBeef Cattle Section, Newe-Ya’ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 30095, IsraelInstitute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, IsraelIn 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 (<i>n</i> = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM) methods (<i>n</i> = 114 cows), for mutations in the <i>FABP4</i> gene that had been suggested to have a large effect on RFI. Combining the whole genome sequence (<i>n</i> = 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.https://www.mdpi.com/2073-4425/14/3/547genomic evaluationgenotyping platformssingle nucleotide polymorphism<i>FABP4</i><i>ZHX2</i>genomic imputation |
| spellingShingle | Moran Gershoni Andrey Shirak Yehoshav Ben-Meir Ariel Shabtay Miri Cohen-Zinder Eyal Seroussi Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation Genes genomic evaluation genotyping platforms single nucleotide polymorphism <i>FABP4</i> <i>ZHX2</i> genomic 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 | genomic evaluation genotyping platforms single nucleotide polymorphism <i>FABP4</i> <i>ZHX2</i> genomic imputation |
| url | https://www.mdpi.com/2073-4425/14/3/547 |
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