OLIVIER HANOTTE's Outputs (49)

Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia (2024)
Journal Article
Morris, K. M., Sutton, K., Girma, M., Sánchez-Molano, E., Solomon, B., Esatu, W., Dessie, T., Vervelde, L., Psifidi, A., Hanotte, O., & Banos, G. (2024). Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia. Frontiers in Genetics, 15, Article 1383609. https://doi.org/10.3389/fgene.2024.1383609

Background:: In sub-Saharan Africa, 80% of poultry production is on smallholder village farms, where chickens are typically reared outdoors in free-ranging conditions. There is limited knowledge on chickens’ phenotypic characteristics and genetics un... Read More about Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia.

Comprehensive analysis of differentially expressed mRNA profiles in chicken jejunum and cecum following Eimeria maxima infection (2024)
Journal Article
Jebessa, E., Bello, S. F., Xu, Y., Cai, B., Tuli, M. D., Girma, M., …Nie, Q. (2024). Comprehensive analysis of differentially expressed mRNA profiles in chicken jejunum and cecum following Eimeria maxima infection. Poultry Science, 103(6), Article 103716. https://doi.org/10.1016/j.psj.2024.103716

Coccidiosis, a protozoan disease that substantially impacts poultry production, is characterized by an intracellular parasite. The study utilized 48 one-day-old Horro chickens, randomly divided into the infected (I) and control (C) groups. The challe... Read More about Comprehensive analysis of differentially expressed mRNA profiles in chicken jejunum and cecum following Eimeria maxima infection.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens (2024)
Journal Article
Kebede, F. G., Derks, M. F., Dessie, T., Hanotte, O., Barros, C. P., Crooijmans, R. P., Komen, H., & Bastiaansen, J. W. (2024). Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens. BMC Genomics, 25(1), Article 284. https://doi.org/10.1186/s12864-024-10193-6

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers... Read More about Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens.

Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing (2024)
Journal Article
Salim, B., Nakao, R., Chatanga, E., Marcuzzi, O., Eissawi, M. A., Almathen, F., …Giovambattista, G. (2024). Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing. BMC Genomics, 25(1), Article 160. https://doi.org/10.1186/s12864-024-10053-3

Introduction
The Ovar-DRB1 gene, a crucial element of the Major Histocompatibility Complex (MHC) Class II region, initiates adaptive immunity by presenting antigens to T-cells. Genetic diversity in sheep, particularly in MHC Class II genes like Ovar... Read More about Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing.

Whole-genome resource sequences of 57 indigenous Ethiopian goats (2024)
Journal Article
Belay, S., Belay, G., Nigussie, H., Jian-Lin, H., Tijjani, A., Ahbara, A. M., …Mwacharo, J. M. (2024). Whole-genome resource sequences of 57 indigenous Ethiopian goats. Scientific Data, 11(1), Article 139. https://doi.org/10.1038/s41597-024-02973-2

Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to th... Read More about Whole-genome resource sequences of 57 indigenous Ethiopian goats.

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress (2024)
Journal Article
Rachman, M. P., Bamidele, O., Dessie, T., Smith, J., Hanotte, O., & Gheyas, A. A. (2024). Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress. Scientific Reports, 14(1), Article 2209. https://doi.org/10.1038/s41598-024-52569-4

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commerc... Read More about Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress.

MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection (2024)
Journal Article
Jebessa, E., Bello, S. F., Guo, L., Tuli, M. D., Hanotte, O., & Nie, Q. (2024). MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection. Frontiers in Immunology, 14, Article 1331532. https://doi.org/10.3389/fimmu.2023.1331532

Coccidiosis stands as a protozoan disease of notable economic impact, characterized by an intracellular parasite that exerts substantial influence over poultry production. This invasion disrupts the integrity of the enteric mucosa, leading to the eme... Read More about MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection.

Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds (2023)
Journal Article
Friedrich, J., Bailey, R. I., Talenti, A., Chaudhry, U., Ali, Q., Obishakin, E. F., …Wiener, P. (2023). Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds. Genetics Selection Evolution, 55(1), Article 91. https://doi.org/10.1186/s12711-023-00861-8

Background: The genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this... Read More about Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds.

Agroecologies defined by species distribution models improve model fit of genotype by environment interactions to identify the best performing chicken breeds for smallholder systems (2023)
Journal Article
Kebede, F. G., Komen, H., Dessie, T., Hanotte, O., Kemp, S., Alemu, S. W., & Bastiaansen, J. W. M. (2023). Agroecologies defined by species distribution models improve model fit of genotype by environment interactions to identify the best performing chicken breeds for smallholder systems. Frontiers in Sustainable Food Systems, 7, Article 1305799. https://doi.org/10.3389/fsufs.2023.1305799

Animal performance is an outcome of genetic effects, environmental influences, and their interaction. Understanding the influences of the environment on performance is important to identify the right breeds for a given environment. Agroecological zon... Read More about Agroecologies defined by species distribution models improve model fit of genotype by environment interactions to identify the best performing chicken breeds for smallholder systems.

Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review (2023)
Journal Article
Kambal, S., Tijjani, A., Ibrahim, S. A., Ahmed, M. K. A., Mwacharo, J. M., & Hanotte, O. (in press). Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Animal Genetics, https://doi.org/10.1111/age.13353

Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic re... Read More about Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review.

Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia (2023)
Journal Article
Zegeye, T., Belay, G., Vallejo-Trujillo, A., Han, J., & Hanotte, O. (2023). Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia. Frontiers in Genetics, 14, Article 1050365. https://doi.org/10.3389/fgene.2023.1050365

The Tigray region, where we found around eight per cent of the indigenous cattle population of Ethiopia, is considered as the historic centre of the country, with the ancient pre-Aksumite and Aksumite civilisations in contact with the civilisations o... Read More about Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia.

Yolk Fatty Acid Content, Lipid Health Indices, and Oxidative Stability in Eggs of Slow-Growing Sasso Chickens Fed on Flaxseed Supplemented with Plant Polyphenol Extracts (2023)
Journal Article
Tadesse, D., Retta, N., Girma, M., Ndiwa, N., Dessie, T., Hanotte, O., …Maak, S. (2023). Yolk Fatty Acid Content, Lipid Health Indices, and Oxidative Stability in Eggs of Slow-Growing Sasso Chickens Fed on Flaxseed Supplemented with Plant Polyphenol Extracts. Foods, 12(9), Article 1819. https://doi.org/10.3390/foods12091819

Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages (2023)
Journal Article
Salim, B., Alasmari, S., Mohamed, N. S., Ahmed, M.-K. A., Nakao, R., & Hanotte, O. (2023). Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages. BMC Genomics, 24, Article 118. https://doi.org/10.1186/s12864-023-09231-6

More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. T... Read More about Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages.

Fourth Report on Chicken Genes and Chromosomes 2022 (2023)
Journal Article
Smith, J., Alfieri, J. M., Anthony, N., Arensburger, P., Athrey, G. N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P. M., Carroll, R., Casono, M. C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L. M., Crooijmans, R., …Zhou, H. (2023). Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenetic and Genome Research, 162(8-9), 405–528. https://doi.org/10.1159/000529376

The chicken continues to hold its position as a leading model organism within many areas of research, as well as being a major source of protein for human consumption. The First Report on Chicken Genes and Chromosomes [Schmid et al., 2000], which was... Read More about Fourth Report on Chicken Genes and Chromosomes 2022.

Analysis of tail morphology and osteology in Ethiopian indigenous sheep (2023)
Journal Article
Amane, A., Belay, G., Kebede, A., Dessie, T., Worku, S., Hanotte, O., & Vila, E. (2023). Analysis of tail morphology and osteology in Ethiopian indigenous sheep. Journal of Archaeological Science: Reports, 47, Article 103776. https://doi.org/10.1016/j.jasrep.2022.103776

Sheep adaptive diversity, including tail morphology, has been shaped by various factors, including natural and/or artificial selection for different traits. The Horn of Africa has historically been a major livestock entry point on the African contine... Read More about Analysis of tail morphology and osteology in Ethiopian indigenous sheep.

Morphological and osteological characterization of indigenous domestic chickens (Gallus gallus domesticus): validation of Rensch’s, Bergmann’s and Allen’s rules (2023)
Journal Article
Gebru, G., Belay, G., Dessie, T., Zenebe Kelkay, M., Birhanie Dagnhegn, M., & Hanotte, O. (2023). Morphological and osteological characterization of indigenous domestic chickens (Gallus gallus domesticus): validation of Rensch’s, Bergmann’s and Allen’s rules. Frontiers in Ecology and Evolution, 11, Article 1032082. https://doi.org/10.3389/fevo.2023.1032082

Ecogeographical habitat heterogeneity in wild endotherm species results in morphological variability associated with physiological mechanisms for maintaining their body temperature at a thermoneutral state in different environments. This habitat-indu... Read More about Morphological and osteological characterization of indigenous domestic chickens (Gallus gallus domesticus): validation of Rensch’s, Bergmann’s and Allen’s rules.

In Vitro Antioxidant Activities of Plant Polyphenol Extracts and Their Combined Effect with Flaxseed on Raw and Cooked Breast Muscle Fatty Acid Content, Lipid Health Indices and Oxidative Stability in Slow-Growing Sasso Chickens (2022)
Journal Article
Tadesse, D., Retta, N., Girma, M., Ndiwa, N., Dessie, T., Hanotte, O., Getachew, P., Dannenberger, D., & Maak, S. (2023). In Vitro Antioxidant Activities of Plant Polyphenol Extracts and Their Combined Effect with Flaxseed on Raw and Cooked Breast Muscle Fatty Acid Content, Lipid Health Indices and Oxidative Stability in Slow-Growing Sasso Chickens. Foods, 12(1), Article 115. https://doi.org/10.3390/foods12010115

Adding flaxseed was found to decrease oxidative stability in feed and increase the antioxidant needs of chicken. This has also been associated with a decrease in the nutritional value and oxidative stability of meat if sufficient dietary antioxidants... Read More about In Vitro Antioxidant Activities of Plant Polyphenol Extracts and Their Combined Effect with Flaxseed on Raw and Cooked Breast Muscle Fatty Acid Content, Lipid Health Indices and Oxidative Stability in Slow-Growing Sasso Chickens.

Genomic adaptation of Ethiopian indigenous cattle to high altitude (2022)
Journal Article
Terefe, E., Belay, G., Han, J., Hanotte, O., & Tijjani, A. (2022). Genomic adaptation of Ethiopian indigenous cattle to high altitude. Frontiers in Genetics, 13, Article 960234. https://doi.org/10.3389/fgene.2022.960234

The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in thes... Read More about Genomic adaptation of Ethiopian indigenous cattle to high altitude.

Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis (2022)
Journal Article
Chen, X., Wang, Z., Chen, Y., Akinci, I., Luo, W., Xu, Y., …Nie, Q. (2022). Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis. Frontiers in Immunology, 13, Article 910860. https://doi.org/10.3389/fimmu.2022.910860

Avian coccidiosis is a common enzootic disease caused by infection of Eimeria species parasites. It causes huge economic losses in the global poultry industry. Current control using anticoccidial drugs or vaccination is limited due to drug resistance... Read More about Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis.

Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing (2022)
Journal Article
Amane, A., Belay, G., Tijjani, A., Dessie, T., Musa, H. H., & Hanotte, O. (2022). Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing. Diversity, 14(11), Article 895. https://doi.org/10.3390/d14110895

Local Sudanese sheep populations inhabiting diverse environmental conditions and holding opposing morphologies provide opportunities for molecular-genetic research. Characterizing their genome is crucial for sustainable breeding improvement and targe... Read More about Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing.

Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia) (2022)
Journal Article
Gebru, G., Belay, G., Vallejo-Trujillo, A., Dessie, T., Gheyas, A., & Hanotte, O. (2022). Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia). Frontiers in Genetics, 13, Article 968961. https://doi.org/10.3389/fgene.2022.968961

The Tigray region is an ancient entry route for the domestic chickens into Africa. The oldest African chicken bones were found in this region at Mezber, a pre-Aksumite rural farming settlement. They were dated to around 800–400 BCE. Since then, the f... Read More about Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia).

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken (2022)
Journal Article
Jebessa, E., Guo, L., Chen, X., Bello, S. F., Cai, B., Girma, M., …Nie, Q. (2022). Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken. Frontiers in Immunology, 13, Article 994224. https://doi.org/10.3389/fimmu.2022.994224

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enh... Read More about Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken.

Natural adaptation and human selection of northeast African sheep genomes (2022)
Journal Article
Ahbara, A. M., Musa, H. H., Robert, C., Abebe, A., Al-Jumaili, A. S., Kebede, A., …Mwacharo, J. M. (2022). Natural adaptation and human selection of northeast African sheep genomes. Genomics, 114(5), Article 110448. https://doi.org/10.1016/j.ygeno.2022.110448

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 northeast African sheep genomes sequenced at an average... Read More about Natural adaptation and human selection of northeast African sheep genomes.

Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken (2022)
Journal Article
Vallejo-Trujillo, A., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J., Hanotte, O., & Gheyas, A. A. (2022). Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken. Frontiers in Ecology and Evolution, 10, Article 866587. https://doi.org/10.3389/fevo.2022.866587

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,... Read More about Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken.

Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle (2022)
Journal Article
Tijjani, A., Salim, B., da Silva, M. V. B., Eltahir, H. A., Musa, T. H., Marshall, K., …Musa, H. H. (2022). Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle. Genomics, 114(4), Article 110423. https://doi.org/10.1016/j.ygeno.2022.110423

Background
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 disease challenges. Here,... Read More about Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle.

Correction to: Population diferentiated copy number variation of Bos taurus, Bos indicus and their African hybrids (2022)
Journal Article
Jang, J., Terefe, E., Kim, K., Lee, Y. H., Belay, G., Tijjani, A., …Kim, H. (2022). Correction to: Population diferentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics, 23, Article 207. https://doi.org/10.1186/s12864-022-08409-8

Following publication of the original article [1], the authors reported that the following missing authors from the authorship list: • Endashaw Terefe • Gurja Belay • Abdulfatai Tijjani • Jian-Lin Han • Olivier Hanotte The corrected authorship list a... Read More about Correction to: Population diferentiated copy number variation of Bos taurus, Bos indicus and their African hybrids.

Author Correction: Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle (2022)
Journal Article
Kwon, T., Kim, K., Caetano-Anolles, K., Sung, S., Cho, S., Jeong, C., …Kim, H. (2022). Author Correction: Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle. BMC Biology, 20, Article 62. https://doi.org/10.1186/s12915-022-01265-8

The original article contained minor errors in Figs. 1 and 3 which have both since been corrected.

Whole genome sequences of 234 indigenous African chickens from Ethiopia (2022)
Journal Article
Gheyas, A., Vallejo-Trujillo, A., Kebede, A., Dessie, T., Hanotte, O., & Smith, J. (2022). Whole genome sequences of 234 indigenous African chickens from Ethiopia. Scientific Data, 9, Article 53. https://doi.org/10.1038/s41597-022-01129-4

Indigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines... Read More about Whole genome sequences of 234 indigenous African chickens from Ethiopia.

The usefulness of maternally inherited genetic markers for phylogeographic studies in village chicken (2022)
Journal Article
Al-Jumaili, A. S., & Hanotte, O. (2023). The usefulness of maternally inherited genetic markers for phylogeographic studies in village chicken. Animal Biotechnology, 34(4), 863-881. https://doi.org/10.1080/10495398.2021.2000429

Phylogeography plays a major role in understanding micro and macroevolutionary processes dealing with evolutionary interpretations of geographical distribution. This field integrates information from molecular genetics, population genetics, demograph... Read More about The usefulness of maternally inherited genetic markers for phylogeographic studies in village chicken.

Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle (2022)
Journal Article
Kwon, T., Kim, K., Caetano-Anolles, K., Sung, S., Cho, S., Jeong, C., …Kim, H. (2022). Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle. BMC Biology, 20(1), Article 20. https://doi.org/10.1186/s12915-021-01206-x

Background: Africa is an important watershed in the genetic history of domestic cattle, as two lineages of modern cattle, Bos taurus and B. indicus, form distinct admixed cattle populations. Despite the predominant B. indicus nuclear ancestry of Afri... Read More about Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle.

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci (2021)
Journal Article
Lv, F., Cao, Y., Liu, G., Luo, L., Lu, R., Liu, M., …Li, M. (2022). Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci. Molecular Biology and Evolution, 39(2), Article msab353. https://doi.org/10.1093/molbev/msab353

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, la... Read More about Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci.

Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens (2021)
Journal Article
Kebede, F. G., Komen, H., Dessie, T., Alemu, S. W., Hanotte, O., & Bastiaansen, J. W. (2021). Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens. Frontiers in Genetics, 12, Article 723360. https://doi.org/10.3389/fgene.2021.723360

Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportu... Read More about Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens.

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids (2021)
Journal Article
Jang, J., Terefe, E., Kim, K., Lee, Y. H., Belay, G., Tijjani, A., …Kim, H. (2021). Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics, 22, Article 531. https://doi.org/10.1186/s12864-021-07808-7

Background: CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results: Here, autosome-wide CNVs were called by read depth of NGS alignme... Read More about Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids.

Large-scale genomic analysis reveals the genetic cost of chicken domestication (2021)
Journal Article
Wang, M. S., Zhang, J. J., Guo, X., Li, M., Meyer, R., Ashari, H., …Zhang, Y. P. (2021). Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biology, 19(1), Article 118. https://doi.org/10.1186/s12915-021-01052-x

Background: Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection... Read More about Large-scale genomic analysis reveals the genetic cost of chicken domestication.

Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens (2021)
Journal Article
Gheyas, A. A., Vallejo-Trujillo, A., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J., & Hanotte, O. (2021). Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens. Molecular Biology and Evolution, 38(10), 4268-4285. https://doi.org/10.1093/molbev/msab156

Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provi... Read More about Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens.

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism (2020)
Journal Article
Kim, K., Kwon, T., Dessie, T., Yoo, D. A., Mwai, O. A., Jang, J., …Kim, H. (2020). The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. Nature Genetics, 52(10), 1099-1110. https://doi.org/10.1038/s41588-020-0694-2

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence an... Read More about The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism.

Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle (2019)
Journal Article
Alshawi, A., Essa, A., Al-Bayatti, S., & Hanotte, O. (2019). Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle. Frontiers in Genetics, 10, Article 609. https://doi.org/10.3389/fgene.2019.00609

The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle hu... Read More about Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle.

Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle (2019)
Journal Article
Tijjani, A., Utsunomiya, Y. T., Ezekwe, A. G., Nashiru, O., & Hanotte, O. (2019). Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle. Frontiers in Genetics, 10, Article 442. https://doi.org/10.3389/fgene.2019.00442

Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variati... Read More about Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle.

Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3 (2019)
Journal Article
Bassano, I., Ong, S. H., Sanz-Hernandez, M., Vinkler, M., Kebede, A., Hanotte, O., …Kellam, P. (2019). Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3. BMC Genomics, 20(1), Article 272. https://doi.org/10.1186/s12864-019-5621-5

Background

The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal spec... Read More about Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3.

c-Myc inhibits myoblast differentiation and promotes myoblast proliferation and muscle fibre hypertrophy by regulating the expression of its target genes, miRNAs and lincRNAs (2019)
Journal Article
Luo, W., Chen, J., Li, L., Ren, X., Cheng, T., Lu, S., …Hanotte, O. (2019). c-Myc inhibits myoblast differentiation and promotes myoblast proliferation and muscle fibre hypertrophy by regulating the expression of its target genes, miRNAs and lincRNAs. Cell Death and Differentiation, 26(3), 426-442. https://doi.org/10.1038/s41418-018-0129-0

© 2018, ADMC Associazione Differenziamento e Morte Cellulare. The transcription factor c-Myc is an important regulator of cellular proliferation, differentiation and embryogenesis. While c-Myc can inhibit myoblast differentiation, the underlying mech... Read More about c-Myc inhibits myoblast differentiation and promotes myoblast proliferation and muscle fibre hypertrophy by regulating the expression of its target genes, miRNAs and lincRNAs.

Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep (2019)
Journal Article
Ahbara, A., Bahbahani, H., Almathen, F., Al Abri, M., Agoub, M. O., Abeba, A., …Mwacharo, J. M. (2019). Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Frontiers in Genetics, 9, Article 699. https://doi.org/10.3389/fgene.2018.00699

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, whic... Read More about Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep.

The role of local adaptation in sustainable production of village chickens (2018)
Journal Article
Bettridge, J. M., Psifidi, A., Terfa, Z. G., Desta, T. T., Lozano-Jaramillo, M., Dessie, T., …Christley, R. M. (2018). The role of local adaptation in sustainable production of village chickens. Nature Sustainability, 1(10), 574-582. https://doi.org/10.1038/s41893-018-0150-9

Village chickens are ubiquitous in smallholder farming systems, contributing to household, local and national economies under diverse environmental, economic and cultural settings. However, they are raised in challenging environments where productivi... Read More about The role of local adaptation in sustainable production of village chickens.

Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species (2018)
Journal Article
Lawal, R. A., Al-Atiyat, R. M., Aljumaah, R. S., Silva, P., Mwacharo, J. M., & Hanotte, O. (2018). Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species. Frontiers in Genetics, 9, Article 264. https://doi.org/10.3389/fgene.2018.00264

© 2018 Lawal, Al-Atiyat, Aljumaah, Silva, Mwacharo and Hanotte. The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic contr... Read More about Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species.

The genome landscape of indigenous African cattle (2017)
Journal Article
Kim, J., Hanotte, O., Okeyo, A. M., Dessie, T., Bashir, S., Diallo, B., …Kim, H. (2017). The genome landscape of indigenous African cattle. Genome Biology, 18(1), Article 34. https://doi.org/10.1186/s13059-017-1153-y

© 2017 The Author(s). Background: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step toward... Read More about The genome landscape of indigenous African cattle.

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary (2016)
Journal Article
Almathen, F., Charruau, P., Mohandesan, E., Mwacharo, J. M., Orozco-terWengel, P., Pitt, D., …Burger, P. A. (2016). Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary. Proceedings of the National Academy of Sciences, 113(24), https://doi.org/10.1073/pnas.1519508113

Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zone... Read More about Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary.

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken (2015)
Journal Article
Wragg, D., Mason, A. S., Yu, L., Kuo, R., Lawal, R. A., Desta, T. T., Mwacharo, J. M., Cho, C.-Y., Kemp, S., Burt, D. W., & Hanotte, O. (2015). Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics, 16, Article 784. https://doi.org/10.1186/s12864-015-1954-x

Background: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry indus... Read More about Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.

Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis (2015)
Journal Article

Co-infections determine patterns of mortality in a population exposed to parasite infection (2015)
Journal Article
Woolhouse, M. E., Thumbi, S. M., Jennings, A., Chase-Topping, M., Callaby, R., Kiara, H., …Toye, P. G. (2015). Co-infections determine patterns of mortality in a population exposed to parasite infection. Science Advances, 1(2), Article e1400026. https://doi.org/10.1126/sciadv.1400026

© 2015 The Authors, some rights reserved. Many individual hosts are infected with multiple parasite species, and this may increase or decrease the pathogenicity of the infections. This phenomenon is termed heterologous reactivity and is potentially a... Read More about Co-infections determine patterns of mortality in a population exposed to parasite infection.

Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl (2013)
Journal Article
Wragg, D., Mwacharo, J. M., Alcalde, J. A., Wang, C., Han, J. L., Gongora, J., Gourichon, D., Tixier-Boichard, M., & Hanotte, O. (2013). Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl. PLoS ONE, 8(8), e71393. https://doi.org/10.1371/journal.pone.0071393

Oocyan or blue/green eggshell colour is an autosomal dominant trait found in native chickens (Mapuche fowl) of Chile and in some of their descendants in European and North American modern breeds. We report here the identification of an endogenous avi... Read More about Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl.