Ren Pengwei, Jing Yadi, Yang Liu, Khan Muhammad Zahoor, Zhang Meixia, Liu Xiang, Ma Weiqing, Ding Zhaoyan, Li Xiangfan, Qi Chao, Liu Zhansheng, Zhang Shuer, Zhu Zhiming, Zheng Nenzhu, Zhu Mingxia
College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Shandong Animal Husbandry Station, Jinan 250010, China.
Poult Sci. 2025 Jun 6;104(9):105404. doi: 10.1016/j.psj.2025.105404.
Artificial selection can enhance desirable traits but may also lead to excessive homozygosity, negatively affecting genetic diversity. Monitoring inbreeding levels in poultry is crucial for maintaining the sustainable development of economic traits. This study investigates the genetic diversity of local domestic duck breeds including Weishan Partridge (WS), Matahu (MT), and Wendeng Black (WD) in Shandong province, with a focus on functional genes associated with economically important traits. We assessed the number and distribution of runs of homozygosity (ROH) and calculated the inbreeding coefficient (F) in three local duck breeds. The Weishan Partridge duck exhibited high genetic diversity, while the WD showed a high inbreeding level, likely due to intensive anthropogenic selection for meat production. Meanwhile, we compared the shared and unique genetic traits of the three breeds at the genomic level based on ROH Islands to obtain significant pathways and candidate genes associated with economically important traits, such as growth and development, lipid metabolism, and immune response. Comparative analysis of genomic selection signatures across breeds revealed distinct patterns of genetic differentiation: the MT breed exhibited selective pressures primarily targeting genes associated with metabolic regulation pathways, the WD breed showed evidence of selection for loci governing muscle development and myogenesis, while the WS breed demonstrated enrichment of selection signals in genomic regions linked to immune system function and anti-inflammatory response mechanisms. Altogether, this study provides valuable insights into the genetic diversity and differentiation of local duck breeds including MT, WS and WD in Shandong Province. The findings are crucial for developing more effective breeding strategies, which will aid in the conservation and optimal utilization of these indigenous breeds.
人工选择可以增强理想性状，但也可能导致过度纯合，对遗传多样性产生负面影响。监测家禽的近亲繁殖水平对于维持经济性状的可持续发展至关重要。本研究调查了山东省当地家鸭品种微山麻鸭（WS）、麻鸭（MT）和文登黑鸭（WD）的遗传多样性，重点关注与经济重要性状相关的功能基因。我们评估了纯合子连续片段（ROH）的数量和分布，并计算了三个当地鸭品种的近亲繁殖系数（F）。微山麻鸭表现出较高的遗传多样性，而文登黑鸭显示出较高的近亲繁殖水平，这可能是由于对肉类生产的强烈人为选择。同时，我们基于ROH岛在基因组水平上比较了这三个品种的共享和独特遗传特征，以获得与经济重要性状相关的显著途径和候选基因，如生长发育、脂质代谢和免疫反应。跨品种基因组选择特征的比较分析揭示了不同的遗传分化模式：麻鸭品种表现出主要针对与代谢调节途径相关基因的选择压力，文登黑鸭品种显示出对控制肌肉发育和成肌的基因座的选择证据，而微山麻鸭品种在与免疫系统功能和抗炎反应机制相关的基因组区域表现出选择信号的富集。总之，本研究为山东省包括麻鸭、微山麻鸭和文登黑鸭在内的当地鸭品种的遗传多样性和分化提供了有价值的见解。这些发现对于制定更有效的育种策略至关重要，这将有助于保护和优化利用这些本土品种。
