Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs
(1) Background: Litter size traits are critical for pig breeding efficiency but pose challenges due to low heritability and sex-limited influences. This study aimed to elucidate the genetic architecture and identify candidate genes for these traits in Large White pigs using genomic selection (GS) an...
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2025-06-01
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| author | Yifeng Hong Xiaoyan He Dan Wu Jian Ye Yuxing Zhang Zhenfang Wu Cheng Tan |
| author_facet | Yifeng Hong Xiaoyan He Dan Wu Jian Ye Yuxing Zhang Zhenfang Wu Cheng Tan |
| author_sort | Yifeng Hong |
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| description | (1) Background: Litter size traits are critical for pig breeding efficiency but pose challenges due to low heritability and sex-limited influences. This study aimed to elucidate the genetic architecture and identify candidate genes for these traits in Large White pigs using genomic selection (GS) and genome-wide association analyses (GWAS). (2) Methods: This study utilized phenotypic data from nine litter size traits in Large White sows. Genotyping-by-sequencing (GBS) was performed to obtain genotype data, retaining 153,782 high-quality SNPs after quality control. Genetic evaluation was conducted using single-step genomic best linear unbiased prediction (ssGBLUP), with genetic parameters (heritability and genetic correlations) estimated via an animal model (repeatability model). To assess prediction accuracy, 10-fold cross-validation was employed to compare traditional BLUP with ssGBLUP. Furthermore, a single-step genome-wide association study (ssGWAS) integrated genomic information and pedigree-based relationship matrices to screen for significant SNPs associated with litter size traits across the genome. Functional analysis of key candidate genes was subsequently conducted based on ssGWAS results. (3) Results: Heritabilities for litter traits ranged from 0.01 to 0.06. ssGBLUP improved genomic prediction accuracy by 6.38–13.33% over BLUP. Six genomic windows explaining 1.07–1.77% of genetic variance were identified via ssGWAS, highlighting <i>GPR12</i> on SSC11 as a key candidate gene linked to oocyte development. (4) Conclusions: This study demonstrates the efficacy of ssGBLUP for low-heritability traits and identifies GPR12 as a pivotal gene for litter size. Prioritizing NHB and LBWT in breeding programs could enhance genetic gains while mitigating adverse effects on piglet health. These findings advance genomic strategies for improving reproductive efficiency in swine. |
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| institution | Kabale University |
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| language | English |
| publishDate | 2025-06-01 |
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| series | Animals |
| spelling | doaj-art-6ea975c7198b455eb07c8c2d54d357ed2025-08-20T03:30:29ZengMDPI AGAnimals2076-26152025-06-011512172410.3390/ani15121724Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White PigsYifeng Hong0Xiaoyan He1Dan Wu2Jian Ye3Yuxing Zhang4Zhenfang Wu5Cheng Tan6College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, WENS Foodstuff Group Co., Ltd., Yunfu 527400, ChinaNational Engineering Research Center for Breeding Swine Industry, WENS Foodstuff Group Co., Ltd., Yunfu 527400, ChinaNational Engineering Research Center for Breeding Swine Industry, WENS Foodstuff Group Co., Ltd., Yunfu 527400, ChinaNational Engineering Research Center for Breeding Swine Industry, WENS Foodstuff Group Co., Ltd., Yunfu 527400, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510640, China(1) Background: Litter size traits are critical for pig breeding efficiency but pose challenges due to low heritability and sex-limited influences. This study aimed to elucidate the genetic architecture and identify candidate genes for these traits in Large White pigs using genomic selection (GS) and genome-wide association analyses (GWAS). (2) Methods: This study utilized phenotypic data from nine litter size traits in Large White sows. Genotyping-by-sequencing (GBS) was performed to obtain genotype data, retaining 153,782 high-quality SNPs after quality control. Genetic evaluation was conducted using single-step genomic best linear unbiased prediction (ssGBLUP), with genetic parameters (heritability and genetic correlations) estimated via an animal model (repeatability model). To assess prediction accuracy, 10-fold cross-validation was employed to compare traditional BLUP with ssGBLUP. Furthermore, a single-step genome-wide association study (ssGWAS) integrated genomic information and pedigree-based relationship matrices to screen for significant SNPs associated with litter size traits across the genome. Functional analysis of key candidate genes was subsequently conducted based on ssGWAS results. (3) Results: Heritabilities for litter traits ranged from 0.01 to 0.06. ssGBLUP improved genomic prediction accuracy by 6.38–13.33% over BLUP. Six genomic windows explaining 1.07–1.77% of genetic variance were identified via ssGWAS, highlighting <i>GPR12</i> on SSC11 as a key candidate gene linked to oocyte development. (4) Conclusions: This study demonstrates the efficacy of ssGBLUP for low-heritability traits and identifies GPR12 as a pivotal gene for litter size. Prioritizing NHB and LBWT in breeding programs could enhance genetic gains while mitigating adverse effects on piglet health. These findings advance genomic strategies for improving reproductive efficiency in swine.https://www.mdpi.com/2076-2615/15/12/1724litter size traitsLarge Whitegenetic parametersGSssGWAS |
| spellingShingle | Yifeng Hong Xiaoyan He Dan Wu Jian Ye Yuxing Zhang Zhenfang Wu Cheng Tan Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs Animals litter size traits Large White genetic parameters GS ssGWAS |
| title | Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs |
| title_full | Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs |
| title_fullStr | Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs |
| title_full_unstemmed | Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs |
| title_short | Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs |
| title_sort | genome selection and genome wide association analyses for litter size traits in large white pigs |
| topic | litter size traits Large White genetic parameters GS ssGWAS |
| url | https://www.mdpi.com/2076-2615/15/12/1724 |
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