Unmasking genetic load: Genomic inbreeding drives growth depression in captive critically endangered Chinese Bahaba (Bahaba taipingensis)

The critically endangered Chinese Bahaba fish, once commercially extinct in the wild, has been saved through captive breeding efforts. However, these breeding programs have revealed concerning genomic issues. Within just two generations of closed breeding from a mere 18 wild ancestors, the fish displayed extreme growth depression, with body length and weight diverging by over three times.

To understand this genomic consequence, scientists analyzed whole-genome sequences from 348 F2 individuals alongside 19 wild counterparts. While overall genetic diversity remained intact, the closed breeding rapidly split the F2 population into eight separate genetic lineages. The research found a significant increase in genomic inbreeding, leading to the exposure of recessive deleterious mutations, which were strongly linked to the growth decline.

By integrating genome-wide association studies, gene-level burden tests, and regions of homozygosity, the team identified key genes involved in skeletal scaffolding and immune regulation, such as fam20b, c-fos, trpv5, and il23r. Additionally, they pinpointed the GH/IGF axis (with socs1a), immune/inflammatory pathways (il23r, nlrp7, cd163, il12rb2), and calcium ion transport pathway as crucial factors contributing to the growth issues.

These findings offer vital insights into the genomic consequences of captive breeding and provide crucial guidance for managing genetic diversity in conservation programs aiming to save endangered species.