Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs
Abstract Background Improvement of protein efficiency (PE) is a key factor for a sustainable pig production, as nitrogen excretion contributes substantially to environmental pollution. Protein efficiency has been shown to be heritable and genetically correlated with performance traits such as feed c...
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| Format: | Article |
| Language: | deu |
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BMC
2025-08-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-025-00993-z |
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| author | Esther Oluwada Ewaoluwagbemiga Audald Lloret-Villas Adéla Nosková Hubert Pausch Claudia Kasper |
| author_facet | Esther Oluwada Ewaoluwagbemiga Audald Lloret-Villas Adéla Nosková Hubert Pausch Claudia Kasper |
| author_sort | Esther Oluwada Ewaoluwagbemiga |
| collection | DOAJ |
| description | Abstract Background Improvement of protein efficiency (PE) is a key factor for a sustainable pig production, as nitrogen excretion contributes substantially to environmental pollution. Protein efficiency has been shown to be heritable and genetically correlated with performance traits such as feed conversion ratio (FCR) and average daily feed intake (ADFI). This study aimed to identify genomic regions associated with these traits through single-variant genome-wide association studies (GWAS) and regional heritability mapping (RHM) using whole-genome sequence variants from low-pass sequencing of more than 1000 Swiss Large White pigs. Results Genomic heritability estimates using ~ 15 million variants were moderate to high, ranging from 0.33 to 0.47. GWAS did not identify significant variants for PE and FCR, but identified 45 variants at suggestive significance levels for ADFI on chromosome 1 and one for ADG on chromosome 14. Similarly, RHM detected no significant regions for PE and FCR, but five suggestive regions for ADFI (chromosome 1) and one for ADG (chromosome 14). However, by combining leading signals from GWAS and RHM, i.e. overlapping leading variants and significant regions, we highlighted putative candidate genes for PE, including PHYKPL, COL23A1, PPFIBP2, GVIN1, SYT9, RBMXL2, ZNF215, and olfactory receptor genes. Conclusions Combining GWAS and RHM allowed us to identify genomic regions that may influence PE and production traits. Our apparent difficulty in detecting significant regions for these traits probably reflects the relatively small sample size, differences in genetic architecture across study designs and experimental conditions, and that polymorphisms explaining large proportions of the trait variation may not segregate in this population. Nevertheless, we identified plausible functional candidate genes in the highlighted regions, including those involved in nutrient sensing, the urea cycle, and metabolic pathways, in particular IGF1-insulin, and that have previously been reported to be associated with nitrogen metabolism in cattle and with muscle and adipose tissue metabolism and feed intake in pigs. We also highlighted a range of noncoding RNAs. Their targets and roles in gene regulation should be further investigated in this context. |
| format | Article |
| id | doaj-art-5c375e9929ed4106a1d6c2f2c12f3f8f |
| institution | Kabale University |
| issn | 1297-9686 |
| language | deu |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj-art-5c375e9929ed4106a1d6c2f2c12f3f8f2025-08-20T03:42:29ZdeuBMCGenetics Selection Evolution1297-96862025-08-0157112410.1186/s12711-025-00993-zSingle-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigsEsther Oluwada Ewaoluwagbemiga0Audald Lloret-Villas1Adéla Nosková2Hubert Pausch3Claudia Kasper4Agroscope, Animal GenoPhenomicsAnimal Genomics, Department of Environmental Systems Science, ETH ZurichAnimal Genomics, Department of Environmental Systems Science, ETH ZurichAnimal Genomics, Department of Environmental Systems Science, ETH ZurichAgroscope, Animal GenoPhenomicsAbstract Background Improvement of protein efficiency (PE) is a key factor for a sustainable pig production, as nitrogen excretion contributes substantially to environmental pollution. Protein efficiency has been shown to be heritable and genetically correlated with performance traits such as feed conversion ratio (FCR) and average daily feed intake (ADFI). This study aimed to identify genomic regions associated with these traits through single-variant genome-wide association studies (GWAS) and regional heritability mapping (RHM) using whole-genome sequence variants from low-pass sequencing of more than 1000 Swiss Large White pigs. Results Genomic heritability estimates using ~ 15 million variants were moderate to high, ranging from 0.33 to 0.47. GWAS did not identify significant variants for PE and FCR, but identified 45 variants at suggestive significance levels for ADFI on chromosome 1 and one for ADG on chromosome 14. Similarly, RHM detected no significant regions for PE and FCR, but five suggestive regions for ADFI (chromosome 1) and one for ADG (chromosome 14). However, by combining leading signals from GWAS and RHM, i.e. overlapping leading variants and significant regions, we highlighted putative candidate genes for PE, including PHYKPL, COL23A1, PPFIBP2, GVIN1, SYT9, RBMXL2, ZNF215, and olfactory receptor genes. Conclusions Combining GWAS and RHM allowed us to identify genomic regions that may influence PE and production traits. Our apparent difficulty in detecting significant regions for these traits probably reflects the relatively small sample size, differences in genetic architecture across study designs and experimental conditions, and that polymorphisms explaining large proportions of the trait variation may not segregate in this population. Nevertheless, we identified plausible functional candidate genes in the highlighted regions, including those involved in nutrient sensing, the urea cycle, and metabolic pathways, in particular IGF1-insulin, and that have previously been reported to be associated with nitrogen metabolism in cattle and with muscle and adipose tissue metabolism and feed intake in pigs. We also highlighted a range of noncoding RNAs. Their targets and roles in gene regulation should be further investigated in this context.https://doi.org/10.1186/s12711-025-00993-z |
| spellingShingle | Esther Oluwada Ewaoluwagbemiga Audald Lloret-Villas Adéla Nosková Hubert Pausch Claudia Kasper Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs Genetics Selection Evolution |
| title | Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs |
| title_full | Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs |
| title_fullStr | Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs |
| title_full_unstemmed | Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs |
| title_short | Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs |
| title_sort | single variant genome wide association study and regional heritability mapping of protein efficiency and performance traits in large white pigs |
| url | https://doi.org/10.1186/s12711-025-00993-z |
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