Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Bahbahani, Hussain; Tijjani, Abdulfatai; Mukasa, Christopher; Wragg, David; Almathen, Faisal; Nash, Oyekanmi; Akpa, G. N.; Mbole-Kariuki, Mary; Malla, Sunir; Woolhouse, Mark E. J.; Sonstegard, Tad S.; Tassell, C. P. van; Blythe, Martin; Huson, Heather J.; Hanotte, Olivier

doi:10.3389/fgene.2017.00068

Cited by 76 publications

(97 citation statements)

References 99 publications

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“…The level of European taurine introgression in the Ethiopian cattle populations was higher than the estimated values for Serere zebu cattle of Uganda (Bahbahani et al . ). On the other hand, compared to our results, a higher (90%) Nellore ancestry was traced in northern Ethiopian cattle populations (Zerabruk et al .…”

Section: Resultsmentioning

confidence: 97%

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Edea

Dadi

Dessie³

et al. 2018

Animal Genetics

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In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (F ST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (F ST ≥ 0.53), representing the top 1% smoothed F ST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.

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Section: Resultsmentioning

confidence: 97%

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Edea

Dadi

Dessie³

et al. 2018

Animal Genetics

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“…Interestingly, for low clusters (K = 2–4), African hybrids display similar proportional ancestry to African indicine. The introgression of indicine into African taurine cattle is predicted to have initially occurred ~4,000 YA, resulting in a consistently high indicine component within African hybrid cattle (Bahbahani et al., ), possibly reinforced by modern admixture with African indicine.…”

Section: Discussionmentioning

confidence: 99%

Domestication of cattle: Two or three events?

Pitt

Sevane

Nicolazzi

et al. 2018

Evolutionary Applications

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Cattle have been invaluable for the transition of human society from nomadic hunter‐gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human‐mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.

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“…Therefore, the low infection risk observed in the most suitable areas for R. appendiculatus (e.g. north-eastern districts) might be explained by the coexistence of putative tick-resistant zebuine-like populations [116], along with a sub-optimal environmental niche for the parasite. Further, we speculate that cattle populations living in regions suitable for T. parva parva development, but with reduced predicted tick presence (e.g.…”

Section: Discussionmentioning

confidence: 99%

Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

Vajana

Barbato

Colli

et al. 2018

Preprint

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63East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, 64and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and 65 caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes 66 their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-67 endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were 68 investigated using molecular data and epidemiological information from 823 indigenous cattle 69 from Uganda. Vector distribution and host infection risk were estimated over the study area and 70 subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We 71 identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, 72 respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. 73 PRKG1 was already described as associated with tick resistance in indigenous South African 74 cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways 75 involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the 76 zebuine origin of the genomic region candidate for tick resistance. 77 Author summary 78The tick-borne parasite Theileria parva parva infects cattle populations of eastern, central 79 and southern Africa, by causing a highly fatal pathology called "East Coast fever". The disease is 80 especially severe for the exotic breeds imported to Africa, as well as outside the endemic areas of 81 East Africa. In these regions, indigenous cattle populations can survive to infection, and this 82 5 tolerance might result from unique adaptations evolved to fight the disease. We investigated this 83 hypothesis by using a method named "landscape genomics", with which we compared the genetic 84 characteristics of indigenous Ugandan cattle coming from areas at different infection risk, and 85 located genomic sites potentially attributable to tolerance. In particular, the method pinpointed 86 two genes, one (PRKG1) involved into inflammatory response and potentially affecting East 87Coast fever vector attachment, the other (SLA2) involved into lymphocytes proliferation, a 88 process activated by T. parva parva infection. Our findings can orientate future research on the 89 genetic basis of East Coast fever-tolerance, and derive from a general method that can be applied 90 to investigate adaptation in analogous host-vector-parasite systems. Characterization of the 91 genetic factors underlying East Coast-fever-tolerance represents an essential step towards 92 enhancing sustainability and productivity of local agroecosystems. 93

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Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Cited by 76 publications

References 99 publications

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Domestication of cattle: Two or three events?

Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

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