Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponia nippon)

Abstract

The crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0–45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.

Effects of the Number of Crested Cushions in Runzhou White-Crested Ducks on Serum Biochemical Parameters

“…Schilling et al [47] found that at the final stage of hatching, embryos have immunity and can mount innate and adaptive immune responses to pathogens. Fu et al [48] found that the crested ibis (Nipponia nippon), an endangered bird worldwide, has a very high embryonic and nestling mortality rate, and comparing living and dead samples using high-throughput sequencing revealed that genes for glycan biosynthesis and metabolism (HYAL1 and HYAL4), as well as the immune system (JAM2), are associated with embryonic and nestling development. Serum immunoglobulins, especially IgA, IgG, and IgM produced by B cells, are important parameters reflecting the humoral immune status of animals and are associated with their important role in immune function and resistance to infection [49,50].…”

Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō

“…Knowledge of population structure, relatedness, and levels of inbreeding can inform breeding decisions and provide crucial insight into the future viability of endangered populations ( Allendorf et al 2010 ). It is therefore important to evaluate the performance of different marker-based measures of inbreeding and understand how they relate to fitness-associated traits such as offspring survival ( Keller 1998 ; Fu et al 2019 ).…”

“…In addition, levels of inbreeding were compared between the descendants of the mainland and Stewart Island founding populations to further investigate the impacts of previous bottlenecks ( Dussex et al 2018 ). Finally, we compared inbreeding estimates between deceased and surviving kākāpō chicks from a recent breeding season to understand potential genetic factors underlying premature mortality ( Fu et al 2019 ).…”