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Growth performance and carcass traits are economically vital in poultry breeding. In Wenchang chickens, reducing excessive abdominal fat represents a critical breeding objective. However, as a typical carcass trait, abdominal fat thickness has traditionally been measurable only post-slaughter, resulting in inefficient and costly selection processes that hinder genetic progress for these traits. To overcome this limitation, we developed an integrated approach combining non-invasive ultrasound phenotyping and multi-model genomic selection to evaluate growth and fat-related traits in Wenchang chickens.
We genotyped 3,737 chickens using the "Jingxin No.1" 55K SNP array and performed longitudinal measurement of abdominal fat thickness (AFT) via ultrasound imaging. A comprehensive evaluation of genomic prediction models revealed that WGBLUP (informed by wssGWAS), and GBLUP models based on LD-pruned whole-genome sequencing (WGS) data significantly outperformed standard GBLUP, with accuracy gains of 5.25% and 6.58%-15.30%, respectively. Among the machine learning algorithms tested, kernel ridge regression (KRR) and support vector regression (SVR) achieved the highest predictive improvement (3.00%-4.15%) while maintaining superior computational efficiency, whereas ensemble methods provide no consistent advantage.
Our work established ultrasound imaging as a scalable, non-invasive phenotyping platform for poultry breeding. Results demonstrated that integrating wssGWAS-derived biological priors with WGS data substantially improves genomic prediction accuracy for complex traits. This integration, enhanced by computationally efficient machine learning algorithms, provides a powerful and practical strategy to accelerate genetic gain.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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