African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

Mwai, Okeyo,Hanotte, Olivier,Kwon, Young-Jun,Cho, Seoae Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.7

At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.

Genetic Diversity of Indigenous Cattle Populations in Bhutan: Implications for Conservation

Dorji, T.,Hanotte, O.,Arbenz, M.,Rege, J.E.O.,Roder, W. Asian Australasian Association of Animal Productio 2003 Animal Bioscience Vol.16 No.7

The Genetic diversity and relationship of native Siri (Bos indicus) cattle populations of Bhutan were evaluated using 20 microsatellite markers. A total of 120 Siri cattle were sampled and were grouped into four populations according to their geographical locations which were named Siri West, Siri South, Siri Central and Siri East cattle. For each, 30 individuals were sampled. In addition, 30 samples each of Indian Jaba (B. indicus), Tibetan Goleng (B. taurus), Nepal Hill cattle (B. indicus), Holstein Friesian (B.taurus) and Mithun (B. frontalis) were typed. The mean number of alleles per loci (MNA) and observed heterozygosity (Ho) were high in the Siri populations ($MNA=7.2{\pm}0.3$ to $8.9{\pm}0.5$ and $Ho=0.67{\pm}0.04$ to $0.73{\pm}0.03$). The smallest coefficient of genetic differentiation and genetic distance ($F_{ST}=0.015$ and $D_A=0.073$) were obtained between Siri West and Siri Central populations. Siri East population is genetically distinct from the other Siri populations being close to the Indian Jaba ($F_{ST}=0.024$ and $D_A=0.084$). A high bootstrap value of 96% supported the close relationship of Siri South, Siri Central and Siri West, while the relationship between Siri East and Jaba was also supported by a high bootstrap value (82%). Data from principal component analysis and individual assignment test were in concordance with the inference from genetic distance and differentiation. In conclusion we identified two separate Siri cattle populations in Bhutan at the genetic level. One population included Siri cattle sampled from the West, Central and South of the country and the other Siri cattle was sampled from the East of the country. We suggest that Siri cattle conservation program in Bhutan should focus on the former population as it has received less genetic influence from other cattle breeds.

- Invited Review - African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

Okeyo Mwai,Olivier Hanotte,권영준,조서애 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.7

At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.

Genetic Characterization of Indigenous Goats of Sub-saharan Africa Using Microsatellite DNA Markers

Chenyambuga, S.W.,Hanotte, O.,Hirbo, J.,Watts, P.C.,Kemp, S.J.,Kifaro, G.C.,Gwakisa, P.S.,Petersen, P.H.,Rege, J.E.O. Asian Australasian Association of Animal Productio 2004 Animal Bioscience Vol.17 No.4

Genetic diversity of sub-Saharan African goats was assessed using 19 microsatellite markers. Breeds were sampled from eastern Africa (Maasai, Kigezi, Mubende, North West Highland, Arsi-Bale), southern Africa (Ndebele, Pafuri) and West Africa (West African Dwarf, Maure, Djallonke). European breeds (Grisons Striped, Toggenburg), Asian breeds (Mongolian Cashmere, Bandipur) and a Middle East breed (Arab) were also included. The mean number of alleles per locus and average gene diversity ranged from 5.26$\pm$0.464 (Djallonke) to 7.05$\pm$0.516 (Mubende) and from 0.542$\pm$0.036 (Pafuri) to 0.672$\pm$0.031 (Ndebele), respectively. The between breeds variation evaluated using $$G_{ST}$$ and $\theta$ were found to account for 14.6% ($\theta$) and 15.7% ($$G_{ST}$$) of the total genetic variation. The $D_{A}$ measure of genetic distance between pairs of breeds indicated that the largest genetic distance was between Pafuri and Djallonke while the lowest genetic distance was between Arsi-Bale and North West Highland. A neighbour-joining tree of breed relationships revealed that the breeds were grouped according to their geographic origins. Principal component analysis supported the grouping of the breeds according to their geographic origins. It was concluded that the relationships of sub-Saharan African goat breeds were according to their geographical locations implying that the goats of eastern Africa, West Africa and southern Africa are genetically distinct. Within each sub-region, goat populations could be differentiated according to morphological characteristics.

The Genetic Diversity of Trans-caucasian Native Sheep Breeds

Hirbo, Jibril,Muigai, Anne,Naqvi, A.N.,Rege, E.D.,Hanotte, Olivier Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.7

The genetic variation in 10 indigenous Caucasian sheep breeds was studied with 14 micro-satellite loci in order to determine the genetic diversity among and between the breeds. Five breeds from Asia, five breeds from Europe and one breed from Africa, were included in order to study any relationships or influences they may have with the Caucasian sheep analyzed. A Karakul population from Uzbekistan was included in the study to see whether there was any Central Asian influence. All the 14 loci were found to be polymorphic in all the breeds, with the exception of ILST0056, which was monomorphic in Imeretian. A total of 231 alleles were generated from all the 688 individuals of the sheep analyzed. The mean number of alleles (MNA) at each locus was 16.5. The total number of alleles detected in all samples ranged from 13 in several loci to 23 in OarJMP029. Out of total 308 Hardy-Weinberg Equilibrium (HWE) tests, 85 gave significant results. After Bonferroni correction for multiple tests, 30 comparisons still remained significant to the experimental levels. The Gala population was the most diverse and Imeretian the least diverse with a MNA of 8.50 and 5.51, respectively. Gene diversity estimates exhibited the same trend and ranged from 0.803 in Gala and 0.623 in Imeretian, but generally there is higher diversity among the Caucasian breeds in comparison to other eference breeds. The closest breeds were Tushin and Bozakh with Da of 0.113 and most distant breeds were $Djallonk{\acute{e}}$ and North Rondalsy with Da of 0.445. Principal Component (PC) analyses were done. PC1 described 14% of the differences. PC2, which described 13% of the differences, further separated the Caucasian breeds from Asian breeds except Karakul and Awasi, and the two British breeds. PC3 described 10% of the differences, allowing better differentiation of the Caucasian breeds. A moderate degree of reliability was observed for individual-breed assignment from the 14 loci using different approaches among which the Bayesian method proved to be the most efficient. About 72% of individuals analyzed were correctly assigned to their respective breeds.

Exploring evidence of positive selection signatures in cattle breeds selected for different traits

Taye, M.,Lee, W.,Jeon, S.,Yoon, J.,Dessie, T.,Hanotte, O.,Mwai, O. A.,Kemp, S.,Cho, S.,Oh, S. J. Springer Science + Business Media 2017 Mammalian genome Vol.28 No.11

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

Kumar, Himansu,Park, Woncheoul,Lim, Dajeong,Srikanth, Krishnamoorthy,Kim, Jun-Mo,Jia, Xin-Zheng,Han, Jian-Lin,Hanotte, Olivier,Park, Jong-Eun,Oyola, Samuel O. Elsevier 2020 Genomics Vol.112 No.2

<P><B>Abstract</B></P> <P>We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by <I>Bacteroidetes</I> and <I>Firmicutes.</I> We identified 2210 common genes in the two groups. LEfSe showed that the distribution of <I>Coprobacter, Geobacter, Cronobacter, Alloprevotella,</I> and <I>Dysgonomonas</I> were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microbial comparison of scavenging chicken's cecum content between high land and low land region of Ethiopia. </LI> <LI> Differential functional annotations of identified microbiota from both regions. </LI> <LI> Antibiotic resistant genes identification and their differential abundance. </LI> </UL> </P>

Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography

Agraw Amane,Gurja Belay,Yao Nasser,Martina Kyalo,Tadelle Dessie,Adebabay Kebede,Tesfaye Getachew,Jean‑Baka Domelevo Entfellner,Zewdu Edea,Olivier Hanotte,Getinet Mekuriaw Tarekegn 한국유전학회 2020 Genes & Genomics Vol.42 No.10

Background Ethiopian sheep living in diferent 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 ArsiBale 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

Integrating Y-Chromosome, Mitochondrial, and Autosomal Data to Analyze the Origin of Pig Breeds

Ramirez, O.,Ojeda, A.,Tomas, A.,Gallardo, D.,Huang, L.S.,Folch, J.M.,Clop, A.,Sanchez, A.,Badaoui, B.,Hanotte, O.,Galman-Omitogun, O.,Makuza, S.M.,Soto, H.,Cadillo, J.,Kelly, L.,Cho, I.C.,Yeghoyan, S. Oxford University Press 2009 Molecular biology and evolution Vol.26 No.9

<P>We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making it difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. Although West African pigs from Nigeria and Benin exclusively harbored European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favored the introduction of Far Eastern breeds into this continent.</P>