Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection
This study aimed to investigate population genetic differences related to reproductive traits between Duroc and Yorkshire (Dutch Large White) pigs using two approaches: linear mixed models that dissect additive and dominant effects, and selective sweep analysis. (1) Methods: Genome-wide single-nucle...
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MDPI AG
2025-07-01
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| Series: | Veterinary Sciences |
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| author | Changyi Chen Yu He Juan Ke Xiaoran Zhang Junwen Fei Boxing Sun Hao Sun Chunyan Bai |
| author_facet | Changyi Chen Yu He Juan Ke Xiaoran Zhang Junwen Fei Boxing Sun Hao Sun Chunyan Bai |
| author_sort | Changyi Chen |
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| description | This study aimed to investigate population genetic differences related to reproductive traits between Duroc and Yorkshire (Dutch Large White) pigs using two approaches: linear mixed models that dissect additive and dominant effects, and selective sweep analysis. (1) Methods: Genome-wide single-nucleotide polymorphism (SNP) data of 3917 Duroc and 3217 Yorkshire pigs were analyzed. The first principal component (PC1) was used as a simulated phenotype to capture population-level variance. Additive and dominant genetic effects were partitioned and evaluated by using the combination of the linear mixed models (LMM) and ADDO’s algorithm (LMM + ADDO). In parallel, selective sweep signals were detected using fixation index (<i>F<sub>ST</sub></i>) and nucleotide diversity (θ<sub>π</sub>) analyses. A comparative assessment was then conducted between the LMM + ADDO and the selective sweep analysis results. Significant loci were annotated using quantitative trait loci (QTL) databases and the Ensembl genome browser. (2) Results: There are 39040 SNPs retained after quality control. Using the LMM + ADDO framework with PC1 as a simulated phenotype, a total of 632 significant SNPs and 184 candidate genes were identified. Notably, 587 SNPs and 171 genes were uniquely detected by the LMM + ADDO method and not among loci detected by the top 5% of <i>F<sub>ST</sub></i> and θ<sub>π</sub> values. Key candidate genes associated with litter size included <i>HSPG2</i>, <i>KAT6B</i>, <i>SAMD8</i>, and <i>LRMDA</i>, while <i>DLGAP1</i>, <i>MYOM1</i>, and <i>VTI1A</i> were associated with teat number traits. (3) Conclusions: This study demonstrates the power of integrating additive and dominant effect modeling with population genetics approaches for the detection of genomic regions under selection. The findings provide novel insights into the genetic architecture of reproductive traits in pigs and have practical implications for understanding the inheritance of complex traits. |
| format | Article |
| id | doaj-art-0700d3d32a9e4eafaa4cbce1d5d2bb57 |
| institution | Kabale University |
| issn | 2306-7381 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
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| series | Veterinary Sciences |
| spelling | doaj-art-0700d3d32a9e4eafaa4cbce1d5d2bb572025-08-20T03:32:28ZengMDPI AGVeterinary Sciences2306-73812025-07-0112765710.3390/vetsci12070657Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep DetectionChangyi Chen0Yu He1Juan Ke2Xiaoran Zhang3Junwen Fei4Boxing Sun5Hao Sun6Chunyan Bai7College of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaCollege of Animal Science, Jilin University, Changchun 130062, ChinaThis study aimed to investigate population genetic differences related to reproductive traits between Duroc and Yorkshire (Dutch Large White) pigs using two approaches: linear mixed models that dissect additive and dominant effects, and selective sweep analysis. (1) Methods: Genome-wide single-nucleotide polymorphism (SNP) data of 3917 Duroc and 3217 Yorkshire pigs were analyzed. The first principal component (PC1) was used as a simulated phenotype to capture population-level variance. Additive and dominant genetic effects were partitioned and evaluated by using the combination of the linear mixed models (LMM) and ADDO’s algorithm (LMM + ADDO). In parallel, selective sweep signals were detected using fixation index (<i>F<sub>ST</sub></i>) and nucleotide diversity (θ<sub>π</sub>) analyses. A comparative assessment was then conducted between the LMM + ADDO and the selective sweep analysis results. Significant loci were annotated using quantitative trait loci (QTL) databases and the Ensembl genome browser. (2) Results: There are 39040 SNPs retained after quality control. Using the LMM + ADDO framework with PC1 as a simulated phenotype, a total of 632 significant SNPs and 184 candidate genes were identified. Notably, 587 SNPs and 171 genes were uniquely detected by the LMM + ADDO method and not among loci detected by the top 5% of <i>F<sub>ST</sub></i> and θ<sub>π</sub> values. Key candidate genes associated with litter size included <i>HSPG2</i>, <i>KAT6B</i>, <i>SAMD8</i>, and <i>LRMDA</i>, while <i>DLGAP1</i>, <i>MYOM1</i>, and <i>VTI1A</i> were associated with teat number traits. (3) Conclusions: This study demonstrates the power of integrating additive and dominant effect modeling with population genetics approaches for the detection of genomic regions under selection. The findings provide novel insights into the genetic architecture of reproductive traits in pigs and have practical implications for understanding the inheritance of complex traits.https://www.mdpi.com/2306-7381/12/7/657additive effectdominant effect<i>F<sub>ST</sub></i>population analysisreproduction traits |
| spellingShingle | Changyi Chen Yu He Juan Ke Xiaoran Zhang Junwen Fei Boxing Sun Hao Sun Chunyan Bai Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection Veterinary Sciences additive effect dominant effect <i>F<sub>ST</sub></i> population analysis reproduction traits |
| title | Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection |
| title_full | Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection |
| title_fullStr | Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection |
| title_full_unstemmed | Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection |
| title_short | Genomic Analysis of Reproductive Trait Divergence in Duroc and Yorkshire Pigs: A Comparison of Mixed Models and Selective Sweep Detection |
| title_sort | genomic analysis of reproductive trait divergence in duroc and yorkshire pigs a comparison of mixed models and selective sweep detection |
| topic | additive effect dominant effect <i>F<sub>ST</sub></i> population analysis reproduction traits |
| url | https://www.mdpi.com/2306-7381/12/7/657 |
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