Signatures of selection in Cameroonian Gudali and Simgud cattle

Abstract Gudali, a West and Central African shorthorn zebu, is an important dual-purpose cattle breed adapted to tropical production systems. It has recently been used in crossbreeding programmes with Italian Simmental cattle to produce the Simgud hybrid, with the aim of combining the adaptive characteristics of Gudali with the higher productive performance of Simmental. However, the genomic consequences of this crossbreeding strategy, particularly with respect to adaptation and selection, remain poorly understood. In this study, we investigated genomic signatures of selection in Gudali and Simgud cattle to identify candidate regions and genes associated with environmental adaptation and production-related divergence. A total of 539 Gudali and 139 Simgud cattle genotyped using the GeneSeek GGP+ Bovine 100K array were subjected to two-step imputation to whole-genome sequence level. Selection signatures were identified using the integrated haplotype score (iHS), Tajima’s D, fixation index (F ST ) and cross-population extended haplotype homozygosity (XP-EHH). Strong iHS signals shared between Gudali and Simgud were detected in intervals enriched for olfactory receptor (OR) and bitter taste receptor (TAS2R) genes, particularly on BTA3, BTA5, BTA7 and BTA15. GO enrichment analysis further supported overrepresentation of pathways associated with G protein-coupled receptor signalling, sensory perception of taste and detection of bitter compounds. In contrast, overlapping XP-EHH and F ST signals identified a differentiated interval on BTA5 containing HMGA2 , MSRB3 , GRIP1 and IRAK3 , genes associated with growth, morphology, oxidative stress and immune regulation. Tajima’s D signals in Gudali co-localised within this broader interval, suggesting ongoing or recent selection affecting partially distinct aspects of haplotype structure and allele frequency change. Comparative analysis of selection signatures identified candidate genomic regions associated with adaptation and productivity in Gudali and Simgud cattle. Shared enrichment of sensory receptor genes suggests retention of adaptive mechanisms related to foraging and environmental perception following crossbreeding, while divergence signals on BTA5 highlight candidate genes potentially associated with morphological, stress-response and production-related differentiation between the two populations.