Genomic insights and the conservation potential of captive breeding: The case of Chinese alligator

Despite 40 years of conservation of the critically endangered Chinese alligator (<i>Alligator sinensis</i>), the genomic underpinnings of its status remained uncharted. Genome sequencing data of 244 individuals uncovered relatively low overall genomic diversity/heterozygosity and long runs of homozygosity, with captive populations exhibiting higher heterozygosity and smaller inbreeding coefficients compared to wild individuals. The decreased level of inbreeding in the captive population demonstrates the contribution of the large captive breeding population. The estimated recent effective population size was around a few dozen. To combat challenges of inbreeding depression and reduced adaptability, we used genome-wide SNP-based kinship analysis on captive populations to enable a genome-informed breeding program that minimizes inbreeding. Long-term field monitoring revealed that the Chinese government greatly advanced the conservation of <i>A. sinensis</i> through conservation measures and reintroduction programs. Our research enriches the understanding of the Chinese alligator's genetic landscape, offering invaluable genomic resources for breeding and conservation strategies.