Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs
The improvement of carcass traits is a key focus in pig genetic breeding programs. To identify quantitative trait loci (QTLs) and genes linked to key carcass traits, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 1118 commercial pigs (Duroc sires and York...
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MDPI AG
2025-04-01
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| author | Zohre Mozduri Graham Plastow Jack Dekkers Kerry Houlahan Robert Kemp Manuel Juárez |
| author_facet | Zohre Mozduri Graham Plastow Jack Dekkers Kerry Houlahan Robert Kemp Manuel Juárez |
| author_sort | Zohre Mozduri |
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| description | The improvement of carcass traits is a key focus in pig genetic breeding programs. To identify quantitative trait loci (QTLs) and genes linked to key carcass traits, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 1118 commercial pigs (Duroc sires and Yorkshire/Landrace F1 dams). This study focused on six phenotypes: iodine value, belly firmness, belly side fat, total side thickness (belly SThK), belly subcutaneous fat (Subq), and belly seam. Phenotypes were measured using image analysis, DEXA, and fatty acid profiling, and genotyping was performed using low-pass sequencing (SkimSeq). After quality control, 18,911,793 single nucleotide polymorphisms (SNPs) were retained for further analysis. A GWAS was conducted using a linear mixed model implemented in GCTA. Key findings include a significant QTL on SSC15 (110.83–112.23 Mb), which is associated with the iodine value, containing genes such as <i>COX15</i>, <i>CHUK</i>, <i>SCD</i>, and <i>HIF1AN</i>, which have known roles in fatty acid metabolism. Additionally, <i>PNKD</i>, <i>VIL1</i>, and <i>PRKAG3</i> (120.74–121.88 Mb on SSC15) were linked to belly firmness, influencing muscle structure and fat composition. Three QTLs for belly side fat were identified on SSC1, SSC2, and SSC3, highlighting genes like <i>SLC22A18</i>, <i>PHLDA2</i>, and <i>OSBPL5</i>, which regulate fat deposition and lipid metabolism. The results provide novel molecular markers that can be incorporated into selective breeding programs to improve pork quality, fat distribution, and meat composition. These findings enhance our understanding of the genetic mechanisms underlying carcass belly traits while offering tools to improve pork quality, optimize fat composition, and align with consumer preferences in the meat production industry. |
| format | Article |
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| institution | DOAJ |
| issn | 2076-2615 |
| language | English |
| publishDate | 2025-04-01 |
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| series | Animals |
| spelling | doaj-art-3bb085e3cfd14ea3985bf46cb9077d472025-08-20T02:58:43ZengMDPI AGAnimals2076-26152025-04-01159125410.3390/ani15091254Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred PigsZohre Mozduri0Graham Plastow1Jack Dekkers2Kerry Houlahan3Robert Kemp4Manuel Juárez5Livestock Gentec Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, CanadaLivestock Gentec Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, CanadaDepartment of Animal Science, Iowa State University, Ames, IA 50011, USAGenesus Genetic Technology Inc., Winnipeg, MB R3P 0H4, CanadaGenesus Genetic Technology Inc., Winnipeg, MB R3P 0H4, CanadaLacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, CanadaThe improvement of carcass traits is a key focus in pig genetic breeding programs. To identify quantitative trait loci (QTLs) and genes linked to key carcass traits, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 1118 commercial pigs (Duroc sires and Yorkshire/Landrace F1 dams). This study focused on six phenotypes: iodine value, belly firmness, belly side fat, total side thickness (belly SThK), belly subcutaneous fat (Subq), and belly seam. Phenotypes were measured using image analysis, DEXA, and fatty acid profiling, and genotyping was performed using low-pass sequencing (SkimSeq). After quality control, 18,911,793 single nucleotide polymorphisms (SNPs) were retained for further analysis. A GWAS was conducted using a linear mixed model implemented in GCTA. Key findings include a significant QTL on SSC15 (110.83–112.23 Mb), which is associated with the iodine value, containing genes such as <i>COX15</i>, <i>CHUK</i>, <i>SCD</i>, and <i>HIF1AN</i>, which have known roles in fatty acid metabolism. Additionally, <i>PNKD</i>, <i>VIL1</i>, and <i>PRKAG3</i> (120.74–121.88 Mb on SSC15) were linked to belly firmness, influencing muscle structure and fat composition. Three QTLs for belly side fat were identified on SSC1, SSC2, and SSC3, highlighting genes like <i>SLC22A18</i>, <i>PHLDA2</i>, and <i>OSBPL5</i>, which regulate fat deposition and lipid metabolism. The results provide novel molecular markers that can be incorporated into selective breeding programs to improve pork quality, fat distribution, and meat composition. These findings enhance our understanding of the genetic mechanisms underlying carcass belly traits while offering tools to improve pork quality, optimize fat composition, and align with consumer preferences in the meat production industry.https://www.mdpi.com/2076-2615/15/9/1254belly traitspork qualityQTLsfat compositionwhole-genome sequencing |
| spellingShingle | Zohre Mozduri Graham Plastow Jack Dekkers Kerry Houlahan Robert Kemp Manuel Juárez Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs Animals belly traits pork quality QTLs fat composition whole-genome sequencing |
| title | Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs |
| title_full | Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs |
| title_fullStr | Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs |
| title_full_unstemmed | Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs |
| title_short | Genome-Wide Association Study for Belly Traits in Canadian Commercial Crossbred Pigs |
| title_sort | genome wide association study for belly traits in canadian commercial crossbred pigs |
| topic | belly traits pork quality QTLs fat composition whole-genome sequencing |
| url | https://www.mdpi.com/2076-2615/15/9/1254 |
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