bioRxiv preprint doi: https://doi.org/10.1101/315184; this version posted May 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 2 3 4 Combining landscape genomics and ecological modelling to 5 investigate local adaptation of indigenous Ugandan cattle to East 6 Coast fever 7 8 9 Elia Vajana1,#a*, Mario Barbato1, Licia Colli1, Marco Milanesi1,2,3, Estelle Rochat4, Enrico 10 Fabrizi5, Christopher Mukasa6, Marcello Del Corvo1, Charles Masembe7, Vincent Muwanika8, 11 Fredrick Kabi9, Tad Stewart Sonstegard10, Heather Jay Huson11, Riccardo Negrini1,12, Stéphane 12 Joost4¶, Paolo Ajmone-Marsan1,13¶, on behalf of The NextGen Consortium^ 13 14 1Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, e Centro di Ricerca sulla 15 Biodiversità e sul DNA Antico (BioDNA), Università Cattolica del S. Cuore, Piacenza, Italy 16 17 2Department of Support, Production and Animal Health, School of Veterinary Medicine, São 18 Paulo State University, Araçatuba, Brazil 19 20 3International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and 21 Bioinformatics, Araçatuba, Brazil 22 23 4Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and 24 Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 25 Lausanne, Switzerland 1 bioRxiv preprint doi: https://doi.org/10.1101/315184; this version posted May 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 26 27 5Dipartimento di Scienze Economiche e Sociali, Università Cattolica del Sacro Cuore, Piacenza, 28 Italy 29 30 6National Animal Genetic Resource Centre and Data Bank, Entebbe, Uganda 31 32 7Department of Zoology, Entomology and Fisheries, Makerere University, Kampala, Uganda 33 34 8Department of Environmental Management, Makerere University, Kampala, Uganda 35 36 9National Livestock Resources Research Institute (NaLIRRI), National Agricultural Research 37 Organisation, Tororo, Uganda 38 39 10Recombinetics, Inc., St. Paul, Minnesota, United States of America 40 41 11Department of Animal Science, Cornell University, Ithaca, New York, United States of 42 America 43 44 12Associazione Italiana Allevatori, Roma 45 46 13PRONUTRIGEN-Centro di Ricerca Nutrigenomica e Proteomica, Università Cattolica del S. 47 Cuore, Piacenza, Italy 48 49 #aCurrent Address: Laboratory of Geographic Information Systems (LASIG), School of 50 Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de 51 Lausanne (EPFL), Lausanne, Switzerland 52 53 54 * Corresponding author 55 E-mail: [email protected] (EV) 56 57 58 ¶These authors contributed equally to this work. 59 60 2 bioRxiv preprint doi: https://doi.org/10.1101/315184; this version posted May 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 61 Short title: Local adaptation to East Coast fever 62 3 bioRxiv preprint doi: https://doi.org/10.1101/315184; this version posted May 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 63 Abstract 64 East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, 65 and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and 66 caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes 67 their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF- 68 endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were 69 investigated using molecular data and epidemiological information from 823 indigenous cattle 70 from Uganda. Vector distribution and host infection risk were estimated over the study area and 71 subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We 72 identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, 73 respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. 74 PRKG1 was already described as associated with tick resistance in indigenous South African 75 cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways 76 involved into lymphocytes’ proliferation. Additionally, local ancestry analysis suggested the 77 zebuine origin of the genomic region candidate for tick resistance. 78 Author summary 79 The tick-borne parasite Theileria parva parva infects cattle populations of eastern, central 80 and southern Africa, by causing a highly fatal pathology called “East Coast fever”. The disease is 81 especially severe for the exotic breeds imported to Africa, as well as outside the endemic areas of 82 East Africa. In these regions, indigenous cattle populations can survive to infection, and this 4 bioRxiv preprint doi: https://doi.org/10.1101/315184; this version posted May 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 83 tolerance might result from unique adaptations evolved to fight the disease. We investigated this 84 hypothesis by using a method named “landscape genomics”, with which we compared the genetic 85 characteristics of indigenous Ugandan cattle coming from areas at different infection risk, and 86 located genomic sites potentially attributable to tolerance. In particular, the method pinpointed 87 two genes, one (PRKG1) involved into inflammatory response and potentially affecting East 88 Coast fever vector attachment, the other (SLA2) involved into lymphocytes proliferation, a 89 process activated by T. parva parva infection. Our findings can orientate future research on the 90 genetic basis of East Coast fever-tolerance, and derive from a general method that can be applied 91 to investigate adaptation in analogous host-vector-parasite systems. Characterization of the 92 genetic factors underlying East Coast-fever-tolerance represents an essential step towards 93 enhancing sustainability and productivity of local agroecosystems. 94 Introduction 95 East Coast fever (ECF) is an endemic vector-borne disease affecting cattle populations of 96 eastern and central Africa. ECF etiological agent is the protozoan emo-parasite protozoan 97 Theileria parva Theiler, 1904, vectored by the hard-bodied tick vector Rhipicephalus 98 appendiculatus Neumann, 1901. The disease is reported to cause morbidity in indigenous 99 populations and high mortality rates among exotic breeds and crossbreds, thus undermining the 100 livestock sector development in the affected countries [1–3]. 101 Cape buffalo (Syncerus caffer Sparrman, 1779) is T. parva native host, being its wild and 102 asymptomatic reservoir [4]. A primordial contact between buffalo-derived T. parva and domestic 5 bioRxiv preprint doi: https://doi.org/10.1101/315184; this version posted May 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 103 bovines is likely to have occurred ~4.500 years before present (YBP) [5]. However, it is hard to 104 define if the host jump affected taurine- or indicine-like cattle first, since no consensus can easily 105 be reached to define who among Bos taurus and B. indicus migrated into ECF endemic regions 106 first [6–8]. Indeed, African taurine cattle might have reached eastern Africa sometime between 107 ~8,000 and 1,500 YBP [7,8], and the most ancient zebuine colonization wave is estimated to have 108 occurred between ~4,000-2,000 YBP from the Asian continent, as suggested by the first certain 109 archaeological record dated 1,750 YBP [6]. Once T. parva spread to domestic populations, 110 coevolution between the parasite and the new hosts likely led to the divergence between buffalo- 111 (T. parva lawracei) and cattle-specific (T. parva parva) parasite strains [9,10], and to the 112 appearance of infection-tolerant indigenous herds [11,12]. 113 Most likely, ECF-tolerance appeared (and is only observable) in areas where environmental 114 conditions guaranteed a constant coexistence between the vector, the parasite and the domestic 115 host. Such a particular situation, together with the evolution of some sort of “innate resistance” 116 [13], plausibly prompted the establishment of an epidemiological state referred to as endemic 117 stability, a condition where hosts become parasite reservoirs with negligible clinical symptoms 118 [14]. However, no clear indication for a genetic control has been provided for ECF-tolerance so 119 far [12], despite host genetic factors were identified for tolerance to tropical theileriosis [15] (a 120 disease caused by