Genomic inbreeding and runs of homozygosity analyses identify shared genomic regions associated with adaptation and production traits in Gudali and Simgud crossbred cattle from Cameroon

Background: Domesticated animal breeds frequently possess large homozygous (or nearly homozygous) regions across their genomes. These homozygous stretches - known as runs of homozygosity (ROH) - can be caused by inbreeding as well as be signatures of positive selection. They moreover provide a highly accurate estimate of inbreeding and inbreeding depression. We analysed ROH in Cameroon’s Gudali and Simgud cattle and identified genomic regions with high ROH frequencies (so-called ROH islands). Further, we investigated their association with body traits (Body length, height at wither, sacrum height and ear length), based on a two-step imputation to whole genome sequence data. Results: We detected a total of 45,312 and 6,646 homozygous segments in local Gudali and crossbred Simgud cattle respectively. The average number of ROH per individual was 83.24 in Gudali and 45.75 in Simgud. Overlapping ROH were evident across the genomes, notably, we detected 133 and 19 ROH islands exceeding 20% frequency within the population. These regions harbour 128 and 20 genes in Gudali and Simgud, respectively. In Gudali, the regions identified are mostly on BTA5 (17.6%) within 46.9-112.7 Mbp, on BTA7 within 49.7-61.1 Mbp (20.4%), and on BTA12 (23.2%) between 26.6-38.5 Mbp. For the Simgud population, 47% of the ROH islands were located on BTA7 between 10.28-51.15 Mbp. The shared region between Gudali and Simgud on BTA7 overlaps with quantitative trait loci reported to be associated with key cattle traits such as heat tolerance (DNAJC18, SLC23A1, RXFP2), immunity (SIL1, TMEM173), growth, reproduction, etc. As expected, genomic inbreeding estimates from ROH (FROH) were higher in Gudali (2.97%) than in Simgud (1.6%). Recent inbreeding, as reflected by medium and long ROH, was negatively associated with body traits, indicating inbreeding depression. Conclusions: Our study investigated the patterns of ROH and their potential associations with production traits in beef cattle. Our findings offer important insights into these patterns in Gudali and Simgud, their association with production and survival traits, and the impact of inbreeding in these populations. These insights contribute to the sustainable management of genetic resources in Cameroon’s indigenous Gudali and provide a valuable baseline for the design of effective breeding programs.