Whole genome sequencing informs SNP-based breeding strategies to safeguard genetic diversity in captive African lions.

Abstract

INTRODUCTION: African lions () face severe population declines, making captive breeding programs essential for conservation. However, genetic data scarcity in such programs elevates inbreeding risks and threatens genetic diversity. METHODS: Using next-generation sequencing (NGS), we analyzed genome-wide genetic markers from 10 captive African lions at Xinjiang Tianshan Wildlife Park. We identified high-confidence SNPs, evaluated population structure, and calculated kinship/inbreeding coefficients alongside identity by descent (IBD) and identity by state (IBS) analyses. RESULTS: We identified 5,051,795 high-confidence SNPs. The population contained distinct genetic subgroups. Six lion pairs exhibited elevated kinship coefficients, with one individual showing inbreeding signs. We developed a science-driven breeding program based on population genetic structure, identity by descent (IBD) analysis, and Identity by State (IBS) analysis. This program prioritizes pairings with low kinship while maintaining a balanced ancestral lineage. DISCUSSION: This study underscores the importance of genomic tools in managing captive populations, offering actionable insights to mitigate inbreeding risks and improve long-term viability. This approach offers a model for optimizing breeding strategies in other endangered species conservation efforts.