Genomic dissection of genetic correlation between stillbirth and gestation length in German Holstein cows

Stillbirth (SB) in dairy cattle is both an animal welfare and an economic issue. The reasons for SB and how traits such as gestation length (GL) influence it are part of ongoing research. Utilizing imputed high-density (HD) and whole-genome sequencing (WGS) genotypes from 34,497 German Holstein cows, this study aimed to identify local genetic correlation in trait-associated genomic regions for SB and GL. For this, regional heritability mapping (RHM) was conducted, alongside analyses of global and local genetic correlation. In the downstream analysis, regions showing significant local genetic correlations within significant RHM windows were searched for candidate genes. Regional heritability mapping of direct effects on GL resulted in 2 significant regions on BTA18 and 19 in first (GL_d1) and second parity (GL_d2). One region on BTA9 was significant for the maternal effect on SB. Significant global genetic correlations were confined to a low negative correlation of -0.17 (SE = 0.04) between SB direct (SBd) and GL_d1. Their local genetic correlations were negative on BTA18 and positive on BTA19, with ZNF415 and SLC43A2 as candidate genes. The Gene Ontology enrichment analysis for SBd and GL_d1 identified biologically relevant pathways, with the largest cluster related to the transport of organic acids and AA. Overall, the study achieved insights into the complex genetic architecture of SB and its interaction with GL. Candidate genes of still unknown function should be considered by future research to further strengthen the understanding of trait interactions.