Integrating Non-Contact 3D Point Cloud Phenotyping and Multi-Locus Genome-Wide Association Studies to Uncover the Genetic Architecture of Body Size in Pigs
4 affiliations
- 1State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- 2National and Regional Livestock Genebank, Guangdong Gene Bank of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
- 3Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- 4School of Life Science, Anhui Medical University, Hefei 230032, China
Abstract
Non-contact 3D point cloud phenotyping reduces the time and animal disturbance of manual livestock measurement, yet the genetic architecture of automatically derived body conformation traits remains underexplored. Here, we extracted body length (BL) and body height (BH) from 3D point cloud data of 510 Wens Black pigs and mapped their genetic basis. Pearson correlations between automated and manual measurements were 0.79 for BL and 0.74 for BH, with mean absolute percentage errors of 2.30% and 3.55%, respectively. The corresponding genetic correlation estimates were 1.00 ± 0.13 for BL and 0.92 ± 0.14 for BH. Combined single- and multi-locus genome-wide association study (GWAS) identified 43 candidate quantitative trait nucleotides (QTNs), including the BL-associated SNP detected at the suggestive significance level by the single-locus model and 42 additional loci at LOD ≥ 3. Among these, eight BL-associated and six BH-associated QTNs were detected by at least two multi-locus methods, including two BL-associated QTNs detected by all four methods. The maximum estimated proportions of phenotypic variance explained by individual QTNs were 6.00% for BL and 4.71% for BH. Functional enrichment implicated skeletal and cellular development pathways, prioritizing ACKR3, PLCB1 and COL11A1 for BL, and BDNF, PLEKHM1, ANKRD11 and RHOBTB2 for BH, as positional candidate genes. These findings demonstrate that 3D point cloud phenotyping captures heritable body-size variation in pigs and provide loci and candidate genes for validation and future genomic breeding.
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BibTeX
@article{qiu2026integrating,
title = {{Integrating Non-Contact 3D Point Cloud Phenotyping and Multi-Locus Genome-Wide Association Studies to Uncover the Genetic Architecture of Body Size in Pigs}},
author = {Yibin Qiu and Yingjun Zou and Ziliang Feng and Qingjun Ren and Fucai Ma and Shiyuan Wang and Meng Lin and Jia-Jin Wu and Enqin Zheng and Jie Yang and Langqing Liu and Hui Zhang},
journal = {Biomolecules},
year = {2026},
month = oct,
doi = {10.3390/biom16111540},
url = {https://www.mdpi.com/2218-273X/16/11/1540},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrating Non-Contact 3D Point Cloud Phenotyping and Multi-Locus Genome-Wide Association Studies to Uncover the Genetic Architecture of Body Size in Pigs
AU - Yibin Qiu
AU - Yingjun Zou
AU - Ziliang Feng
AU - Qingjun Ren
AU - Fucai Ma
AU - Shiyuan Wang
AU - Meng Lin
AU - Jia-Jin Wu
AU - Enqin Zheng
AU - Jie Yang
AU - Langqing Liu
AU - Hui Zhang
PY - 2026
DA - 2026/10/22
JO - Biomolecules
DO - 10.3390/biom16111540
UR - https://www.mdpi.com/2218-273X/16/11/1540
AB - Non-contact 3D point cloud phenotyping reduces the time and animal disturbance of manual livestock measurement, yet the genetic architecture of automatically derived body conformation traits remains underexplored. Here, we extracted body length (BL) and body height (BH) from 3D point cloud data of 510 Wens Black pigs and mapped their genetic basis. Pearson correlations between automated and manual measurements were 0.79 for BL and 0.74 for BH, with mean absolute percentage errors of 2.30% and 3.55%, respectively. The corresponding genetic correlation estimates were 1.00 ± 0.13 for BL and 0.92 ± 0.14 for BH. Combined single- and multi-locus genome-wide association study (GWAS) identified 43 candidate quantitative trait nucleotides (QTNs), including the BL-associated SNP detected at the suggestive significance level by the single-locus model and 42 additional loci at LOD ≥ 3. Among these, eight BL-associated and six BH-associated QTNs were detected by at least two multi-locus methods, including two BL-associated QTNs detected by all four methods. The maximum estimated proportions of phenotypic variance explained by individual QTNs were 6.00% for BL and 4.71% for BH. Functional enrichment implicated skeletal and cellular development pathways, prioritizing ACKR3, PLCB1 and COL11A1 for BL, and BDNF, PLEKHM1, ANKRD11 and RHOBTB2 for BH, as positional candidate genes. These findings demonstrate that 3D point cloud phenotyping captures heritable body-size variation in pigs and provide loci and candidate genes for validation and future genomic breeding.
SN - 2218-273X
ER -