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3.
Sci Data ; 9(1): 53, 2022 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-35165296

RESUMO

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. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes.


Assuntos
Galinhas , Genoma , Animais , Galinhas/genética , Etiópia , Polimorfismo de Nucleotídeo Único
4.
BMC Biol ; 20(1): 20, 2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-35039029

RESUMO

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 African admixed cattle, B. indicus mitochondria have not been found on the continent. This discrepancy between the mitochondrial and nuclear genomes has been previously hypothesized to be driven by male-biased introgression of Asian B. indicus into ancestral African B. taurus. Given that this hypothesis mandates extreme demographic assumptions relying on random genetic drift, we propose a novel hypothesis of selection induced by mitonuclear incompatibility and assess these hypotheses with regard to the current genomic status of African admixed cattle. RESULTS: By analyzing 494 mitochondrial and 235 nuclear genome sequences, we first confirmed the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle: the absence of B. indicus mitochondria and the predominant B. indicus autosomal ancestry. We applied approximate Bayesian computation (ABC) to assess the posterior probabilities of two selection hypotheses given this observation. The results of ABC indicated that the model assuming both male-biased B. indicus introgression and selection induced by mitonuclear incompatibility explains the current genomic discrepancy most accurately. Subsequently, we identified selection signatures at autosomal loci interacting with mitochondria that are responsible for integrity of the cellular respiration system. By contrast with B. indicus-enriched genome ancestry of African admixed cattle, local ancestries at these selection signatures were enriched with B. taurus alleles, concurring with the key expectation of selection induced by mitonuclear incompatibility. CONCLUSIONS: Our findings support the current genome status of African admixed cattle as a potential outcome of male-biased B. indicus introgression, where mitonuclear incompatibility exerted selection pressure against B. indicus mitochondria. This study provides a novel perspective on African cattle demography and supports the role of mitonuclear incompatibility in the hybridization of mammalian species.


Assuntos
Cromossomos , Hibridização Genética , Alelos , Animais , Teorema de Bayes , Bovinos/genética , Genótipo , Masculino , Mamíferos
5.
Anim Biotechnol ; : 1-19, 2022 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-35073494

RESUMO

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.

6.
Mol Biol Evol ; 39(2)2022 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-34893856

RESUMO

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, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.


Assuntos
Genoma , Carneiro Doméstico , Animais , Ásia , Europa (Continente) , Variação Genética , Irã (Geográfico) , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Ovinos/genética , Carneiro Doméstico/genética
7.
J Anim Breed Genet ; 139(2): 161-169, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-34520084

RESUMO

Western Baggara cattle breed (WBCB) is an East African zebu inhabiting Sudan, well-known as beef-producing cattle. We investigated herein two phenotypically and geographically distinct populations of this breed, namely Nyalawi and Daeinawi, which are renowned for their unique meat production capabilities and adaptation attributes, with the aim to contribute to our understanding of their maternal genetic diversity and demography dynamics. Genetic polymorphism analysis of the full-length D-loop mtDNA region revealed 44 and 35 polymorphic sites defining 28 and 24 distinct haplotypes in the Nyalawi and the Daeinawi, respectively. Observed genetic diversity is high within the population with a low level of genetic differentiation between populations. Approximate Bayesian computation via the calculation of Bayesian skyline plots and neutrality tests support past expansion with a higher maternal effective population size (Ne ) in Nyalawi compared with the Daeinawi population and a population expansion beginning around 4,500 YBP and 3,500 YBP, respectively, before the arrival of zebu into the continent.


Assuntos
Bovinos , DNA Mitocondrial , Variação Genética , Animais , Teorema de Bayes , Bovinos/genética , DNA Mitocondrial/genética , Haplótipos , Filogenia , Densidade Demográfica , Sudão
8.
Front Genet ; 12: 723360, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34567075

RESUMO

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 opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes.

9.
BMC Genomics ; 22(1): 531, 2021 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-34253178

RESUMO

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 alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. CONCLUSION: For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.


Assuntos
Variações do Número de Cópias de DNA , Genoma , Animais , Bovinos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Fenótipo , Polimorfismo de Nucleotídeo Único
10.
BMC Biol ; 19(1): 118, 2021 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-34130700

RESUMO

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 that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS: We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION: This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.


Assuntos
Galinhas , Domesticação , Animais , Animais Domésticos/genética , Galinhas/genética , Genoma , Genômica , Humanos
11.
Mol Biol Evol ; 38(10): 4268-4285, 2021 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-34021753

RESUMO

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) provides a powerful avenue to identify the main environmental drivers of selection. Here, we applied an integrative approach combining ENM with genome-wide selection signature analyses (XPEHH and Fst) and genotype-environment association (redundancy analysis), with the aim of identifying the genomic signatures of adaptation in African village chickens. By dissecting 34 agro-climatic variables from the ecosystems of 25 Ethiopian village chicken populations, ENM identified six key drivers of environmental challenges: One temperature variable-strongly correlated with elevation, three precipitation variables as proxies for water availability, and two soil/land cover variables as proxies of food availability for foraging chickens. Genome analyses based on whole-genome sequencing (n = 245), identified a few strongly supported genomic regions under selection for environmental challenges related to altitude, temperature, water scarcity, and food availability. These regions harbor several gene clusters including regulatory genes, suggesting a predominantly oligogenic control of environmental adaptation. Few candidate genes detected in relation to heat-stress, indicates likely epigenetic regulation of thermo-tolerance for a domestic species originating from a tropical Asian wild ancestor. These results provide possible explanations for the rapid past adaptation of chickens to diverse African agro-ecologies, while also representing new landmarks for sustainable breeding improvement for climate resilience. We show that the pre-identification of key environmental drivers, followed by genomic investigation, provides a powerful new approach for elucidating adaptation in domestic animals.


Assuntos
Galinhas , Ecossistema , Adaptação Fisiológica/genética , Animais , Galinhas/genética , Epigênese Genética , Genoma , Genômica
12.
Trop Anim Health Prod ; 53(2): 212, 2021 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-33738653

RESUMO

Abergelle, Arado, Begait, Irob, and Raya are important native cattle populations that are well adapted to the harsh natural conditions in Tigray, Ethiopia. However, little is known about their phenotypic characteristics and inter-population variability. Understanding the phenotypic characteristics is the crucial step in an effort of maintaining genetic diversity and conserving important traits for adaptation. A total of 1650 native matured cattle from the five populations were used to investigate the phenotypic characteristics and variability based on 21 qualitative traits and 21 body measurements using uni- and multivariate, and discriminant analysis. All the qualitative traits and body measurements showed highly significant breed difference except the tail base thickness. Values for most of the body measurements were higher in Begait cattle compared to the other cattle populations. The stepwise discriminant analysis extracted eighteen variables for characterizing the female populations and thirteen variables for the male populations. The pair-wise Mahalanobis distance showed the highest morphological distance between Begait and Irob, and the closest distance between Abergelle and Irob cattle populations. High correct assignment to source population was obtained for both sexes of all breeds except Abergelle and Irob. The discriminant function graph discerned each population with no clear distinction between Abergelle and Irob. These results indicate that the five cattle populations under investigation are clustered into four distinct breeds. However, the present phenotypic characterization should be confirmed with molecular genetic diversity investigation to use as a base in their conservation, breeding, and selection strategies.


Assuntos
Fenótipo , Animais , Bovinos/genética , Análise Discriminante , Etiópia , Feminino , Masculino
13.
Genome Biol Evol ; 13(3)2021 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-33501931

RESUMO

Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.


Assuntos
Genômica , Ovinos/genética , Sequenciamento Completo do Genoma , Adaptação Fisiológica/genética , Altitude , Animais , Cruzamento , Etiópia , Genoma , Ruminantes/genética , Seleção Genética
14.
Mol Biol Evol ; 38(3): 838-855, 2021 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-32941615

RESUMO

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.


Assuntos
Adaptação Biológica/genética , Resistência à Doença/genética , Introgressão Genética , Ovinos/genética , Animais , Evolução Biológica , Mudança Climática , Variação Genética , Filogeografia , Pneumonia/imunologia , Ovinos/imunologia
15.
Front Genet ; 11: 543890, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33193617

RESUMO

Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek's Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity [body weight and body condition score (BCS)]. Combined data from the two chicken ecotypes, Horro (n = 384) and Jarso (n = 376), were jointly analyzed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22-0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection.

16.
Nat Genet ; 52(10): 1099-1110, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32989325

RESUMO

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 analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750-1,050 yr ago, which has shaped the genome of today's cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism.


Assuntos
Adaptação Fisiológica/genética , Cruzamento , Genoma/genética , Sequenciamento Completo do Genoma , África , Alelos , Animais , Bovinos , Genótipo , Temperatura Alta/efeitos adversos , Humanos , Mosaicismo , Polimorfismo de Nucleotídeo Único/genética , Reprodução/genética , Taurina/genética
17.
Curr Biol ; 30(20): 4085-4095.e6, 2020 10 19.
Artigo em Inglês | MEDLINE | ID: mdl-32822607

RESUMO

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.


Assuntos
DNA Mitocondrial/genética , Genoma/genética , Polimorfismo de Nucleotídeo Único/genética , Carneiro Doméstico/genética , Cromossomo Y/genética , Animais , Cruzamento , Linhagem da Célula/genética , Mapeamento Cromossômico , Variação Genética/genética , Masculino , Mitocôndrias/genética , Fenótipo , Filogenia , Ovinos , Carneiro Doméstico/classificação , Sequenciamento Completo do Genoma
18.
Genes Genomics ; 42(10): 1169-1178, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32803704

RESUMO

BACKGROUND: Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. OBJECTIVE: The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. METHODS: A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. RESULTS: Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. CONCLUSION: The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations.


Assuntos
Variação Genética/genética , Estudo de Associação Genômica Ampla , Ovinos/genética , Cauda/anatomia & histologia , Animais , Etiópia , Genoma/genética , Genótipo , Humanos , Filogeografia , Polimorfismo de Nucleotídeo Único/genética , Grupos Populacionais/genética , Ovinos/anatomia & histologia
19.
Anim Biotechnol ; : 1-11, 2020 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-32787620

RESUMO

Local chicken populations are a major source of food in the rural areas of Algeria. However, their origin has not been well characterized. The objectives of this study were to assess genetic diversity and maternal origin of domestic chicken from five agro-ecological regions of western Algeria: coastal (CT), inland plains (IP), highlands (HL), mountains (MT) and sahara (SH, including Oasis, Req and Erg regions). A set of 88 mitochondrial DNA (mtDNA) D-loop sequences including the hypervariable region I (HV1) were analyzed. From the 397 bp D-loop sequence, 20 variable sites that defined 13 haplotypes were identified in Algerian domestic chicken. The haplotype and nucleotide diversity were estimated as 0.597 and 0.003, respectively. Phylogenetic and network analyses indicated the presence of two clades or haplogroups (A and E). Only one clade A haplotype was observed exclusively in the population of mountains, while, Clade E haplotypes were found in almost all Algerian chicken with twelve different haplotypes. These findings suggest that Algerian chickens derived from the most ubiquitous haplogroup which have its root in the Indian subcontinent. Our results provide important information about the origin of the North-West African chicken and the historical dispersal of the first chicken populations into African continent.

20.
Sci Data ; 7(1): 224, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32647128

RESUMO

The Infectious Diseases of East African Livestock (IDEAL) project was a longitudinal cohort study of calf health which was conducted in Western Kenya between 2007-2010. A total of 548 East African shorthorn zebu calves were recruited at birth and followed at least every 5 weeks during the first year of life. Comprehensive clinical and epidemiological data, blood and tissue samples were collected at every visit. These samples were screened for over 100 different pathogens or infectious exposures, using a range of diagnostic methods. This manuscript describes this comprehensive dataset and bio-repository, and how to access it through a single online site ( http://data.ctlgh.org/ideal/ ). This provides extensive filtering and searching capabilities. These data are useful to illustrate outcomes of multiple infections on health, investigate patterns of morbidity and mortality due to parasite infections, and to study genotypic determinants of immunity and disease.


Assuntos
Bancos de Espécimes Biológicos , Doenças Transmissíveis/veterinária , Gado , Animais , Bovinos , Bases de Dados Factuais , Quênia , Estudos Longitudinais
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