olivier hanotte | University of Nottingham (original) (raw)

Papers by olivier hanotte

Scientific reports, Jan 26, 2024

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long ar... more 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 commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance. It is important to recognize the value of indigenous livestock populations from various geographic regions. These animals have adapted to their local agro-climatic conditions, making them important genetic resources for conservation efforts. By protecting these populations, we can help preserve their unique genetic traits and ensure the sustainability of our agricultural practices. Native tropical breeds are particularly crucial. As climate change and global warming are forcing many temperate regions to experience tropic-like conditions, such breeds may hold genetic solutions for climate resilience. Nigeria is a tropical lowland country where poultry farming plays a crucial role in the economy and livelihood of local people. About 45% of the Nigerian population is involved in poultry production, mostly small or medium-scale farming, and Nigeria ranks second for its chicken population size (180 M birds) within Africa 1,2. However, despite the importance of poultry farming for the country's economy, over half of its chickens are still raised in extensive backyard farming systems. Moreover, about 80% of the chickens reared in backyard farming in Nigeria are represented by unimproved local breeds 3. Being unimproved, they have poor productivity, but otherwise have very desirable qualities such as hardiness to thrive under harsh tropical environments, the ability to forage for food, the ability to hatch on their own and brood, and considerable tolerance to endemic disease challenges 4. Besides this, their egg and meat products are preferred by local people 5. These local chickens, commonly called Nigerian Indigenous Chickens (NICs), represent important genetic resources for the sustainable development of the poultry programme in Nigeria to cater for future needs arising from climate challenges and consumer demands.

Frontiers in Immunology, Jan 14, 2024

Coccidiosis stands as a protozoan disease of notable economic impact, characterized by an intrace... more 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 emergence of severe lesions and diminishing the efficiency of feed utilization in chickens. MicroRNA (miRNA) are short, non-coding RNA molecules with approximately 21-24 nucleotides long in size that play essential roles in various infectious diseases and inflammatory responses. However, the miRNA's expression patterns and roles in the context of Eimeria maxima infection of chicken intestines remain unclear. miRNA sequencing was employed to assess the miRNA expression profile in chicken jejunum during E. maxima infection. In this study, we analyzed miRNA expression profiles related to the host's immune response in the chicken jejunum during E. maxima infection. At 4 days infection and control (J4I versus J4C), 21 differentially expressed miRNAs in the jejunum were identified, comprising 9 upregulated and 12 downregulated miRNAs. Furthermore, in the jejunum, at 7 days infection and control (J7I versus J7C) groups, a total of 35 significantly differentially expressed miRNAs were observed, with 13 upregulated and 22 downregulated miRNAs. The regulatory networks were constructed between differentially expressed miRNA and mRNAs to offer insight into the interaction mechanisms between chickens and E. maxima coccidian infection. Furthermore, within the comparison group, we obtained 946, 897, and 281 GO terms that exhibited significant enrichment associated with host immunity in the following scenarios, J4I vs. J4C, J7I vs. J7C, and J4I vs. J7I, respectively. The KEGG pathway analysis indicated notable enrichment of differentially expressed miRNAs in the jejunum, particularly in J4I vs. J4C; enriched pathways included metabolic pathways, endocytosis, MAPK signaling pathway, regulation of actin cytoskeleton, and cytokine-cytokine receptor interaction. Moreover, in J7I vs. J7C, the KEGG pathway was significantly enriched, including metabolic pathways, protein processing in the endoplasmic Frontiers in Immunology frontiersin.org 01

16 Minisatellite Analysis in Conservation Genetics TERRY BURKE, OLIVIER HANOTTE, AND IRIS VAN PIJ... more 16 Minisatellite Analysis in Conservation Genetics TERRY BURKE, OLIVIER HANOTTE, AND IRIS VAN PIJLEN A minisatellite ... In: Burke, T., C. Dolf, AJ Jeffreys, and R. Wolff, eds. ... Mus domesticus) MHC locus probe in the red-winged blackbird (Agelaius phoeniceus) (Gibbs et al ...

Genomics, Apr 1, 1991

We report here for the first time the large-scale isolation of hypervariable minisatellite DNA se... more We report here for the first time the large-scale isolation of hypervariable minisatellite DNA sequences from a nonhuman species, the Indian peafowl (Pauo cristatus). A sizeselected genomic DNA fraction, rich in hypervariable minisatellites, was cloned into Charomid 9-36. This library was screened using two multilocus hypervariable probes, 33.6 and 33.15 and also, in a "probe-walking" approach, with five of the peafowl minisatellites initially isolated. Forty-eight positively hybridizing clones were characterized and found to originate from 30 different loci, 18 of which were polymorphic. Five of these variable minisatellite loci were studied further. They all showed Mendelian inheritance. The heterozygosities of these loci were relatively low (range 22-78%) in comparison with those of previously cloned human loci, as expected in view of inbreeding in our semicaptive study population. No new length allele mutations were observed in families and the mean mutation rate per locus is low (cO.004, 95% confidence maximum). These loci were also investigated by cross-species hybridization in related taxa. The ability of the probes to detect hypervariable sequences in other species within the same avian family was found to vary, from those probes that are species-specific to those that are apparently general to the family. We also illustrate the potential usefulness of these probes for paternity analysis in a study of sexual selection, and discuss the general application of specific hypervariable probes in behavioral and evolutionary studies.

Proceedings of the National Academy of Sciences of the United States of America, Jun 12, 2003

Animal Genetics, Jun 1, 1999

The applicability of bovine autosomal microsatellite markers for population genetic studies on Af... more The applicability of bovine autosomal microsatellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per marker was 5. 0 (SE = 0. 2) and the mean heterozygosity per marker was 0. 61 (SE = 0. 03). Considering the overall high level of polymorphism, it was concluded that most bovine microsatellite markers are applicable in African buffalo.

Animal Genetics, Apr 24, 2013

The Green-legged Partridgelike (GP) fowl, an old native Polish breed, is characterised by reseda ... more The Green-legged Partridgelike (GP) fowl, an old native Polish breed, is characterised by reseda green-coloured shanks rather than yellow, white, slate or black commonly observed across most domestic breeds of chicken. Here, we investigate the origin, genetic relationships and structure of the GP fowl using mtDNA D-loop sequencing and genomewide SNP analysis. Genome-wide association analysis between breeds enables us to verify the genetic control of the reseda green shank phenotype, a defining trait for the breed. Two mtDNA D-loop haplogroups and three autosomal genetic backgrounds are revealed. Significant associations of SNPs on chromosomes GGA24 and GGAZ indicate that the reseda green leg phenotype is associated with recessive alleles linked to the W and Id loci. Our results provide new insights into the genetic history of European chicken, indicating an admixed origin of East European traditional breeds of chicken on the continent, as supported by the presence of the reseda green phenotype and the knowledge that the GP fowl as a breed was developed before the advent of commercial stocks.

Genetics, Jul 1, 2006

Historical hybridization events between the two subspecies of cattle, Bos taurus and B. indicus, ... more Historical hybridization events between the two subspecies of cattle, Bos taurus and B. indicus, have occurred in several regions of the world, while other populations have remained nonadmixed. We typed closely linked X chromosome microsatellites in cattle populations with differing histories of admixture from Africa, Europe, the Near East, and India. Haplotype breakdown will occur as admixed populations age, and longer ancestral haplotypes will remain intact in more recently admixed populations compared to older ones. We genotyped male animals from these populations, obtaining unambiguous haplotypes, and measured levels of linkage disequilibrium (LD) and ancestral mosaicism. Extensive LD, likely to be the result of ongoing admixture, was discovered in hybrid cattle populations from the perimeter of the tsetse zone in West Africa. A Bayesian method to assign microsatellite allele ancestry was used to designate the likely origin of each chromosomal segment and assess the relative ages of admixture in the populations. A gradient of the age of admixture in the African continent emerged, where older admixture has produced more fragmented haplotypes in the south, and longer intact haplotypes, indicating more recent hybridization, feature in the northwest.

Animal Genetics, Feb 1, 2006

SummaryMicrosatellite markers are commonly used for population genetic analyses of livestock. How... more SummaryMicrosatellite markers are commonly used for population genetic analyses of livestock. However, up to now, combinations of microsatellite data sets or comparison of population genetic parameters from different studies and breeds has proven difficult. Often different genotyping methods have been employed, preventing standardization of microsatellite allele calling. In other cases different sets of markers have been genotyped, providing differing estimates of population genetic parameters. Here, we address these issues and illustrate a general two‐step regression approach in cattle using three different sets of microsatellite data, to combine population genetics estimates of diversity and admixture. This regression‐based method is independent of the loci genotyped but requires common breeds in the data sets. We show that combining microsatellite data sets can provide new insights on the origin and geographical distribution of genetic diversity and admixture in cattle, which will facilitate global management of this livestock species.

Animal Genetics, Apr 24, 2009

SummaryThe isolation of chicken minisatellites is reported. Two charomid libraries were construct... more SummaryThe isolation of chicken minisatellites is reported. Two charomid libraries were constructed from fractions of size‐selected MboI‐digested genomic DNA. A total of 5985 colonies were screened with the multilocus probes 33.6 and 33.15; 137 positives were obtained (2.35%). A total of 55 clones were tested against four unrelated chickens; 30 revealed variable single locus patterns. More detailed characterization was made of 15 probes, which were tested against four families comprising a total of 53 offspring. Of parent/offspring comparisons 51% were informative for segregation. No mutations were detected. Three minisatellites were linked on the same autosome, implying that these loci may occur in clusters, and one was Z chromosome‐linked. Heterozygosity and allelic variability were measured in 67 individuals to several different strains and breeds. Mean heterozygosity ranged from 50 to 84%. Minisatellite loci appear to be highly variable in the chicken and should provide highly informative markers in intraspecific crosses in genome mapping studies.

Revue Scientifique Et Technique De L Office International Des Epizooties, Apr 1, 2015

Vector-borne diseases in cattle and small ruminants (e.g. trypanosomosis, Rift Valley fever and E... more Vector-borne diseases in cattle and small ruminants (e.g. trypanosomosis, Rift Valley fever and East Coast fever) are associated with major economic losses in tropical countries, and particularly on the African continent. A variety of control strategies (e.g. management, vaccination and/or acaricide treatments) are used to minimise their negative impacts. These strategies are often associated with environmental, technical and/or economic drawbacks. However, several indigenous livestock populations have been reported to show a level of genetic tolerance or resistance to such disease challenges (e.g. trypanotolerant N'Dama cattle and Djallonké sheep). Use of these populations represents a sustainable alternative approach to minimising the negative impact of such infection/infestation on livestock production. This review summarises the current understanding of the genetic control of these adaptations, identifies knowledge gaps and critically examines the possible impacts of genomics approaches to the genetic improvement of tolerance and/or resistance to vector-borne diseases.

Journal of Animal Science, Sep 1, 2016

Frontiers in Genetics

The Tigray region, where we found around eight per cent of the indigenous cattle population of Et... more 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 of the Fertile Crescent and the Indian subcontinent. Here, we used whole genome sequencing data to characterise the genomic diversity, relatedness, and admixture of five cattle populations (Abergelle, Arado, Begait, Erob, and Raya) indigenous to the Tigray region of Ethiopia. We detected 28 to 29 million SNPs and 2.7 to 2.9 million indels in each population, of which 7% of SNPs and 34% of indels were novel. Functional annotation of the variants showed around 0.01% SNPs and 0.22%–0.27% indels in coding regions. Enrichment analysis of genes overlapping missense private SNPs revealed 20 significant GO terms and KEGG pathways that were shared by or specific to breeds. They included important genes associated with morphology (SCN4A, TAS1R2 and...

WIAS Annual Conference 2021: Resilience, Apr 27, 2021

Animal Biotechnology, 2022

Phylogeography plays a major role in understanding micro and macroevolutionary processes dealing ... more 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, demography, and phylogeny for the interpretation of the geographical distribution of lineages. The full mtDNA sequence and W chromosome polymorphisms were exploited to assess the usefulness of two maternally-inherited genetic markers for phylogeographic studies of village chickens. We studied 243 full mtDNA sequences from three countries (Iraq, n = 27; Ethiopia, n = 211; and Saudi Arabia, n = 5) and a 13-kb fragment of the W chromosome from 20 Iraqi and 137 Ethiopian female chickens. The results show a high level of genetic diversity for the mtDNA within and among countries as well as within populations. On the other hand, sequence analysis of the W chromosome shows low genetic diversity both within and among populations. Six full mtDNA haplogroups (A, B, C1, C2, D1, and E1) were observed and 25 distinct W haplotypes. The results support the effectiveness of full mtDNA sequences but not the W chromosome in tracing the maternal historical genome background with, however, weak within a country phylogeographic signal.

Journal of Animal Science, 2016

Nature Communications, Nov 27, 2023

Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral c... more Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.