Publications in VIVO

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Hanotte, Olivier Principal Scientist - Quantitative Geneticist, ILRI

ILRI

Ethiopia

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selected publications

article
- Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens. Frontiers in Genetics. 11:543890. 2020
- The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. Nature Genetics. 52:1099-+. 2020
- Historical introgression from wild relatives enhanced climatic adaptation and resistance to pneumonia in sheep.. Molecular Biology and Evolution. 2020
- Author Correction: 863 genomes reveal the origin and domestication of chicken.. Cell Research. 30:824-825. 2020
- Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens. bioRxiv. 2020
- Paternal Origins and Migratory Episodes of Domestic Sheep. Current Biology. 30:4085-+. 2020
- Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography.. Genes & Genomics. 42:1169-1178. 2020
- IDEAL, the Infectious Diseases of East African Livestock project open access database and biobank.. Scientific Data. 7:224. 2020
- 863 genomes reveal the origin and domestication of chicken. Cell Research. 30:693-701. 2020
- Reflections on IDEAL: What we have learnt from a unique calf cohort study. Preventive Veterinary Medicine. 181:105062. 2020
- Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nature Communications. 11:2815. 2020
- Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens.. Genetics Selection Evolution. 52:29. 2020
- Genetic diversity and population structure of six ethiopian cattle breeds from different geographical regions using high density single nucleotide polymorphisms. Livestock Science. 234:103979. 2020
- The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa.. BMC Genetics. 21:30. 2020
- Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes.. Genomics. 112:1988-1999. 2020
- The wild species genome ancestry of domestic chickens.. BMC Biology. 18:13-13. 2020
- Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed.. Frontiers in Genetics. 10:1095. 2019
- Genome Diversity and Signatures of Selection for Production and Performance Traits in Dromedary Camels.. Frontiers in Genetics. 10:893. 2019
- The wild species genome ancestry of domestic chickens. bioRxiv. 711366. 2019
- Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle. Frontiers in Genetics. 10:609. 2019
- Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia.. PLOS ONE. 14. 2019
- Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle.. Frontiers in Genetics. 10:442. 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. 20:1-14. 2019
- Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Frontiers in Genetics. 9:699. 2019
- Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia. bioRxiv. 493940. 2018
- Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus. Frontiers in Genetics. 9:627. 2018
- The role of local adaptation in sustainable production of village chickens. NATURE SUSTAINABILITY. 1:574-582. 2018
- Polymorphisms in MC1R and ASIP Genes are Associated with Coat Color Variation in the Arabian Camel.. Journal of Heredity. 109:700-706. 2018
- Whole-genome resequencing of red junglefowl and indigenous village chicken reveal new insights on the genome dynamics of the species. Frontiers in Genetics. 9:264. 2018
- Signatures of positive selection in African Butana and Kenana dairy zebu cattle. PLOS ONE. 13. 2018
- Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance. Animal Science Journal. 88:1889-1901. 2017
- Exploring evidence of positive selection signatures in cattle breeds selected for different traits.. Mammalian Genome. 28:528-541. 2017
- Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu.. Frontiers in Genetics. 8:68-68. 2017
- Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama. BMC Genomics. 18:371. 2017
- The genome landscape of indigenous African cattle. Genome Biology. 18:34-34. 2017
- Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef. BMC Genetics. 18:11-11. 2017
- An integrated surveillance system for zoonotic diseases in western Kenya 2017
- Diversity of LEI0258 microsatellite locus in indigenous Ethiopian chickens 2017
- Seroprevalence of respiratory viral pathogens of indigenous calves in Western Kenya.. Research in Veterinary Science. 108:120-124. 2016
- Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes. Genetics Selection Evolution. 48:74. 2016
- P5004 Identification of signatures of selection and assessing the diversity of East African Shorthorn Zebu mitochondrial DNA.. Journal of Animal Science. 94:117-117. 2016
- Mapping genomic regions associated with resistance to infectious diseases in Ethiopian chicken 2016
- Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary.. Proceedings of the National Academy of Sciences of the United States of America. 113:6707-6712. 2016
- Multi-locus genotyping reveals absence of genetic structure in field populations of the brown ear tick (Rhipicephalus appendiculatus) in Kenya.. Ticks and Tick-borne Diseases. 7:26-35. 2016
- Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics. 16:784-784. 2015
- The epidemiology of tick-borne haemoparasites as determined by the reverse line blot hybridization assay in an intensively studied cohort of calves in western Kenya. Veterinary Parasitology. 210:69-76. 2015
- Identification of Novel Loci Associated with Gastrointestinal Parasite Resistance in a Red Maasai x Dorper Backcross Population. PLOS ONE. 10. 2015
- Co-infections determine patterns of mortality in a population exposed to parasite infection.. Science Advances. 1. 2015
- Variation and covariation in strongyle infection in East African shorthorn zebu calves. Parasitology. 142:499-511. 2015
- Evolving hunting practices in Gabon: lessons for community-based conservation interventions 2015
- From Bacteria to Elephants: effects of land-use legacies on biodiversity and ecosystem processes in the Serengeti-Mara Ecosystem 2015
- Genomics selection in livestock: ILRI?ICARDA perspectives 2015
- Genetic Relationships among Four Saudi Arabian Sheep Populations. Iranian Journal of Applied Animal Science. 4:775-779. 2014
- Infection-interactions in Ethiopian village chickens.. Preventive Veterinary Medicine. 117:358-366. 2014
- Identification of SNP Markers for Resistance to Salmonella and IBDV in Indigenous Ethiopian Chickens 2014
- A longitudinal assessment of the serological response to Theileria parva and other tick-borne parasites from birth to one year in a cohort of indigenous calves in western Kenya. Parasitology. 141:1289-1298. 2014
- Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya. Heredity. 113:297-305. 2014
- The impact of co-infections on the haematological profile of East African Short-horn Zebu calves. Parasitology. 141:374-388. 2014
- Parasite Co-Infections and Their Impact on Survival of Indigenous Cattle. PLOS ONE. 9. 2014
- Review Panel of the Centre Commissioned External Review (CCER) on Livestock Systems Research at the International Centre for Agricultural Research in the Dry Areas (ICARDA) 2014
- Prevalence and molecular characterisation of Eimeria species in Ethiopian village chickens. BMC Veterinary Research. 9:208-208. 2013
- High levels of mitochondrial cytochrome b sequence diversity are present within the Anthus similis complex in sub-Saharan Africa. Ostrich. 84:145-151. 2013
- Mortality in East African shorthorn zebu cattle under one year: predictors of infectious-disease mortality. BMC Veterinary Research. 9:175-175. 2013
- Parasite co-infections show synergistic and antagonistic interactions on growth performance of East African zebu cattle under one year.. Parasitology. 140:1789-1798. 2013
- Hematological profile of East African short-horn zebu calves from birth to 51 weeks of age. Comparative Haematology International. 22:1029-1036. 2013
- Maternal antibody uptake, duration and influence on survival and growth rate in a cohort of indigenous calves in a smallholder farming system in western Kenya.. Veterinary Immunology and Immunopathology. 155:129-134. 2013
- Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl.. PLOS ONE. 8. 2013
- Bluetongue and epizootic haemorrhagic disease virus in local breeds of cattle in Kenya.. Research in Veterinary Science. 94:769-773. 2013
- Signature of artificial selection and ecological landscape on morphological structures of Ethiopian village chickens 2013
- Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers. Molecular Ecology. 22:2683-2697. 2013
- Trypanosomosis: a priority disease in tsetse-challenged areas of Burkina Faso. Tropical Animal Health and Production. 45:497-503. 2013
- Design and descriptive epidemiology of the Infectious Diseases of East African Livestock (IDEAL) project, a longitudinal calf cohort study in western Kenya. BMC Veterinary Research. 9. 2013
- Genetic differentiation of Ethiopian and Nigerian village chicken 2013
- Trypanotolerance in N’Dama x Boran crosses under natural trypanosome challenge: effect of test-year environment, gender, and breed composition. BMC Genetics. 13:87-87. 2012
- Micro- and minisatellite-expressed sequence tag (EST) markers discriminate between populations of Rhipicephalus appendiculatus ☆. Ticks and Tick-borne Diseases. 3:128-136. 2012
- Pastoralists' indigenous selection criteria and other breeding practices of the long-horned Ankole cattle in Uganda.. Tropical Animal Health and Production. 44:557-565. 2012
- Current state of knowledge on indigenous chicken genetic resources of the tropics: Domestication, distribution and documentation of information on the genetic resources. Worlds Poultry Science Journal. 68:11-19. 2012
- Accuracy of pastoralists’ memory‐based kinship assignment of Ankole cattle: a microsatellite DNA analysis. Journal of Animal Breeding and Genetics. 129:30-40. 2012
- Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep. Animal Genetics. 43:63-71. 2012
- Current state of knowledge on phenotypic characteristics of indigenous chickens in the tropics. Worlds Poultry Science Journal. 67:507-516. 2011
- Expression of trypanotolerance in N'Dama x Boran crosses under field challenge in relation to N'Dama genome content. 2011
- Productivity and morphology of Ankole cattle in three livestock production systems in Uganda 2011
- East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis.. Animal Genetics. 42:125-133. 2011
- Genetic diversity and differentiation of Ankole cattle populations in Uganda inferred from microsatellite data. Livestock Science. 135:140-147. 2011
- Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Molecular Phylogenetics and Evolution. 58:374-382. 2011
- Genetic Structure of Hartebeest Populations Straddling a Transition Zone between Morphotypes 2011
- Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection. Proceedings of the National Academy of Sciences of the United States of America. 108:9304-9309. 2011
- Characterization of sheep populations of Kenya using microsatellite markers : implications for conservation and management of indigenous sheep populations. South African Journal of Animal Science. 39:93-96. 2010
- Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding and Genetics. 127:339-347. 2010
- Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequences.. Animal Genetics. 41:548-550. 2010
- Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers.. Animal Genetics. 41:242-252. 2010
- Lack of Phylogeographic Structure in Nigerian Village Chickens Revealed by Mitochondrial DNA D-loop Sequence Analysis. International Journal of Poultry Science. 9:503-507. 2010
- Sheep genetic diversity in Bhutan using microsatellite markers. Animal Science Journal. 81:145-151. 2010
- Genetic diversity and relationship of three native chicken populations from Papua New Guinea using microsatellite analysis 2010
- Geographic and breed distribution patterns of an A/G Polymorphism resent in the Mx gene suggests balanced selection in village chickens 2010
- Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.. BMC Genetics. 10:86-86. 2009
- Integrating Y-Chromosome, Mitochondrial, and Autosomal Data to Analyze the Origin of Pig Breeds. Molecular Biology and Evolution. 26:2061-2072. 2009
- Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus.. BMC Evolutionary Biology. 9:136-136. 2009
- Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.. Science. 324:528-532. 2009
- Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.. Science. 324:528-532. 2009
- Genetic diversity and zebu genes introgression in cattle population along the coastal region of the Bight of Benin. Animal Genetic Resources Information. 44:45-55. 2009
- Contrasting evolution of diversity at two disease-associated chicken genes.. Immunogenetics. 61:303-314. 2009
- Characterization of sheep populations of Kenya using microsatellite markers: Implications for conservation and management of indigenous sheep populations. South African Journal of Animal Science. 39:93-96. 2009
- Delivering systematic information on indigenous farm animal genetic resources of developing countries 2009
- Erratum: Contrasting evolution of diversity at two disease-associated chicken genes (Immunogenetics DOI: 10.1007/s00251-009-0359-x). Immunogenetics. 61:421-422. 2009
- Genetic Diversity and Origin of Gansu Indigenous Sheep Breeds Determined by Mitochondrial DNA D-loop Sequence. Chinese Journal of Animal and Veterinary Sciences. 2009
- Identification and Characterization of a Polymorphic Mono-Nucleotide Microsatellite within 16S rRNA Gene in Chicken Mitochondrial Genome. Philippine Agricultural Scientist. 92:353-361. 2009
- Identification and characterization of a perfect mono-nucleotide microsatellite within 16S rRNA gene in chicken mtDNA genome 2009
- Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proceedings of the National Academy of Sciences of the United States of America. 106:18644-18649. 2009
- Mitochondrial DNA origin of indigenous malagasy chicken.. Annals of the New York Academy of Sciences. 1149:77-79. 2008
- Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region.. Genetics Selection Evolution. 40:467-490. 2008
- CONSERVATION PRIORITIES FOR ETHIOPIAN SHEEP BREEDS COMBINING THREAT STATUS BREED MERITS AND CONTRIBUTIONS TO GENETIC DIVERSITY. Genetics Selection Evolution. 40:433-447. 2008
- Indigenous sheep resources of Ethiopia: types, production systems and farmers preferences. Animal Genetic Resources Information. 43:25-39. 2008
- Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping. BMC Genomics. 9:129-129. 2008
- Individual-breed assignments in caprine populations using microsatellite DNA analysis. Small Ruminant Research. 75:154-161. 2008
- Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity. Genetics Selection Evolution. 40:433-447. 2008
- Extent and implications of incorrect offspring-sire relationships in pastoral production system in Kajiado District, Kenya 2008
- Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region. Genetics Selection Evolution. 40:467-490. 2008
- Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proceedings of the National Academy of Sciences of the United States of America. 105:10308-10313. 2008
- Reply to Storey et al.: More DNA and dating studies needed for ancient El Arenal-1 chickens. Proceedings of the National Academy of Sciences of the United States of America. 105:E100-E100. 2008
- Understanding the yak pastoralism in Central Asian Highlands: Mitochondrial DNA evidence for origin, domestication and dispersal of domestic yak 2008
- Population structure, genetic variation and morphological diversity in indigenous sheep of Ethiopia.. Animal Genetics. 38:621-628. 2007
- Genetic relationships among Kenyan and other East African indigenous chickens. Animal Genetics. 38:485-490. 2007
- Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle. Animal Genetics. 38:595-600. 2007
- Cytokine mRNA profiling of peripheral blood mononuclear cells from trypanotolerant and trypanosusceptible cattle infected with Trypanosoma congolense. Physiological Genomics. 28:53-61. 2006
- Globally dispersed Y chromosomal haplotypes in wild and domestic sheep.. Animal Genetics. 37:444-453. 2006
- Linkage disequilibrium between alleles at highly polymorphic mini- and micro-satellite loci of Theileria parva isolated from cattle in three regions of Kenya. International Journal for Parasitology. 36:937-946. 2006
- Combination of multiple microsatellite data sets to investigate genetic diversity and admixture of domestic cattle.. Animal Genetics. 37:1-9. 2006
- Assessing the relative ages of admixture in the bovine hybrid zones of Africa and the Near East using X chromosome haplotype mosaicism. Genetics. 173:1503-1510. 2006
- Microsatellite DNA polymorphism of the Long Horned Ankole cattle in Uganda 2006
- The genetic diversity of trans-Caucasian native sheep breeds. Asian-australasian Journal of Animal Sciences. 19:943-952. 2006
- High differentiation among populations of the woody legume Sesbania sesban in sub-Saharan Africa: Implications for conservation and cultivation during germplasm introduction into agroforestry systems. Forest Ecology and Management. 210:225-238. 2005
- Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics. Veterinary Immunology and Immunopathology. 105:247-258. 2005
- Genetic diversity and differentiation of Mongolian and Russian yak populations.. Journal of Animal Breeding and Genetics. 122:117-126. 2005
- Genomics and breeding for highly productive and disease resistance livestock in the tropics 2005
- Genetic diversity and relationship of domestic Bactrian camels (Camelus bactrianus) in China and Mongolia. JOURNAL OF CAMEL PRACTICE AND RESEARCH. 11:97-99. 2004
- Targeted generation of 16 sequence-tagged sites for bovine chromosome region 5q21-q25 by microdissection.. Chromosome Research. 12:309-315. 2004
- Population parameters for traits defining trypanotolerance in an F2 cross of N'Dama and Boran cattle. Livestock Production Science. 84:219-230. 2003
- Weitzman's Approach and Conservation of Breed Diversity: an Application to African Cattle Breeds. Conservation Biology. 17:1299-1311. 2003
- An approach to the optimal allocation of conservation funds to minimize loss of genetic diversity between livestock breeds. Ecological Economics. 45:377-392. 2003
- Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N’Dama and susceptible East African Boran cattle. Proceedings of the National Academy of Sciences of the United States of America. 100:7443-7448. 2003
- Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification. Animal Genetics. 34:26-32. 2003
- Genetic diversity of indigenous cattle populations in Bhutan: Implications for conservation 2003
- Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites.. Heredity. 90:10-16. 2003
- Analysis of genetic Diversity and relationships of Tanzania local goat populations using microsatellite DNA markers. Tanzania Journal of Agricultural Sciences. 5:29-38. 2002
- African pastoralism: genetic imprints of origins and migrations.. Science. 296:336-339. 2002
- High frequency of polyandry in a lek mating system. BEHAVIORAL ECOLOGY. 13:209-215. 2002
- Identification of two polymorphic microsatellite repeats on a bovine TNFA-containing BAC clone.. Animal Genetics. 32:105-106. 2001
- Zebu cattle of Kenya: Uses, performance, farmer preferences, measures of genetic diversity and options for improved use 2001
- Interleukin-12 p35 encoding gene of cattle and sheep harbours a polymorphic T stretch in intron 4.. Animal Genetics. 31:283-285. 2000
- Geographic and breed distribution of an Msp I PCR-RFLP in the bovine growth hormone (bGH) gene.. Animal Genetics. 31:210-213. 2000
- Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-Saharan African cattle breeds.. Molecular Ecology. 9:387-396. 2000
- Linkage mapping of the bovine lysosomal alpha-mannosidase (MANB) gene.. Animal Genetics. 30:227-228. 1999
- Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer). Animal Genetics. 30:214-220. 1999
- DNA markers for forage and livestock improvement 1999
- Establishment of bovine chromosome region specific high resolution maps using microdissection.. Animal Biotechnology. 10:113-118. 1999
- Radiation hybrid maps of candidate trypanotolerance chromosomal regions in cattle. ARCHIV FUR TIERZUCHT-ARCHIVES OF ANIMAL BREEDING. 42:123-125. 1999
- Radiation hybrid maps of candidate trypanotolerance regions in cattle 1999
- Resistance to trypanosomosis: of markers, genes and mechanisms. ARCHIV FUR TIERZUCHT-ARCHIVES OF ANIMAL BREEDING. 42:36-41. 1999
- Satellite DNA polymorphisms and AFLP correlate with Bos indicus-taurus hybridization. Animal Genetics. 30:265-273. 1999
- A polymorphic Y chromosome microsatellite locus in cattle. Animal Genetics. 28:318-319. 1997
dataset
document
editorial article
- Variation in chicken populations may affect the enzymatic activity of lysozyme.. Animal Genetics. 41:213-217. 2010
- Time to Tap Africa's Livestock Genomes. Science. 328:1640-1641. 2010
- Application of New World Camelidae microsatellite primers for amplification of polymorphic loci in Old World camelids. Animal Genetics. 31:404-406. 2000
review
- African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World. Asian-australasian Journal of Animal Sciences. 911-921. 2015
- The History of African Village Chickens: an Archaeological and Molecular Perspective. African Archaeological Review. 97-114. 2013