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

Abstract

<b>Background</b><br/> Humpless <i>Bos taurus</i> 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 <i>Bos taurus</i> and <i>Bos indicus</i>. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds.<br/> <b>Methods</b><br/> Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European <i>Bos taurus</i>, 4 <i>Bos indicus</i>, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s <i>F</i> statistic. The linkage disequilibrium and effective population size (<i>Ne</i>) were estimated for the pure cattle populations.<br/> <b>Results</b><br/> The first two principal components differentiated <i>Bos indicus</i> from European <i>Bos taurus</i>, and African <i>Bos taurus</i> from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African <i>Bos taurus</i> or admixtures of African <i>Bos taurus</i> and <i>Bos indicus</i>. The African zebu breeds had highest proportions of <i>Bos indicus</i> ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African <i>Bos taurus</i>, ranged from 42 to 70% or 23 to 61% <i>Bos indicus</i> ancestry. The African <i>Bos taurus</i> populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on <i>r</i>² and <i>r</i>²_adj showed a decline in <i>Ne</i> 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.<br/> <b>Conclusion</b><br/> African indigenous cattle breeds have a large genetic diversity and are either pure African <i>Bos taurus</i> or admixtures of African <i>Bos taurus</i> and <i>Bos indicus</i>. 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.