The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

Abstract

EAT and AAI, along eigenvector 1, which explains ~15% of the total variation. AFT Muturu and N'Dama are close to EAT along the eigenvector 1. Most of the AFH cattle cluster together regardless of their breed memberships, leaving only Ankole, Mursi and Sheko outside the main cluster toward the AFT Muturu and N'Dama. The PCA results also show that Muturu and N'Dama, our representative of AFT population, are separated from the other cattle groups (eigenvector 2, ~2.5% of total variation). Sheko positions close to the AFH, as similarly reported in other studies 5,43 . Genetic clustering analysis using ADMIXTURE 44 corroborates the pattern found in PCA (Fig. 2b and Extended Data Fig. 2). Most of AFH show a similar proportion of taurine ancestry, around 25% on average. Only a few AFH breeds have elevated taurine ancestry: Ankole (53.37 ± 1.49%), Sheko (46.28 ± 2.03%) and Mursi (35.90 ± 2.16%). (Fig. 2b).Genetic distance and diversity. Pairwise F st were calculated to estimate the genetic distances between populations (n = 38) (Extended Data Fig. 3). Taurine (EUT, AST and AFT) show F st values of 0.1568 and 0.3287 on average against AFH and AAI, respectively.Across AFH, pairwise F st between breeds is close to zero, regardless of their phenotypic classification as African Zebu, Sanga or Zenga. Muturu and N'Dama show F st value of 0.1769, 0.1847 and 0.3734 against AFH, EAT and AAI, respectively.The genome-wide autosomal SNPs show reduced levels of heterozygosity in the taurine (0.0021 ± 0.0005/bp) compared to all other populations (0.0048 ± 0.0008/bp). Heterozygosity values of AFH are similarly higher across populations (0.0046 ± 0.0003/bp). AAI shows a higher level of heterozygosity compared to AFH (0.0052 ± 0.0014/bp) (Extended Data Fig. 4). The degree of inbreeding measured by runs of homozygosity (ROH) shows that taurine, including Muturu and N'Dama, have a higher level of inbreeding compared to the other and Ethiopia), the University of Khartoum (Sudan), and the National Biotechnology Development Agency (NABDA) (Nigeria). The following institutions and their personnel provided help for the sampling of the African cattle: ILRI Kapiti Ranch, Ministry of Animal Resources, Fisheries and Range (Sudan), Ol Pejeta Conservancy (Kenya), Institute of Biodiversity (Ethiopia), the Directors of Veterinary Services and the cattle keepers from Ethiopia, Kenya, Uganda and Sudan. ILRI livestock genomics program is supported by the

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

“…Genome-wide variations such as SNPs and small INDELs of cattle were identified in previous studies [ 8 , 9 ]. These small variations have been studied for understanding cattle evolution including population structure, selection, demographic history and introgression [ 7 , 10 , 11 ]. In case of structural variation, a large proportion in the genome is comprised of CNVs which have great effects on changing of gene structure, dosage and expression level [ 12 , 13 ].…”

Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers

“…Studies show that genetic intermixing is caused by rigorous transportation of domestic animals like goats, cattle, and sheep from place to place as a result of their valuable resource for economic trade or cultural exchange (Tarekegn et al, 2018). Notably, recent study has revealed the impact of African cattle pastoralism in admixture of cattle across the continent, and this admixture or intermixing has been well observed in the African humped cattle (Kim et al, 2020). It is generally known that most of the genetic variation in cattle elucidated by matrilineal genetic information is attributable to geographical differences (Hanotte et al, 2002), which can be sourced at the regional or continental levels (Dadi et al, 2009) rather than by their morphological disparities or differences in their origins (Álvarez et al, 2017).…”

Novel functional sequences uncovered through a bovine multi-assembly graph

“…Bovine DNA sequences are typically aligned to the Hereford-based reference genome to discover and genotype variable sites. Reference-guided read alignment and variant genotyping has revealed millions of polymorphic variants that segregate within and between taurine and indicine cattle breeds [6][7][8] . However, using the linear reference in this alignment approach is susceptible to reference allele bias, particularly for DNA samples that are greatly diverged from the reference 9,10 .…”