Identification and Characterization of Copy Number Variations Regions in West African Taurine Cattle

SIMPLE SUMMARY: Native West African (WA) taurine (Bos taurus) cattle are trypanotolerant; i.e., they have the ability to suppress the establishment of trypanosomes. Cattle trypanotolerance is a heritable trait—partially additive in nature—that can share mechanisms with tick resistance. Copy Number Variations (CNVs) are genomic alterations affecting gene structure, gene expression, and performance. However, the relationship between CNV regions and trypanotolerance and tick resistance in WA taurine cattle has not been approached thusfar. Here, we identify and characterize CNV regions in a sample of WA taurine cattle using WA zebu as an outgroup. The CNV regions identified spanned genes that are mainly involved in innate immunity. However, their relationship with genomic regions, previously reported to be associated with trypanotolerance and tick resistance, was not clear. Therefore, CNV alterations may not be the main genomic features underlying such traits. ABSTRACT: A total of 106 West African taurine cattle belonging to the Lagunaire breed of Benin (33), the N’Dama population of Burkina Faso (48), and N’Dama cattle sampled in Congo (25) were analyzed for Copy Number Variations (CNVs) using the BovineHDBeadChip of Illumina and two different CNV calling programs: PennCNV and QuantiSNP. Furthermore, 89 West African zebu samples (Bororo cattle of Mali and Zebu Peul sampled in Benin and Burkina Faso) were used as an outgroup to ensure that analyses reflect the taurine cattle genomic background. Analyses identified 307 taurine-specific CNV regions (CNVRs), covering about 56 Mb on all bovine autosomes. Gene annotation enrichment analysis identified a total of 840 candidate genes on 168 taurine-specific CNVRs. Three different statistically significant functional term annotation clusters (from ACt1 to ACt3) involved in the immune function were identified: ACt1 includes genes encoding lipocalins, proteins involved in the modulation of immune response and allergy; ACt2 includes genes encoding coding B-box-type zinc finger proteins and butyrophilins, involved in innate immune processes; and Act3 includes genes encoding lectin receptors, involved in the inflammatory responses to pathogens and B- and T-cell differentiation. The overlap between taurine-specific CNVRs and QTL regions associated with trypanotolerant response and tick-resistance was relatively low, suggesting that the mechanisms underlying such traits may not be determined by CNV alterations. However, four taurine-specific CNVRs overlapped with QTL regions associated with both traits on BTA23, therefore suggesting that CNV alterations in major histocompatibility complex (MHC) genes can partially explain the existence of genetic mechanisms shared between trypanotolerance and tick resistance in cattle. This research contributes to the understanding of the genomic features of West African taurine cattle.