All Outputs (49)

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.

Domestic chicken diversity: Origin, distribution, and adaptation (2021)
Journal Article
Lawal, R. A., & Hanotte, O. (2021). Domestic chicken diversity: Origin, distribution, and adaptation. Animal Genetics, 52(4), 385-394. https://doi.org/10.1111/age.13091

Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditi... Read More about Domestic chicken diversity: Origin, distribution, and adaptation.

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.

The wild species genome ancestry of domestic chickens (2020)
Journal Article
Lawal, R. A., Martin, S. H., Vanmechelen, K., Vereijken, A., Silva, P., Al-Atiyat, R. M., …Hanotte, O. (2020). The wild species genome ancestry of domestic chickens. BMC Biology, 18(1), Article 13 (2020). https://doi.org/10.1186/s12915-020-0738-1

BACKGROUND: Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds.The domestic chicken Gallus gallus domesticus is the most common livestock specie... Read More about The wild species genome ancestry of domestic chickens.

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.