Whole Genome Sequencing Informs SNP-Based Breeding Strategies to Safeguard Genetic Diversity in Captive African Lions

Wanzhao Chen ^1,2 Ronghe Xing ³ Panpan Xia ^1,2 Yujie Yang ^1,2 Chao Ma ^3* Lining Xia ^1,2*

• ¹ College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, Xinjiang Uyghur Region, China
• ² Xinjiang Key Laboratory of New Drug Research and Development for Herbivores, Urumqi, China
• ³ Zoo Urumqi, Urumqi, China

African lions (Panthera leo) have experienced significant population declines, with captive breeding programs critical for their conservation. However, such programs often lack genetic data, increasing risks of inbreeding and reduced genetic diversity. This study employed next-generation sequencing (NGS) to analyze genome-wide genetic markers in 10 captive African lions at Xinjiang Tianshan Wildlife Park. We identified 5,051,795 high-confidence SNPs, assessed population structure, and calculated kinship coefficients and inbreeding coefficients. Results revealed distinct genetic subgroups and elevated kin-ship coefficient in six lion pairs, with one individual showing signs of inbreeding. 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. 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.