Biology subjects

Hanotte, O.

Publications and source records attributed to Hanotte, O..

8 recordsLinked to original sources

bioRxiv2026

The genomic basis of heat stress adaptation in indigenous Ethiopian cattle from arid and hot-humid climates

African zebu cattle (Bos indicus) exhibit remarkable adaptation to extreme thermal conditions, yet the genomic bases of this resilience are not fully elucidated. Ethiopia provides a unique natural setting where closely related zebu populations have divergently adapted to hot-arid (DHETZ) and hot-humid (HHETZ) climates. In this study, we performed whole-genome sequencing of 46 Ethiopian zebu cattle from five populations and compared them with Asian zebu, Sudanese zebu, African taurine, and European taurine breeds. By integrating genome-wide SNP analysis, population genetic structure assessment, and multiple selection scans (iHS, Hp, XP-EHH, and XP-CLR), we identified distinct and shared selection signatures between DHETZ and HHETZ cattle. Ethiopian zebu closely clustered with Sudanese zebu but showed clear divergence from Asian zebu and taurine breeds. Although DHETZ and HHETZ cattle exhibited minimal genetic differentiation, reflecting their shared ancestry, each group displayed unique selection signals. DHETZ cattle showed strong selection in genes involved in oxidative stress regulation, protein folding, mitochondrial function, and vascular remodeling (e.g., SESN2, DNAJC8, GRPEL2, ABLIM3, and AFAP1L1). In contrast, HHETZ cattle displayed signatures in genes associated with immune responses, energy metabolism, and angiogenesis inhibition (e.g., MYD88, PRKACA, PRKACB, and WIF1). Several genes, including VEGFC, TNIP3, and DMXL2, were under selection in both groups, suggesting conserved mechanisms of thermotolerance and reproductive adaptation. These findings reveal a dual pattern of genomic adaptation: while core heat-response pathways are shared, population-specific signatures reflect distinct metabolic and vascular strategies for coping with arid versus humid heat stress. This study provides novel insights into the genomic architecture of environmental adaptation in tropical cattle and offers valuable markers for breeding climate-resilient livestock.

genomics↗

bioRxiv2023

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into 3 enterotypes, with one particularly enriched at high altitudes. We assembled 9,977 taxonomically and functionally diverse metagenome-assembled genomes, the vast majority of which were not found in a dataset of previously published chicken microbes, or in the Genome Taxonomy Database. The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argues for further discoveries in other agro-ecologies.

microbiology↗

bioRxiv2021

Genomic signatures of desert adaptation at gene-rich regions in zebu cattle from the African drylands

Sudan, the largest country in Africa, acts as a corridor between North and sub-Saharan Africa along the river Niles. It comprises warm arid and semi-arid grazing lands, and it is home to the second-largest African population of indigenous livestock. Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector diseases challenges. We investigated genome diversity in six indigenous African zebu breeds sampled in Sudan (Aryashai, Baggara, Butana, Fulani, Gash, and Kenana). We adopted three genomic scan approaches to identify candidate selective sweeps regions (ZHp, FST, XP-EHH). We identified a set of gene-rich selective sweep regions shared across African and Asian zebu or unique to Sudanese zebu. In particular, African and Asian zebu candidate gene-rich regions are detected on chromosomes 2, 5 and 7. They include genes involved in immune response, body size and conformation, and stress response to heat. In addition, a 250 kb selective sweep on chromosome 16 was detected exclusively in five Sudanese zebu populations. This region spans seven genes, including PLCH2, PEX10, PRKCZ and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Together, these genes may contribute to the zebu cattle resilience to heat, nutritional and water shortages. Our results highlight the putative importance of selection at gene-rich genome regions, which might be under a common regulatory genetic control, as an evolutionary mechanism for rapid adaptation to the complexity of environmental challenges.

evolutionary biology↗

bioRxiv2021

A framework for defining livestock ecotypes based on ecological modelling and exploring genomic environmental adaptation: the example of Ethiopian village chicken

In evolutionary ecology, an ecotype is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining Ecological Niche Modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within- ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. A few biological pathways were shared amongst most ecotypes and the involved genes showed functions important for scavenging chickens, e.g. neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using Redundancy Analysis (RDA) allowed for correlating [~]33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype x environment (GxE) interactions.

genetics↗

bioRxiv2021

The natural adaptation and human selection history of African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous African sheep genomes sequenced at an average depth of [~]54x for 130 samples (Ethiopia, Libya) and [~]10x for 20 samples (Sudan), representing sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups that correspond to altitudinal geographic origins and tail morphotypes. Comparative genomic analysis identified targets of selection spanning conserved haplotype structures overlapping genes and gene families relating to hypoxia responses, caudal vertebrae and tail skeleton length, ear morphology, and tail fat-depot structure. Our findings provide novel insights underpinning variation and response to human selection and environmental adaptation, and possible pleiotropic gene interactions in indigenous African sheep genomes, which guaranteed the successful establishment of the species on the continent.

genomics↗

bioRxiv2020

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

Elucidating the genetic basis of environmental adaptation in indigenous livestock populations has important implications for sustainable breeding improvement. It requires a detailed untangling of relevant environmental pressures and fine resolution detection of genomic signatures of selection associated with these environmental parameters. Here, we uniquely employed an integrative approach, combining Ecological Niche Modelling (ENM) with (i) genome-wide analyses of positive signatures of selection (SSA) and (ii) genotype-environment association (GEA) analyses to unravel the environmental adaptation of Ethiopian indigenous chickens. We first examined 34 agro-ecological and climatic variables and identified six main environmental selection drivers (one temperature - strongly correlated to elevation, three precipitation, and two soil/land variables). We then performed genomic analyses using high-density SNP data from whole-genome sequencing of 245 Ethiopian chickens from 25 different populations. Environmental genomic association analyses (SSA and GEA) identify a few strongly supported selected genomic regions, often with clusters of candidate genes, related to altitude-induced stresses (hypoxia, thrombosis, and cold temperatures), water scarcity, and the challenges of scavenging feeding behaviour. These analyses support a predominantly oligogenic control of environmental adaptation and possible regulation by one or few genetic elements only. Our study shows that the pre-identification of the key environmental drivers of adaptation, followed by a detailed genomic investigation of the associated genetic mechanisms provides a powerful new approach for elucidating the effect of natural selection in domestic animals. These results represent new landmarks to inform sustainable poultry breeding improvement.

genomics↗

bioRxiv2019

The wild species genome ancestry of domestic chickens

Hybridization and/or introgression play a key role in the evolutionary history of animal species. It is commonly observed in several orders in wild birds. The domestic chicken Gallus gallus domesticus is the commonest livestock species exploited for the benefit of mankind. The origin of its diversity remains unsettled. Here, we report a genome-wide analyses for signatures of introgression within domestic village chicken. We first established the genome-wide phylogeny and divergence time across the genus Gallus, showing the sister relationships between Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii and that the Green junglefowl is the first diverging lineage within the genus Gallus. Then, by analysing the whole-genome sequences of geographically diverse chicken populations, we reveal extensive bidirectional introgression between Grey junglefowl and domestic chicken and to a much less extent with Ceylon junglefowl. A single case of Green junglefowl G. varius introgression was identified. These introgressed regions include biological functions related to the control of gene expression. Our results show that while the Red junglefowl is the main ancestral species, introgressive hybridization episodes have impacted the genome and contributed to the diversity of domestic chicken, although likely at different level across its geographic range.

evolutionary biology↗

bioRxiv2018

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.

genetics↗