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Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding
This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits of 16,970 com...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606632/ https://www.ncbi.nlm.nih.gov/pubmed/37895191 http://dx.doi.org/10.3390/genes14101839 |
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author | Lee, Dong Jae Kim, Yoonsik Dinh, Phuong Thanh N. Chung, Yoonji Lee, Dooho Kim, Yeongkuk Lee, Soo Hyun Choi, Inchul Lee, Seung Hwan |
author_facet | Lee, Dong Jae Kim, Yoonsik Dinh, Phuong Thanh N. Chung, Yoonji Lee, Dooho Kim, Yeongkuk Lee, Soo Hyun Choi, Inchul Lee, Seung Hwan |
author_sort | Lee, Dong Jae |
collection | PubMed |
description | This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits of 16,970 commercial Hanwoo. We found 33, 2, 1, and 3 significant SNPs associated with carcass weight (CW), backfat thickness (BFT), eye muscle area (EMA), and marbling score (MS), respectively. In CW and EMA, the most significant missense SNP was identified at 19,524,263 on BTA14 and involved the PRKDC. A missense SNP in the ZFAND2B, located at 107,160,304 on BTA2 was identified as being involved in BFT. For MS, missense SNP in the ACVR2B gene, located at 11,849,704 in BTA22 was identified as the most significant marker. The contribution of the most significant missense SNPs to genetic variance was confirmed to be 8.47%, 2.08%, 1.73%, and 1.19% in CW, BFT, EMA, and MS, respectively. We generated favorable and unfavorable haplotype combinations based on the significant SNPs for CW. Significant differences in GEBV (Genomic Estimated Breeding Values) were observed between groups with each favorable and unfavorable haplotype combination. In particular, the missense SNPs in PRKDC, MRPL9, and ANKFN1 appear to significantly affect the protein’s function and structure, making them strong candidates as causal mutations. These missense SNPs have the potential to serve as valuable markers for improving carcass traits in Hanwoo commercial farms. |
format | Online Article Text |
id | pubmed-10606632 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-106066322023-10-28 Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding Lee, Dong Jae Kim, Yoonsik Dinh, Phuong Thanh N. Chung, Yoonji Lee, Dooho Kim, Yeongkuk Lee, Soo Hyun Choi, Inchul Lee, Seung Hwan Genes (Basel) Article This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits of 16,970 commercial Hanwoo. We found 33, 2, 1, and 3 significant SNPs associated with carcass weight (CW), backfat thickness (BFT), eye muscle area (EMA), and marbling score (MS), respectively. In CW and EMA, the most significant missense SNP was identified at 19,524,263 on BTA14 and involved the PRKDC. A missense SNP in the ZFAND2B, located at 107,160,304 on BTA2 was identified as being involved in BFT. For MS, missense SNP in the ACVR2B gene, located at 11,849,704 in BTA22 was identified as the most significant marker. The contribution of the most significant missense SNPs to genetic variance was confirmed to be 8.47%, 2.08%, 1.73%, and 1.19% in CW, BFT, EMA, and MS, respectively. We generated favorable and unfavorable haplotype combinations based on the significant SNPs for CW. Significant differences in GEBV (Genomic Estimated Breeding Values) were observed between groups with each favorable and unfavorable haplotype combination. In particular, the missense SNPs in PRKDC, MRPL9, and ANKFN1 appear to significantly affect the protein’s function and structure, making them strong candidates as causal mutations. These missense SNPs have the potential to serve as valuable markers for improving carcass traits in Hanwoo commercial farms. MDPI 2023-09-22 /pmc/articles/PMC10606632/ /pubmed/37895191 http://dx.doi.org/10.3390/genes14101839 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 Lee, Dong Jae Kim, Yoonsik Dinh, Phuong Thanh N. Chung, Yoonji Lee, Dooho Kim, Yeongkuk Lee, Soo Hyun Choi, Inchul Lee, Seung Hwan Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding |
title | Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding |
title_full | Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding |
title_fullStr | Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding |
title_full_unstemmed | Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding |
title_short | Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding |
title_sort | identification of missense variants affecting carcass traits for hanwoo precision breeding |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606632/ https://www.ncbi.nlm.nih.gov/pubmed/37895191 http://dx.doi.org/10.3390/genes14101839 |
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