Abstract
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(ROH)) 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.