Uncovering the genetic diversity of native bovine from South Angola

Abstract

cattle in Angola and how they relate to other breeds. In Africa we find Bos taurus and Bos indicus cattle and a hybrid also known as Sanga cattle. The most dominant cattle in Angola are Sanga which name varies according to the location and native language of the region, existing 11 different denominations, which conservation status in unknown. Sampling was performed between 2023 and 2024 in different provinces. Here we report the results of the first sequenced samples originated from Namibe (N = 4) and Cunene (N = 2), that resemble with Sanga cattle called Mucubal in Namibe and Kwanhama in Cunene. A total of 339Gb of data, was generated that was compared with public data of Angus, Hereford, N’Dama and Djankole breeds. After quality control, mapping (BWA), and SNP calling (samtools, bcftools) with a minimum 10× coverage and observation in at least 3 reads, ~17 million high-confidence SNPs were identified. Principal component analysis (PCA) was performed to assess the population structure, using PLINK. Admixture analysis from k = 2 to k = 6, was performed using Fastmixture to investigate ancestry; and Linkage disequilibrium (LD) decay was estimated using PopLDdecay to investigate diversity and selection. The PCA analysis, one with African breeds and 2 others composed by Angus and Hereford samples respectively. If in the PCA Angolan samples were clustered together with other African cattle, these present lower extent of LD. The analysis of admixture shows several haplotypes in the ancestry of all the samples. Nevertheless, Angolan breeds display higher degree of ancestry with other African cattle. In conclusion, these results suggest that cattle from these provinces share a common genetic background, which is like other African cattle breeds. Importantly these seem to harbour higher level of genetic diversity. Future perspectives include sequencing further samples in these provinces as well as from other provinces of the country.