The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

Abstract

Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

“…Purebred reference breeds were five African Bos taurus samples (N’Dama, N’Dama1, Lagune, Baoule, and Somba), a pooled Indian Bos indicus sample (N = 105), and six European Bos taurus dairy breeds (Guernsey, Holstein, Jersey, Ayrshire, Friesian, and Montbeliarde, N = 125) as described in detail by Gebrehiwot et al [ 2 ], with the origin of samples in Table 1 . The pooled Bos indicus sample included 12 Bos indicus breeds from India, selected from 525 indigenous samples such that within-breed relationships were minimal [ 31 ].…”

“…For the 713 k dataset ( K = 7), the ancestral populations were a pooled African Bos taurus population (N = 36) comprising both N’Dama samples and the Baoule, the pooled Bos indicus population (N = 105), and the European Bos taurus Ayshire, Guernsey, Holstein, Jersey, N = 20, each, and Friesian (N = 25). The reference breeds were chosen based on known crossbreeding history in the African countries where samples were collected, and based on previous studies, which had checked breed purity and suitability for analysis in African populations [ 2 , 15 , 37 ]. Pooling of reference breeds was only performed when little genetic variation was found between breeds according to Gebrehiwot et al [ 2 ], who used the same data.…”

“…The reference breeds were chosen based on known crossbreeding history in the African countries where samples were collected, and based on previous studies, which had checked breed purity and suitability for analysis in African populations [ 2 , 15 , 37 ]. Pooling of reference breeds was only performed when little genetic variation was found between breeds according to Gebrehiwot et al [ 2 ], who used the same data.…”

“…Africa has large populations of livestock with many different indigenous cattle populations [ 1 ]. In a recent synthesis of public domain and new genotype data, Gebrehiwot et al [ 2 ] found that the sampled African indigenous cattle populations, with the exception of some pure African Bos taurus breeds found in West Africa, are admixtures between Bos indicus and African Bos taurus , and that West and Southern African populations showed a lower Bos indicus content than East African populations. Several African countries have introduced exotic cattle breeds over the last century with the objective of increasing the productivity of indigenous breeds [ 1 ].…”

“…Molecular genetic markers, such as single nucleotide polymorphisms (SNPs), can be used for parentage assignment and pedigree reconstruction [ 14 , 15 ], or to obtain estimates of breed composition in crossbred populations, using genotypes from reference purebred populations that may have contributed to the crossbred population. Studies of breed compositions in cattle have been mostly based on microsatellites [ 16 , 17 ] or medium- to high-density SNP assays [ 2 , 18 , 19 ]. However, the major limitation to a wider use of molecular markers in developing countries is the cost of genotyping, and the expected value of the information gained by genotyping must exceed the cost of obtaining the genotypes [ 20 ].…”