Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever

Abstract

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.

Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle

“…Overall, the results of genes functions/annotation analysis reveal 19 genes related to the immune system response; 5 genes for Jenoubi, 15 genes for Rustaqi, and 1 overlapping gene between Jenoubi and Rustaqi breeds. This gene is PRKG1 associated with tick resistance in cattle (Mapholi et al, 2016; Vajana et al, 2018). These immune response genes were involved in both the acquired and innate immune responses, for example, IRF8 (Rustaqi; BTA18) and ABCC2 (Rustaqi; BTA26) linked to the acquired immune response to protozoan and bacterial infections (Giagu, 2016) and gastrointestinal nematodes (Li et al, 2011), respectively; PARM1 , an innate immune response gene (Jenoubi breed; BTA6), associated with anti-apoptotic activity especially during fertility stage (Cochran et al, 2013); and ATG7 (innate response gene, Jenoubi; BTA22), linked to the autophagy process (Aboelenain et al, 2015).…”

Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline

“…samβada is written in C++ with a particular emphasis on high-performance computing (HPC). Since its publication, samβada, as applied alone or in combination with other methods, proved useful to target putative genomic regions underlying local adaptation in a wide variety of species, including domestic animals such as swine and cattle (Cesconeto et al, 2017;Vajana et al, 2018), wild animals such as the freshwater sculpin and European pond turtle (Lucek, Keller, Nolte, & Seehausen, 2018;Pereira, Teixeira, & Velo-Antón, 2018), and many different plant species including the European beech and the cow-tail fir (Cuervo-Alarcon et al, 2018;Shih, Chang, Chung, Chiang, & Hwang, 2018).…”

Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens

“…Along with the agro-climatic data, any other environmental variable (e.g. epidemiological) may be included (59).…”