EXPLORING LIVESTOCK EVOLUTIONARY HISTORY, DIVERSITY, ADAPTATION AND CONSERVATION THROUGH LANDSCAPE GENOMICS AND ECOLOGICAL MODELLING

Attività antropiche e pressioni di mercato stanno rapidamente riducendo la biodiversità. Per questa ragione, conservare il patrimonio ecosistemico, tassonomico e genetico risulta fondamentale al fine di garantire potenziale adattativo alle specie, e, in ultima analisi, un futuro sostenibile per il pianeta. Al fine di minimizzare la perdita di biodiversità, numerosi metodi sono stati proposti per priorizzare ecosistemi, specie e popolazioni. Il presente lavoro di tesi fornisce in primo luogo una revisione di tali approcci, proponendo un albero decisionale volto a favorirne un corretto utilizzo. Secondariamente, la variabilità genomica neutrale del bufalo d’acqua (Bubalus bubalis L.) è investigata per mezzo di un pannello di marcatori SNP a media densità, rivelando due centri di domesticazione (India Nord-occidentale, Cina-Indocina) e possibili rotte di migrazione per gli ecotipi ‘river’ e ‘swamp’. L’adattamento locale ad East Coast Fever, patologia endemica delle popolazioni bovine in Africa Sub-sahariana, è stato inoltre studiato in bovini autoctoni Ugandesi (Bos taurus L.) combinando tecniche di modellizzazione delle nicchie ecologiche e di genomica del paesaggio. L’approccio ha portato ad indentificare PRKG1 e SLA2 come possibili geni di adattamento. I risultati sono discussi alla luce delle possibili implicazioni nella conservazione del bufalo e nella gestione delle risorse genetiche animali Ugandesi.Biodiversity is quickly disappearing due to human impact on the biosphere, and to market pressure. Consequently, the protection of both wild and domestic species needs to become a priority in order to preserve their evolutionary potential and, ultimately, guarantee a sustainable future for coming human generations. To date, tens of methods have been proposed to prioritize biodiversity for conservation purposes. Here, an ontology for priority setting in conservation biology is provided with the aim of supporting the selection of the most opportune methodologies given specific conservation goals. Further, two case studies are presented characterizing neutral and adaptive genomic diversity in water buffalo (Bubalus bubalis L.) and indigenous Ugandan cattle (Bos taurus L.), respectively. In particular, two independent domestication centres (North-western India and Indochina) and separate migration routes are suggested for the ‘river’ and ‘swamp’ water buffalo types. In the case of indigenous Ugandan cattle, the integration of species distribution modelling and landscape genomics techniques allowed the identification of PRKG1 and SLA2 as candidate genes for local adaptation to East Coast Fever, a vector-borne disease affecting bovine populations of Sub-Saharan Africa. Results are discussed for their implications in water buffalo conservation and Ugandan cattle adaptive management

Big dairy data to unravel effects of environmental, physiological and morphological factors on milk production of mountain-pastured Braunvieh cows

The transhumance system, which consists in moving animals to high mountain pastures during summer, plays a considerable role in preserving both local biodiversity and traditions, as well as protecting against natural hazard. In cows, particularly, milk production is observed to decline as a response to food shortage and climatic stress, leading to atypical lactation curves that are barely described by current lactation models. Here, we relied on 5 million monthly milk records from over 200 000 Braunvieh and Original Braunvieh cows to devise a new model accounting for transhumance, and test the influence of environmental, physiological and morphological factors on cattle productivity. Counter to expectations, environmental conditions in the mountain showed a globally limited impact on milk production during transhumance, with cows in favourable conditions producing only 10% more compared with cows living in detrimental conditions, and with precipitation in spring and altitude revealing to be the most production-affecting variables. Conversely, physiological factors such as lactation number and pregnancy stage presented an important impact over the whole lactation cycle with 20% difference in milk production, and alter the way animals respond to transhumance. Finally, the considered morphological factors (cow height and foot angle) presented a smaller impact during the whole lactation cycle (10% difference in milk production). The present findings help to anticipate the effect of climate change and to identify problematic environmental conditions by comparing their impact with the effect of factors that are known to influence lactation

Spatial Areas of Genotype Probability of Cattle Genomic Variants Involved in the Resistance to East Coast Fever: A Tool to Predict Future Disease-Vulnerable Geographical Regions

East Coast Fever (ECF) is a livestock disease caused by Theileria parva, a protozoan transmitted by the vector tick Rhipicephalus appendiculatus. This disease causes high mortality in cattle populations of Central and Eastern Africa, especially in exotic breeds. Here, we highlight genomic regions likely involved into tolerance/resistance mechanisms against ECF, and we introduce the estimation of their Spatial Area of Genotype Probability (SPAG) to delimit areas where the concerned genotypes are predicted to be present. During the NEXTGEN project, 803 Ugandan cattle were geo-referenced and genotyped (54K SNPs), while 532 tick occurrences were retrieved from a published database. To get a proxy of the parasite selective pressure, we used WorldClim bioclimatic variables to model vector ecological niche. Landscape genomics models were then used to detect cattle genotypes associated with vector probability of presence, and to estimate their SPAGs. Finally, climate change scenarios for 2070 were considered to compare the predicted shift in the vector niche with the estimated current SPAG. The analysis revealed two main areas of presence of possibly resistance-related genotypes, one South and one East of Lake Victoria. Climate change will probably shift tick niche southwards in the Eastern regions of Lake Victoria, inducing a critical area that currently does not show the candidate genotypes, but where disease will likely spread in the future. The combined use of SPAGs and niche maps could therefore facilitate the identification of regions of concern and to direct future targeted breeding schemes

Effect of climate change on the spatial distribution of genomic variants involved in the resistance to East Coast Fever in Ugandan cattle

East Coast Fever (ECF) is a major livestock disease caused by Theileria parva Theiler, 1904, an emo-parasite protozoan transmitted by the tick Rhipicephalus appendiculatus Neumann, 1901. This disease provokes high mortality in cattle populations of East and Central Africa, especially in exotic breeds and crossbreds (Olwoch et al., 2008). Here, we use landscape genomics (Joost et al., 2007) to highlight genomic regions likely involved into tolerance/resistance mechanisms against ECF, and we introduce Spatial Areas of Genotype Probability (SPAG) to delimit territories where favourable allelic variants are predicted to be present. Between 2010 and 2012, the NEXTGEN project (nextgen.epfl.ch) carried out the geo-referencing and genotyping (54K SNPs) of 803 Ugandan cattle, among which 496 were tested for T. parva presence. Moreover, 532 additional R. appendiculatus occurrences were obtained from a published database (Cumming, 1998). Current and future values of 19 bioclimatic variables were also retrieved from the WorldClim database (www.worldclim.org/). In order to evaluate the selective pressure of the parasite, we used MAXENT (Phillips et al., 2006; Muscarella et al., 2014) and a mixed logistic regression (Bates et al., 2014) to model and map the ecological niches of both T. parva and R. appendiculatus. Then, we used a correlative approach (Stucki et al., 2014) to detect molecular markers positively associated with the resulting probabilities of presence and built the corresponding SPAG. Finally, we considered bioclimatic predictors representing two different climate change scenarios for 2070 - one moderate and one severe - to forecast the simultaneous shift of both SPAG and vector/pathogen niches. While suitable ecological conditions for T. parva are predicted to remain constant, the best environment for the vector is predicted around Lake Victoria. However, when considering future conditions, parasite occurrence is expected to decrease because of the contraction of suitable environments for the tick in both scenarios. Landscape genomics’ analyses revealed several markers significantly associated with a high probability of presence of the tick and of the parasite. Among them, we found the marker ARS-BFGL-NGS-113888, whose heterozygous genotype AG showed a positive association. Interestingly, this marker is located close to the gene IRAK-M, an essential component of the Toll-like receptors involved in the immune response against pathogens (Kobayashi et al., 2002). If the implication of this gene into resistance mechanisms against ECF is confirmed, the corresponding SPAG (Figure 1) represents either areas where the variant of interest shows a high probability to exist now, or areas where ecological characteristics are the most favorable to induce its presence under future climatic conditions. Beyond the results presented here, the combined use of SPAG and niche maps could help identifying critical geographical regions that do not present the favourable genetic variant in the present, but where a parasite is likely to expand its range in the future. This may represent a valuable tool to support the identification of current resistant populations and to direct future targeted crossbreeding schemes

Genomic diversity and disease prevalence in Ugandan cattle

Ugandan cattle are represented by three main types: the long-horned Ankole, the short-horned zebu, and the Ankole-zebu crosses called “Nganda”. In the course of the EU-funded project Nextgen, Ugandan cattle have been extensively sampled over the whole country to investigate the association between genotypes and resistance/tolerance to endemic diseases (e.g. tsetse fly- and tick-born diseases)

Genomic diversity and Population Structure of Ugandan Taurine and Zebuine Cattle Breeds

An extensive sampling of Ugandan cattle was carried out in the course of the European project Nextgen to identify possible associations between genotypes, livestock endemic diseases and environmental variables. As a prior to the GWAS and selection signatures analyses planned within the project, we analyzed the population structure of Ugandan cattle genotyped with both 54K and 800K HD SNP panels in the context of the worldwide cattle genomic diversity

Modeling the spatial distribution of Theileria parva (Theiler 1904), causative agent of East Coast Fever disease in cattle

Theileria parva is a protozoan emo-parasite affecting sub-Saharan Bos taurus and Bos indicus populations. It is the causative agent of East Coast Fever, a major cattle disease causing the death of ~1.1∙106 animals per year and an annual loss of ~168∙106 USD (Norval et. al., 1992). T. parva geographical occurrence is bound to the presence of susceptible bovine host populations, the main tick vector Rhipicephalus appendiculatus (Neumann 1901), as well as suitable ecological conditions for the survival of both the vector and the parasite. While tick habitat requirements have been extensively investigated (see e.g. Cumming, 2002), studies focusing solely on the environmental conditions determining the parasite occurrence are still lacking. The goal of the study is to define T. parva ecological fundamental niche, thus fostering our understanding of the environmental requirements needed to maintain the parasite-vector-host biological system

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

East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance

Supplementary Figure 4

Additional ADMIXTURE analysis: results

Syncerus caffer distribution model

Data and analyses (R code) used to obtain the discussed Syncerus caffer model are provided. README information is provided in the archive