Animal Genetic Resources, 2012, 50, 13–20. © Food and Agriculture Organization of the United Nations, 2012 doi:10.1017/S2078633612000070 Genetic diversity analysis of the mitochondrial D-loop of Nigerian indigenous sheep B.O. Agaviezor1,2,3, M.A. Adefenwa3,4, S.O. Peters1,3, A. Yakubu5, O.A. Adebambo1, M.O. Ozoje1, C.O.N. Ikeobi1, B.M. Ilori1, M. Wheto1, O.O. Ajayi1, S.A. Amusan1, M. Okpeku6, M. De Donato3 and I.G. Imumorin3 Department of Animal Breeding and Genetics, Federal University of Technology, Abeokuta, Nigeria, Nigeria; 2Department of Animal Science and Fisheries, University of Port Harcourt, Port Harcourt, Nigeria; 3Department of Animal Science, Cornell University, Ithaca, NY 14853, USA; 4Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria; 5Department of Animal Science, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria; 6Department of Livestock Production, Niger Delta University, Amasomma, Bayelsa State, Nigeria 1 Summary Indigenous livestock resources are strategic in the socio-economics of rural agricultural systems to ensure food security in resourcepoor countries. Therefore, better understanding of genetic variation holds the key to future utilization through conservation. We report the first analysis of genetic diversity of Nigerian sheep based on the D-loop region of the Ovis aries mitochondrial genome using 1 179 bases between sites 15 437 and 16 616 base pairs. A sample of 290 animals made up of Balami, West African Dwarf (WAD), Uda and Yankasa breeds were randomly collected from across Nigeria. Ninety-six haplotypes were observed with a high mean haplotype diversity of 0.899 ± 0.148. Gene diversity was highest in Uda (0.921 ± 0.021) and lowest in WAD (0.852 ± 0.061). Population specific FST indices varied from 0.00133 in Uda to 0.00335 in WAD. Yankasa had the highest number of polymorphic sites (201), while the least was in Uda (96). Analysis of molecular variance revealed that 0.23 percent of the variation is found among populations compared with 99.77 percent variation found within populations. The phylogenetic tree indicates that the mitochondrial lineages of these sheep breeds originated from a common source consistent with first divergence of Yankasa followed by WAD, while Balami and Uda remain more closely related. These results suggest that evolutionary divergence of Nigerian sheep breeds based on mitochondrial DNA D-loop sequence may be coincident with geographical distribution in Nigeria and suggest significant interbreeding. This could have implications for managing improvement and conservation strategies and long-term conservation of Nigerian indigenous sheep. Keywords: mitochondrial DNA, genetic distance, genetic diversity, Nigerian sheep Résumé Les ressources des animaux d’élevage indigènes représentent une valeur stratégique dans la socio-économie des systèmes agricoles ruraux qui permettrait de garantir la sécurité alimentaire dans les pays pauvres en ressources. Par conséquent, l’utilisation future de ces ressources par le biais de la conservation dépend d’une meilleure compréhension de la variation génétique. Nous signalons la première analyse de la diversité génétique des moutons nigériens basée sur la région de la boucle D du génome mitochondrial d’Ovis aries en utilisant 1 179 bases entre les sites 15 437 et 16 616 paires de bases. Des échantillons de 290 animaux provenant des races Balami, West African Dwarf, Uda et Yankasa ont été collectés au hasard dans tout le Nigéria. On a observé 96 haplotypes avec une moyenne élevée de diversité d’haplotype de 0,899 ± 0,148. On a relevé la diversité génétique la plus élevée chez les moutons Uda (0,921 ± 0,021) et la plus faible chez les moutons West African Dwarf (0,852 ± 0,061). Les indices spécifiques de population FST variaient entre 0,00133 pour les Uda et 0,00335 pour les West African Dwarf. Les moutons Yankasa présentaient le nombre le plus élevé de sites polymorphiques (201) tandis que le plus bas a été repéré chez les Uda (96). L’analyse de la variance moléculaire a indiqué que 0,23 pour cent de la variation se trouve parmi les populations tandis que 99,7 pour cent se situe au sein des populations. L’arbre phylogénétique indique que les lignées mitochondriales de ces races de moutons proviennent d’une source commune cohérente avec la première divergence des Yankasa suivie par les West African Dwarf, tandis que les races Balami et Uda restent plus étroitement apparentées. Ces résultats semblent indiquer que la divergence évolutive des races de moutons indigènes basée sur la séquence de la boucle D d’ADN mitochondrial pourrait coïncider avec la distribution géographique au Nigéria et suggérer un croisement considérable. Cette conclusion pourrait avoir des retombées dans la gestion des stratégies d’amélioration et de conservation et dans la conservation à long terme des moutons indigènes du Nigéria. Mots-clés: DNA mitochondrial, distance génétique, diversité génétique, moutons nigériens Resumen Los recursos ganaderos autóctonos son de carácter estratégico en los aspectos socioeconómicos de los sistemas agrícolas para garantizar la seguridad alimentaria en los países de escasos recursos. Por lo tanto, conocer mejor la importancia de la variabilidad genética es vital para su futura utilización, por medio de la conservación. Se presenta el primer análisis de la diversidad genética en ovejas de Correspondence to: Dr Ikhide G. Imumorin, Department of Animal Science, Cornell University, 267 Morrison Hall, Ithaca, NY 14853, USA. email: igi2@cornell.edu 13 14 B.O. Agaviezor et al. Nigeria basado en la región de control (D-loop) del Ovis aries del genoma mitocondrial, utilizando 1.179 bases entre las posiciones 15.437 y 16.616 de pares de bases. Una muestra de 290 animales, compuesta por las razas Balami, West African Dwarf (WAD), Uda y Yankasa, fue tomada al azar de toda Nigeria. Se observaron noventa y seis (96) haplotipos, con una alta diversidad media en cuanto a éstos de 0,899 ± 0,148. La diversidad genética fue mayor en la raza Uda (0,921 ± 0,021) y menor en la raza WAD (0,852 ± 0,061). Los índices de población específicos FST variaron de 0.00133 en la raza Uda a 0,00335 en la raza WAD. La raza Yankasa presentó el mayor número de posiciones polimórficas (201), mientras que el menor lo mostró la raza Uda (96). Análisis de la varianza molecular reveló que 0,23% de la variación se encuentra entre las poblaciones, en comparación con el 99,77% de variación que se encuentra dentro de las poblaciones. El árbol filogenético indica que los linajes mitocondriales de las razas ovinas partieron de un origen común en conformidad con la primera divergencia de la raza Yankasa, seguida por WAD, mientras que las razas Balami y Uda se encuentran más estrechamente relacionadas. Estos resultados demuestran que la divergencia evolutiva de las poblaciones ovinas de Nigeria, basados en el ADN mitocondrial de la región control, puede coincidir con la distribución geográfica en Nigeria e indican una tasa importante de cruzamiento entre ellas. Esto podría tener ventajas desde el punto de vista de la gestión de la mejora y las estrategias de conservación y preservación a largo plazo de las ovejas autóctonas de Nigeria. Palabras clave: ADN mitocondrial, distancia genética, diversidad genética, oveja nigeriana Submitted 1 November 2011; accepted 24 January 2012 Introduction Animal genetic resources are defined as animal species that are used, or may be used for the production of food and fibre (FAO, 2007). Livestock currently contribute about 30 percent of agricultural gross domestic product in developing countries, with a projected increase to about 40 percent by 2030. The World Bank has estimated that it will be necessary to increase meat production by about 80 percent between 2000 and 2030 (FAO, 2011). Sheep are very important in the socio-economic lives of the people of Nigeria (Abdullahi, 2002). However, their potential value is not realized because of low productivity resulting from high mortality and poor performance among others. Geographical isolation, natural and artificial selection for physical or productive characters, genetic drift, mutations and interpopulation gene flows have altered gene frequencies over many generations (Pariset et al., 2011), and this could affect fitness and adaptive potentials of animals (Luikart and Allendorf, 1996). The current loss of genetic resources concerns not only the extinction of traditional breeds, but also the loss of genetic diversity within breeds (Taberlet et al., 2011). In terms of biodiversity, conservation and utilization, these genetic resources require further identification and evaluation to assess their potential contribution to food and agricultural production in the future. The initial step in characterization is identification of distinct populations using information on their geographic and ecological isolation, traditional nomenclatures (traditionally recognized populations), phenotypic distinctness and the level of genetic differentiation among the populations (Gizaw et al., 2011). Since the beginning of the 1990s, molecular data have become more relevant to the characterization of genetic diversity (Groeneveld et al., 2010), and the identification of genetically distinct breeds is commonly based on these state-of-the-art techniques (Gizaw et al., 2011). Mitochondrial DNA (mtDNA) diversity is a useful molecular tool in establishing phylogenetic relationships among breeds and at species level (Tanaka et al., 2011; Zhao et al., 2011). According to Ajmone-Marsan and The GLOBALDIV Consortium (2010), studies of mtDNA, microsatellite DNA profiling and Y-chromosomes have revealed many details about the process of domestication, diversity retained by breeds and the relationships between breeds. Although a preliminary study of natural genetic variation among Nigerian sheep breeds using microsatellite markers was reported by Adebambo et al. (2004), the full extent of molecular variation and diversity remain largely unknown, and studies based on other molecular markers capable of unraveling phylogenetic history and development to better understand the genetic structure of the Nigerian sheep population are scarce. As part of efforts to better understand the genetics of Nigerian sheep for improvement and conservation goals, we report the first study undertaken to assess population structure and genetic diversity of Nigerian sheep using D-loop sequence of the ovine mitochondrial genome. Materials and methods Study area and study population This study was carried out using samples collected across all over Nigeria. Nigeria is located in West Africa on the Gulf of Guinea between latitude 10° north of the equator and longitude 8° east of Greenwich Meridian with a total area of 923 768 km2. Nigeria is bounded by Niger, Benin and Cameroon Republics on the North, West and East, respectively (Figure 1). The five agro-ecological zones include Sahel and Sudan Savannah, Guinea Savannah, derived Guinea Savannah and Rainforest/Mangrove swamp. For the purposes of sampling, Sahel and Sudan savannas were combined into Sahelo-Sudan; derived Guinea and Guinea Genetic diversity analysis of Nigerian indigenous sheep Figure 1. Map of Nigeria showing sampled locations. savannas were combined into Guinea savanna and sampling was carried out from three main agro-ecological zones of Sahelo-Sudan Savannah, Guinea Savannah and Rainforest/ Mangrove swamp. Two hundred and ninety sheep were sampled from the three main agro-ecological zones of Nigeria comprising 98 Balami, 43 Uda, 110 Yankasa and 39 West African Dwarf (WAD) breeds. Approximately 5 ml of blood was collected into heparinized tubes from the jugular vein of the sheep, stored on ice before transfer to the laboratory for analysis. DNA extraction, polymerase chain reaction amplification and sequencing DNA was extracted from 50–100 µl of whole blood using the ZymoBeadTM Genomic DNA Kit (Zymo Research Corp. Irvine, CA, USA) according to the manufacturer’s recommendations. Quantification of DNA yield and assessment of quality were done using the Nanodrop ND-100 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The DNA was amplified via polymerase chain reaction (PCR) in a MyCyclerTM Thermal Cycler (Biorad, Hercules, CA, USA) using primers designed from published ovine sequences (Genbank Accession Number AF010406) (Hiendleder et al., 1998): tRNA-proline (5-CAGTGCCTT GCTTTGGTTAAGC-3) and tRNA-phenylalanine (5-CA CCATCAACCC CAAAGCTGAAG-3). The total volume of 20 µl amplification reactions contained 20–50 ng template DNA, 2.0 µl each of forward and reverse primers, and 16 µl nuclease-free water in a BIONEER AccuPower® TLA PCR Premix (containing NTPs, MgCl2 and DNA polymerase) (BIONEER Corporation, Alameda, CA, USA). PCR used the following protocol: initial denaturation at 94°C for 5 min, 35 cycles of amplification at 94°C for 30 s, annealing at 62°C for 30 s, extension at 72°C for 1 min, final extension at 72°C for 5 min and held at 4°C until analysis. Ten microlitres of the PCR product were separated in a 1.5 percent agarose gel prestained with 0.5 µg/ml ethidium bromide. Electrophoresis was carried out at room temperature for 40 min at 100 V using a Bio-Rad Power PacTM electrophoresis apparatus (Biorad). The resulting amplified bands were visualized with UV light and photographed using the AlphalmagerTM 2200 electrophoresis documentation and analysis system (Cell Biosciences, CA, USA), and were scored using GENEMate Quanti-Marker 100 bp DNA ladder (BioExpress, UT, USA). Amplified PCR products were sequenced with the Applied Biosystems Automated 3730 DNA Analyzer (Applied Biosytems, Foster City, CA, USA) using the Big Dye Terminator chemistry and AmpliTaq-FS DNA polymerase. Sequencing reactions used tRNA-proline primer (5-CAGTGCCTTGCTTTGGTTAAGC-3). Statistical analysis Sequence alignment of the 1 179 bp PCR-amplified fragment (after excluding the 75 nt tandem-repeat elements) was done using DNA alignment software (Fluxus Technology, http:// www.fluxus-engineering.com/). A pair-wise distance matrix 15 16 B.O. Agaviezor et al. Table 1. Standard diversity indices for mtDNA analysis of Nigerian sheep breeds. Indices Balami Number of gene copies 98 Number of haplotypes (h) 49 Number of loci 297 Number of polymorphic sites (S) 195 Sum of square frequency 0.0889 Hyplotype diversity (Hd) 0.9205 ± 0.0219 Mismatch observed mean 13.175 Mismatch observed variance 690.468 Parameters of the spatial expansion assuming constant deme size Tau 19.213 Theta 5.784 M 0.425 between mtDNA sequences were computed using the nucleotide p-distance (Nei and Kumar, 2000), and a neighbourjoining (NJ) tree constructed on the basis of these distances using the MEGA 3.0 software (Kumar, Tamura and Nei, 2004). A median joining network (Bandelt, Forster and Rohl, 1999) was drawn from haplotypes using the program Network 4.1.0.9 (www.fluxus-engineering.com). Indices of sequence variation and haplotype structure were calculated using the DnaSP 4.00 program (Rozas et al., 2003) including nucleotide diversity (π), number of haplotypes (nh), haplotype diversity (Hd) and number of polymorphic sites (S). An analysis of molecular variance (AMOVA) was computed to test significant differences in mitochondrial diversity between Nigerian sheep breeds using ARLEQUIN 3.01 (Excoffier, Laval and Schneider, 2005). Results Table 1 shows values for standard diversity indices for the study of mtDNA of the Nigerian sheep. A total of 96 haplotypes were observed among the populations. Haplotypes 2, 3, 9, 12, 13, 14, 15, 16, 17, 18, 22, 23, 25, 31, 34, 36, 37 and 63 were shared among the different populations with haplotypes 2, 9, 12 and 15, common to all the populations. However, haplotype 2 had the highest distribution among the four populations studied (Tables 2 and 3). Number of polymorphic sites varied across the populations with the highest value in Yankasa (201) and the lowest in Uda (96). Gene diversity was high in all the populations. Values ranged from 0.9601 ± 0.0170 in Uda to 0.8522 ± 0.0611 in WAD. A variation in mismatch observed mean was noticed in this study, with WAD having the highest value of 18.214. Uda WAD Yankasa 43 27 297 96 0.0622 0.9601 ± 0.0170 11.218 150.985 39 15 297 190 0.1772 0.8522 ± 0.0611 18.214 2078.648 110 39 297 201 0.1425 0.8654 ± 0.0288 10.764 642.036 0.689 6.267 938.614 0.945 1.481 8.815 0.594 2.288 1166.750 Parameters of spatial expansion assuming constant deme size is shown in Table 1. Tau ranged from 0.594 in Yankasa to 19.213 in Balami. However, Uda had the highest value of 6.267 for Theta, with the lowest value seen in WAD. Higher variation in M was also observed with values ranging from 0.425 in Balami to 9338.613 in Uda. The AMOVA is shown in Table 4. The AMOVA analysis revealed that 0.23 percent of the variation is found among populations compared with 99.77 percent variation found within populations. Population-specific FST indices are presented in Table 5. FST values are very low and range from 0.00133 in Uda to 0.00335 in WAD. The fixation index FST is 0.00226. The estimation of population size change for Nigerian sheep breeds using pair-wise comparison is shown in Figure 2. In all the populations, a sharp variation for both observed and expected pair-wise differences was observed. The fluctuation was highest among Uda. Figure 3 shows the median joining network for the haplotypes observed among Nigerian sheep. The network shows a grouping of the haplotypes into two haplogroups. The unweighted pair group method analysis (UPGMA) tree of Nigerian sheep mtDNA sequences is shown in Figure 4. The tree shows that all the breeds originated from a common source. However, Yankasa diverged first. This was followed by WAD and lastly Balami and Uda, although separated but are more genetically closely related. Discussion Variation among all the standard diversity indices was observed across the four Nigerian sheep breeds studied. Table 2. Haplotypes shared among populations. Uda WAD Yankasa Balami Uda WAD 14 (2, 3, 9, 12, 14, 15, 17, 18, 22, 23, 25, 34, 36, 37) 5 (2, 9, 12, 14, 15) 14 (1, 2, 3, 9, 12, 13, 14, 15, 16, 18, 21, 31, 34, 37) 5 (2, 9, 12, 14, 15) 9 (2, 3, 9, 12, 15, 18, 34, 37) 6 (2, 9, 12, 14, 15, 63) Genetic diversity analysis of Nigerian indigenous sheep Table 3. Distribution of haplotypes among the populations studied. Haplotype 1, 13 2 3 4–8, 10–11, 19–20, 24, 26–30, 32– 33, 35, 38–49 9 12 13 14 15 16 17, 20, 25, 36 18 21 22 34 37 50–62 63 64–72 73–77, 79–89, 91–96 78 90 Balami Uda WAD Yankasa 1 26 1 1 0 7 1 0 0 11 0 0 1 38 2 0 6 5 2 3 4 2 1 4 5 1 1 1 0 0 0 0 0 0 3 4 0 1 3 0 1 2 0 2 2 1 1 0 0 0 0 0 3 2 0 1 2 0 0 0 0 0 0 0 0 1 1 0 0 0 11 3 1 3 5 4 0 4 6 0 2 1 0 1 0 1 3 2 Table 4. AMOVA analysis. Among population Within population Total Df Sum of squares 3 Population Balami Uda WAD Yankasa FST 0.00180 0.00133 0.00335 0.00274 Fixation index FST: 0.00226. The highest number of polymorphic sites in Yankasa could be attributed to the fact that it is the most populous sheep breed in Nigeria spread across different agro-ecological zones of the country (Adebambo et al., 2004). The mismatch distribution analyses and the genetic diversity analyses suggest that these breeds must have undergone relatively recent population expansion (Qing et al., 2009). The values of haplotype and nucleotide diversities observed in this study are a little higher than haplotype diversity of 0.792 ± 0.37 and nucleotide diversity of 0.00392 ± 0.00046 observed by Wang et al. (2006) from analysis of mtDNA variation and matrilineal structure in blue sheep populations of Helan Mountain, China. However, the values of haplotype diversity are comparable to 0.857 ± 0.137 to 1.000 ± 0.052 reported by Sulaiman, Wu and Zhao (2011). Mohammadhashemi et al. (2010) also reported that sequence analysis of the mtDNA from Moghani breed with another Iranian sheep showed high genetic diversity with some Iranian sheep breeds. Pariset et al. (2011) observed that mtDNA analysis showed higher levels of sheep nucleotide diversity in the South-East, which was congruent with the proximity to the Source of variation Table 5. Population specific FST indices. Variance components Percentage of variation 1.543 0.00102 0.23 286 123.900 0.48910 99.77 289 125.443 0.44993 domestication centre. In a related study in goats, Benjelloun et al. (2011) reported very high haplotype diversity obtained for the Moroccan goats, and this, according to the same authors, could have resulted from the capture of a large part of the wild diversity during domestication. The AMOVA showed that 0.23 percent of the genetic variation among Nigerian sheep breeds is attributed to among populations compared with 99.77 percent due to variation within populations. A higher variation within than among Nigerian sheep breeds suggests high levels of femalemediated gene flow (Tserenbataa et al., 2004). More so, the results of pair-wise computations and AMOVA indicates that some breeds are differentiated relative to a random collection of genotypes and reflect differences in the spatial distribution of genetic variation (Wang et al., 2006). Similar to these findings, Pariset et al. (2011) reported that the major mitochondrial variation was distributed within breeds (95.04 percent), while it was lower among regions (0.90 percent) and among breeds within regions (4.06 percent). The genetic differentiation fixation index (FST) among the Nigerian sheep breeds was low. The highest FST value in Nigerian WAD sheep could be the results of its presence only in the southern part of the country. Reduced differentiation could be attributed to shrinkage of grazing area, indiscriminate cross-breeding/intermixing between breeds and lack of appropriate breeding and management policies. Although there are no strict breeding rules, geographical isolation between the investigated sheep from different regions has probably led to the moderate level of differentiation among them since genetic drift and natural selection are two main factors that give rise to genetic differentiation among populations (Qing et al., 2009). The observed FST values indicate significant inbreeding from subdivision of the breeds. The degree of subdivision suggests gene flow between the breeds (Kantanen et al., 1995). If gene flow is greater than one, it could play a uniform action of resisting the action of genetic drift and preventing differentiation between populations (Qing et al., 2009). According to Gizaw et al. (2011), an important characteristic to note in genetic diversity in livestock populations is that the variation within a population is much larger than that between the populations. This is well exemplified in the study of Ethiopian sheep where the diversity between Ethiopian sheep populations accounted for only 4.6 percent of the overall genetic diversity (global FST value = 0.046 ± 17 18 B.O. Agaviezor et al. 0.004), the rest being accounted for by within-population variation. The variation in the number of haplotypes and gene copies analysed contributes to unravelling genetic diversity among Nigerian sheep breeds. Despite the high haplotype diversity observed in Uda, the higher number of polymorphic sites in Yankasa compared with other breeds is likely to have contributed to Yankasa’s adaptation ability. Out of the 96 haplotypes observed in this study, only 5 haplotypes are common to all the breeds with haplotype 2 having the highest frequency. This probably points to the existence of evolutionary relationship among them; and equally suggests evidence linking the four Nigerian sheep breeds to a common ancestor or a small number of founders. In a related study in buffalo, few haplotypes of South Kanara and Toda were found to be quite distinct from the commonly found haplotypes, indicating that these might have been ancestral to all the present-day haplotypes (Kathiravan et al., 2011). Relatively divergent haplotypes within breeds and geographical locations suggests that gene flow has occurred on a regional scale at some time in the recent past and that the breeds have not been subdivided by long-term biogeographic barriers (Luikart and Allendorf, 1996). Similar mean haplotype diversity of 0.945 and mean nucleotide diversity and 0.013 from genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mtDNA analyses further support the results of this study (Cinkulov et al., 2008). In a related study in goats, Vacca et al. (2010) reported that the animals showed a high genetic haplotype diversity, as 35 haplotypes were each represented by a single sequence and only a few haplotypes were shared among the animals, thereby lending credence to the findings of Naderi et al. (2007) that it is common to find haplotypes represented by one individual or shared by only a few subjects, because mtDNA variation is a more frequent component within breeds than between them. The significant differentiation in the haplotype frequencies among Nigerian sheep breeds suggest that little gene flow currently exist among the breeds (Luikart and Allendorf, 1996). Figure 2. Estimation of population size changes for Nigerian sheep breeds. The median joining network separated the 96 haplotypes into two major haplogroups. The UPGMA tree separated the four Nigerian sheep breeds according to their geographical locations and population sizes in the country. Balami and Uda are northern breeds which are also fewer than WAD which is a southern breed compared with Yankasa with a wider geographical spread across the country. Evidence from the phylogenetic tree supports first divergence of Yankasa followed by WAD and later by Uda and Balami. However, Zhao et al. (2011) reported that FS value was −13.17574 (P = 0.00000) for haplogroup A in Chinese large-fat-tailed sheep breeds, which suggested one expansion event in this population’s demographic history. Analysis of mismatch distribution also revealed an almost multi-modal distribution of mtDNA D-loop for haplogroup B. FS value was −6.39666 (P = 0.00000) for haplogroup B, which showed no population expansion and relatively stable population size because of no significant difference from neutrality. Genetic diversity analysis of Nigerian indigenous sheep Figure 3. A median joining network for the haplotypes observed among Nigerian sheep. Circles represent haplotypes and have a size proportional to frequency. Mutational differences are shown on lines. population sizes with a rough grouping of the northern breeds (Balami and Uda) and the southern breeds (WAD and Yankasa). The evolutionary divergence into distinct entities of Nigerian sheep breeds based on mtDNA D-loop sequence appear to closely follow their geographical distribution in Nigeria, and this could have implications for management, improvement and conservation strategies in Nigerian sheep. Figure 4. UPGMA tree of Nigerian sheep mtDNA sequences. The present information could be used to strengthen the monitoring, characterization and conservation of animal genetic resources towards the sustainable rearing of the autochtonuous sheep breeds. However, further studies involving the use of endogenous retroviruses (Chessa et al., 2009) as a new class of genetic markers, combined with existing knowledge from microsatellite (Agaviezor et al. accepted. Adebambo et al., 2004) will help to unravel the history of domestication of Nigerian sheep. Statement of Interest: The authors wish to state that there is no conflict of interest as regards this manuscript. Acknowledgements Financial support from College of Agriculture and Life Sciences, Cornell University through a partnership with University of Agriculture, Abeokuta, Nigeria is gratefully acknowledged. Special thanks to Prof. W. Ron Butler for the opportunity given to the first two authors as visiting graduate students at Cornell University. Conclusions Genetic diversity among Nigerian indigenous sheep breeds is eroding due to indiscriminate cross-breeding/intermixing between breeds, and lack of appropriate breeding and management policies. The highest number of polymorphic loci in Yankasa compared with other breeds suggests wider genetic variation that can be exploited in its improvement. In addition, the four Nigerian sheep breeds studied separated genetically based on their geographical locations and References Abdullahi, M. 2002. 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