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Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle

Whole-genome sequence (WGS) data are increasingly being applied into genomic predictions, offering a higher predictive ability by including causal mutations or single-nucleotide polymorphisms (SNPs) putatively in strong linkage disequilibrium with causal mutations affecting the trait. This study aim...

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Autores principales: Lopez, Bryan Irvine M., An, Narae, Srikanth, Krishnamoorthy, Lee, Seunghwan, Oh, Jae-Don, Shin, Dong-Hyun, Park, Woncheoul, Chai, Han-Ha, Park, Jong-Eun, Lim, Dajeong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859490/
https://www.ncbi.nlm.nih.gov/pubmed/33552124
http://dx.doi.org/10.3389/fgene.2020.603822
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author Lopez, Bryan Irvine M.
An, Narae
Srikanth, Krishnamoorthy
Lee, Seunghwan
Oh, Jae-Don
Shin, Dong-Hyun
Park, Woncheoul
Chai, Han-Ha
Park, Jong-Eun
Lim, Dajeong
author_facet Lopez, Bryan Irvine M.
An, Narae
Srikanth, Krishnamoorthy
Lee, Seunghwan
Oh, Jae-Don
Shin, Dong-Hyun
Park, Woncheoul
Chai, Han-Ha
Park, Jong-Eun
Lim, Dajeong
author_sort Lopez, Bryan Irvine M.
collection PubMed
description Whole-genome sequence (WGS) data are increasingly being applied into genomic predictions, offering a higher predictive ability by including causal mutations or single-nucleotide polymorphisms (SNPs) putatively in strong linkage disequilibrium with causal mutations affecting the trait. This study aimed to improve the predictive performance of the customized Hanwoo 50 k SNP panel for four carcass traits in commercial Hanwoo population by adding highly predictive variants from sequence data. A total of 16,892 Hanwoo cattle with phenotypes (i.e., backfat thickness, carcass weight, longissimus muscle area, and marbling score), 50 k genotypes, and WGS imputed genotypes were used. We partitioned imputed WGS data according to functional annotation [intergenic (IGR), intron (ITR), regulatory (REG), synonymous (SYN), and non-synonymous (NSY)] to characterize the genomic regions that will deliver higher predictive power for the traits investigated. Animals were assigned into two groups, the discovery set (7324 animals) used for predictive variant detection and the cross-validation set for genomic prediction. Genome-wide association studies were performed by trait to every genomic region and entire WGS data for the pre-selection of variants. Each set of pre-selected SNPs with different density (1000, 3000, 5000, or 10,000) were added to the 50 k genotypes separately and the predictive performance of each set of genotypes was assessed using the genomic best linear unbiased prediction (GBLUP). Results showed that the predictive performance of the customized Hanwoo 50 k SNP panel can be improved by the addition of pre-selected variants from the WGS data, particularly 3000 variants from each trait, which is then sufficient to improve the prediction accuracy for all traits. When 12,000 pre-selected variants (3000 variants from each trait) were added to the 50 k genotypes, the prediction accuracies increased by 9.9, 9.2, 6.4, and 4.7% for backfat thickness, carcass weight, longissimus muscle area, and marbling score compared to the regular 50 k SNP panel, respectively. In terms of prediction bias, regression coefficients for all sets of genotypes in all traits were close to 1, indicating an unbiased prediction. The strategy used to select variants based on functional annotation did not show a clear advantage compared to using whole-genome. Nonetheless, such pre-selected SNPs from the IGR region gave the highest improvement in prediction accuracy among genomic regions and the values were close to those obtained using the WGS data for all traits. We concluded that additional gain in prediction accuracy when using pre-selected variants appears to be trait-dependent, and using WGS data remained more accurate compared to using a specific genomic region.
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spelling pubmed-78594902021-02-05 Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle Lopez, Bryan Irvine M. An, Narae Srikanth, Krishnamoorthy Lee, Seunghwan Oh, Jae-Don Shin, Dong-Hyun Park, Woncheoul Chai, Han-Ha Park, Jong-Eun Lim, Dajeong Front Genet Genetics Whole-genome sequence (WGS) data are increasingly being applied into genomic predictions, offering a higher predictive ability by including causal mutations or single-nucleotide polymorphisms (SNPs) putatively in strong linkage disequilibrium with causal mutations affecting the trait. This study aimed to improve the predictive performance of the customized Hanwoo 50 k SNP panel for four carcass traits in commercial Hanwoo population by adding highly predictive variants from sequence data. A total of 16,892 Hanwoo cattle with phenotypes (i.e., backfat thickness, carcass weight, longissimus muscle area, and marbling score), 50 k genotypes, and WGS imputed genotypes were used. We partitioned imputed WGS data according to functional annotation [intergenic (IGR), intron (ITR), regulatory (REG), synonymous (SYN), and non-synonymous (NSY)] to characterize the genomic regions that will deliver higher predictive power for the traits investigated. Animals were assigned into two groups, the discovery set (7324 animals) used for predictive variant detection and the cross-validation set for genomic prediction. Genome-wide association studies were performed by trait to every genomic region and entire WGS data for the pre-selection of variants. Each set of pre-selected SNPs with different density (1000, 3000, 5000, or 10,000) were added to the 50 k genotypes separately and the predictive performance of each set of genotypes was assessed using the genomic best linear unbiased prediction (GBLUP). Results showed that the predictive performance of the customized Hanwoo 50 k SNP panel can be improved by the addition of pre-selected variants from the WGS data, particularly 3000 variants from each trait, which is then sufficient to improve the prediction accuracy for all traits. When 12,000 pre-selected variants (3000 variants from each trait) were added to the 50 k genotypes, the prediction accuracies increased by 9.9, 9.2, 6.4, and 4.7% for backfat thickness, carcass weight, longissimus muscle area, and marbling score compared to the regular 50 k SNP panel, respectively. In terms of prediction bias, regression coefficients for all sets of genotypes in all traits were close to 1, indicating an unbiased prediction. The strategy used to select variants based on functional annotation did not show a clear advantage compared to using whole-genome. Nonetheless, such pre-selected SNPs from the IGR region gave the highest improvement in prediction accuracy among genomic regions and the values were close to those obtained using the WGS data for all traits. We concluded that additional gain in prediction accuracy when using pre-selected variants appears to be trait-dependent, and using WGS data remained more accurate compared to using a specific genomic region. Frontiers Media S.A. 2021-01-21 /pmc/articles/PMC7859490/ /pubmed/33552124 http://dx.doi.org/10.3389/fgene.2020.603822 Text en Copyright © 2021 Lopez, An, Srikanth, Lee, Oh, Shin, Park, Chai, Park and Lim. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Lopez, Bryan Irvine M.
An, Narae
Srikanth, Krishnamoorthy
Lee, Seunghwan
Oh, Jae-Don
Shin, Dong-Hyun
Park, Woncheoul
Chai, Han-Ha
Park, Jong-Eun
Lim, Dajeong
Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
title Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
title_full Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
title_fullStr Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
title_full_unstemmed Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
title_short Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
title_sort genomic prediction based on snp functional annotation using imputed whole-genome sequence data in korean hanwoo cattle
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859490/
https://www.ncbi.nlm.nih.gov/pubmed/33552124
http://dx.doi.org/10.3389/fgene.2020.603822
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