Genomic Evaluation of the Genetic Structure and Analysis of Selective Evolutionary Signatures of Xupu Goose

As an elite indigenous poultry breed under national protection in China, the Xupu goose is renowned for its large body size, superior fatty liver production, premium meat quality, and high tolerance to roughage. To elucidate its genomic architecture, genetic diversity, and evolutionary selection signatures, we conducted whole-genome resequencing on 15 purposively selected, unrelated male Xupu geese. An average of 6.79 Gb of high-quality sequence data was generated per individual, yielding approximately 4.27 million single-nucleotide polymorphisms (SNPs) with a transition/transversion (Ti/Tv) ratio of 2.49. Population genomic analyses revealed that while the population retains a moderate genetic reservoir (<i>H_E</i> = 0.298), it exhibits a distinct heterozygote deficit (<i>H_O</i> = 0.217) and a moderate genomic inbreeding coefficient <i>F_ROH</i> = 0.204). This structural pattern underscores the genetic impact of historical ex situ closed-flock conservation and the consequent formation of cryptic family lineages. Furthermore, genome-wide integrated haplotype score (iHS) scans detected distinct regions under recent positive selection. Functional annotation of these regions highlighted candidate genes tightly associated with the breed's hallmark traits, specifically lipid metabolism and hepatic fat deposition (<i>ACSS2</i>, <i>ACSS3</i>, <i>PECR</i>), alongside muscle development (<i>CMYA5</i>, <i>MTPN</i>, <i>LEPR</i>). Conclusively, this study delineates a comprehensive genomic landscape of the Xupu goose, providing a robust foundational resource for future germplasm conservation, molecular marker development, and precision breeding programs.