Tan Lizhi, Cai Xinyu, Kong Yuan, Liu Zexuan, Wen Zilong, Bu Lina, Wang Yuzhan, Liu Xiaojun, Zhang Zhiwu, Han Jianlin, Wang Dandan, Zhao Yiqiang
State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
J Anim Sci Biotechnol. 2025 Aug 11;16(1):114. doi: 10.1186/s40104-025-01245-2.
Compared to many other vertebrates, chickens have a high reproductive efficiency in terms of egg production. The classic traits for evaluating egg-laying performance include age at first egg, egg number, clutch size, laying rate, etc. These egg-laying traits were not specifically designed to characterize egg production efficiency and stability. By considering the stage-specific variations in the egg production curve, this study aims to investigate the genetic mechanisms that directly influence the efficiency of egg production at each stage of the laying cycle.
Using whole-genome sequencing data, we perform comprehensive genome-wide association study for 39 traits that focus on egg production efficiency and stability in the Gushi chicken. We showed that the haplotype-based approach is more effective for genetic mapping and capturing polygenic architecture. By combining the signals of Singleton Density Score (SDS), which is a population-genetic statistic designed to detect recent selection by leveraging the distribution of singletons, and association analyses, multiple egg-laying traits related to egg production efficiency were found to have experienced polygenic selection. Consistently, functional analysis of associated genes demonstrates that egg production efficiency benefits from multiple physiological functions. Furthermore, our results identified the CNNM2 gene, known for its role in magnesium homeostasis, plays a dual role in egg production variance, promoting variability during the up-stage while reducing it during the sustained-stage to optimize egg production efficiency.
Collectively, our multiple genome analyses reveal a complex genetic mechanism underlying more efficient and stable egg production, and establish chicken genetics as a model for studying reproductive efficiency across species.
与许多其他脊椎动物相比，鸡在产蛋方面具有较高的繁殖效率。评估产蛋性能的经典性状包括开产日龄、产蛋数、窝蛋数、产蛋率等。这些产蛋性状并非专门设计用于表征产蛋效率和稳定性。通过考虑产蛋曲线的阶段特异性变化，本研究旨在探究直接影响产蛋周期各阶段产蛋效率的遗传机制。
利用全基因组测序数据，我们针对固始鸡的39个聚焦于产蛋效率和稳定性的性状进行了全面的全基因组关联研究。我们表明基于单倍型的方法在基因定位和捕捉多基因结构方面更有效。通过结合单例密度评分（SDS）的信号（SDS是一种群体遗传统计量，旨在通过利用单例的分布来检测近期选择）和关联分析，发现多个与产蛋效率相关的产蛋性状经历了多基因选择。一致地，对相关基因的功能分析表明产蛋效率受益于多种生理功能。此外，我们的结果确定了以其在镁稳态中的作用而闻名的CNNM2基因在产蛋变异中起双重作用，在上升阶段促进变异性，而在持续阶段降低变异性以优化产蛋效率。
总体而言，我们的多重基因组分析揭示了更高效和稳定产蛋背后的复杂遗传机制，并将鸡遗传学确立为研究跨物种繁殖效率的模型。
