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

## TL;DR

This study uses whole-genome sequencing to analyze the genetic diversity and evolutionary traits of the Xupu goose, a Chinese breed at risk of decline.

## Contribution

The study provides a genomic foundation for conservation and breeding by identifying selection signatures and candidate genes linked to fatty liver and muscle traits.

## Key findings

- Xupu goose shows moderate genetic diversity but signs of historical inbreeding.
- Candidate genes related to lipid metabolism (ACSS2, ACSS3, PECR) and muscle development (CMYA5, MTPN, LEPR) were identified.
- Conservation efforts have prevented recent inbreeding despite lineage differentiation.

## Abstract

The Xupu goose is an economically valuable indigenous breed in China, celebrated for its large body size and exceptional fatty liver capacity. However, as an “at-risk” population, it requires urgent conservation efforts. In this study, we conducted whole-genome sequencing on 15 Xupu geese to evaluate their genetic diversity and uncover the genomic basis of their unique traits. We found that while the breed retains a moderate genetic reservoir, it carries a legacy of historical inbreeding driven by past population bottlenecks. Importantly, our results indicate that current conservation practices have successfully prevented severe recent inbreeding, despite the natural emergence of distinct family lineages. Furthermore, we identified key candidate genes strongly linked to lipid metabolism and muscle development. These findings provide crucial scientific guidance for optimizing future mating strategies and lay the genomic groundwork for the precision breeding of this vital waterfowl.

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 (HE = 0.298), it exhibits a distinct heterozygote deficit (HO = 0.217) and a moderate genomic inbreeding coefficient FROH = 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 (ACSS2, ACSS3, PECR), alongside muscle development (CMYA5, MTPN, LEPR). 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.