Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya

Abstract

The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (⩾12.5%), moderate (1.56%<X<12.5%) and non-introgressed (⩽1.56%) according to the European taurine genetic proportion. The non-European taurine introgressed animals (n=425) show an unfluctuating zebu and taurine ancestry of 0.84±0.009 s.d. and 0.16±0.009 s.d., respectively, with significant differences in African taurine (AT) and Asian zebu backgrounds across chromosomes (P<0.0001). In contrast, no such differences are observed for the European taurine ancestry (P=0.1357). Excluding European introgressed animals, low and nonsignificant genetic differentiation and isolation by distance are observed among sub-locations (Fst=0.0033, P=0.09; r=0.155, P=0.07). Following a short population expansion, a major reduction in effective population size (Ne) is observed from approximately 240 years ago to present time. Our results support ancient zebu × AT admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression.

Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide

“…The principal component assessment agreed with previous findings, which partitioned bovine breeds into three distinct groups representing European taurines, African taurines and indicines [14–18, 23, 24] (Fig. 1).…”

“…Cluster analysis () and the principal component analysis were mutually supportive and highlighted the presence of three genetic backgrounds for the populations studied. The classification of the bovine populations into a triangle-like structure is well-established [14–18, 23, 24]. As already mentioned, the Nguni and Afrikaner cattle were observed on the gradient between the indicines and African taurines, but more towards the African taurines, which indicates that the genomes of these breeds include more African taurine genetic background than indicine genetic background.…”

“…Based on analyses with microsatellite markers, Hanotte et al [11] and Freeman et al [13] predicted that Sanga cattle resulted from the crossbreeding of African taurine and zebu cattle around 700 AD, which was confirmed by studies based on single nucleotide polymorphisms (SNPs) [14–18]. However, in spite of these studies, the genetic composition of South African Sanga cattle remains uncertain [19].…”

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

“…We detected significant differences in levels of indicine admixture among chromosomes in Ethiopian cattle. This aligns with a recent study by Mbole-Kariuki et al (2014) who detected significant differences in African taurine and Asian zebu backgrounds among chromosomes, but little variation among animals in East African shorthorn zebu populations that contained the ancient zebu and African taurine admixture. The relatively low level of variability in indicine ancestry among the Ethiopian populations supports the ancient zebu introgression into African cattle breeds.…”

Review: Sustainability of crossbreeding in developing countries; definitely not like crossing a meadow…

“…In Kenya, Murray et al (2013) performed genomic analysis on a sample of 500 East African Shorthorn Zebu and reported average introgression levels around 2%, with 20% of calves showing levels of introgression consistent with crossing with European breeds ⩽5 generations ago. A study of the same data revealed a greater rate of European introgression in closer proximity to animal markets (Mbole-Kariuki et al, 2014). A study of African village chickens from multiple locations (Leroy et al, 2012) reported evidence of introgression in some of the countries, including Morocco and Cameroon, whereas finding negligible gene flow in some other countries such as Benin or Ghana.…”