Genome wide association analysis revealed novel candidate genes for body measurement traits in indigenous Gudali and crossbred Simgud in Cameroon

Background : The genetics of Central African cattle have not been well-explored in terms of their potential for improved productivity. We therefore performed a genome wide association analysis (GWAS) on a total of 856 animals genotyped with the GGP Bovine 100K array, to identify genes or genomic regions of importance in body measurements in a local zebu (Gudali) and its crossbreed with the European Simmental (Simgud), using mixed linear model (MLM). Results : SNP-based heritability of the four body traits under study varied between 0.23 ± 0.12 for the height at wither (HAW) to 0.44 ± 0.11 for the sacrum height (SH). The genetic correlation ranged from 0.19 ± 0.14 between HAW and ear length (EL), to 0.81 ± 0.06 between HAW and SH. For the phenotypic correlation, the ranges were 0.58 ± 0.00 between body length (BL) and EL to 0.90 ± 0.06 between HAW and BL. The maximum LD was 0.465 for Gudali and decreased by half (0.23) at a distance of 50,708 bp, while for the Simgud population the maximum LD was 0.47 and decreased to half (0.23) at 99,201 bp. Interestingly, we observed long ranges of LD throughout the Gudali and Simgud genome up to more than 1 mbp distant. These features are of great potential interest in association analysis and genetic improvement initiatives. We identified 59 SNPs associated to body traits. These SNPs were mapped within or near some 189 genes throughout the genome, with the CDCA2, EBF2, ADGRD1, NDUFAF1, DPPA4 and DPPA2 genes showing a pleiotropic effect since they were found associated with 2 or more traits. Conclusions : This study identified a number of novel genes/loci associated with pathways influencing growth and body traits, disease resistance and immunity, reproduction and milk production. Overall, the identified genes could be considered as candidate genes in any attempt to improve growth, disease resistance and production in tropical cattle managed under extensive conditions. These genes or genomic regions should be targeted for any future cattle breeding in Cameroon.