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R esearch
(Published online:
18-08-2015)
9.
Genetic diversity and phylogenetic relationships in local cattle
breeds of Senegal based on autosomal microsatellite markers
-
Ndèye
Penda Ndiaye, Adama Sow, Guiguigbaza-Kossigan Dayo, Saliou Ndiaye,
Germain Jerôme Sawadogo and Mbacké Sembène
Veterinary World, 8(8): 994-1005
doi:
10.14202/vetworld.2015.994-1005
Ndèye Penda Ndiaye:
Department of Animal Biology, FST (UCAD), Dakar Fann-PO 5005,
Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar
Fann-PO 5077, Senegal;
ndeye1.ndiaye@ucad.edu.sn
Adama Sow:
Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar
Fann-PO 5077, Senegal;
wosamada@yahoo.fr
Guiguigbaza-Kossigan Dayo:
CIRDES,
Bobo Dioulasso 01-PO 454, Burkina Faso;
charlesdayo@yahoo.fr
Saliou Ndiaye:
ENSA,
University of Thiès, Thiès RP-PO A 296, Senegal;
drsaliou@gmail.com
Germain Jerôme Sawadogo:
Laboratory of Endocrinology and Radio-immunology, EISMV, Dakar
Fann-PO 5077, Senegal;
gemgemswadogo@yahoo.fr
Mbacké Sembène: Department of Animal
Biology, FST (UCAD), Dakar Fann-PO 5005, Laboratory CBGP, IRD,
Dakar Bel Air- PO 1386, Senegal;
mbacke.sembene@ird.fr
Received:
27-03-2015, Revised: 09-07-2015, Accepted: 20-07-2015, Published
online: 18-08-2015
Corresponding author:
Ndèye
Penda Ndiaye, e-mail: ndeye1.ndiaye@ucad.edu.sn
Citation:
Ndiaye
NP, Sow A, Dayo GK, Ndiaye S, Sawadogo GJ, Sembène M (2015)
Genetic diversity and phylogenetic relationships in local cattle
breeds of Senegal based on autosomal microsatellite markers,
Veterinary World 8(8): 994-1005.
Abstract
Aim: In Senegal,
uncontrolled cross-breeding of cattle breeds and changes in
production systems are assumed to lead to an increase of gene flow
between populations. This might constitute a relevant threat to
livestock improvement. Therewith, this study was carried out to
assess the current genetic diversity and the phylogenetic
relationships of the four native Senegalese cattle breeds (Gobra
zebu, Maure zebu, Djakoré, and N’Dama).
Methods: Genomic DNA was isolated from blood samples of 120
unrelated animals collected from three agro-ecological areas of
Senegal according to their phenotypic traits. Genotyping was done
using 11 specific highly polymorphic microsatellite makers
recommended by Food and Agriculture Organization. The basic
measures of genetic variation and phylogenetic trees were computed
using bioinformatics’ software.
Results: A total of 115 alleles were identified with a number
of alleles (Na) at one locus ranging from 6 to 16. All loci were
polymorphic with a mean polymorphic information content of 0.76.
The mean allelic richness (Rs) lay within the narrow range of 5.14
in N’Dama taurine to 6.10 in Gobra zebu. While, the expected
heterozygosity (H E)
per breed was high in general with an overall mean of 0.76±0.04.
Generally, the heterozygote deficiency (FIS)
of 0.073±0.026 was relatively due to inbreeding among these cattle
breeds or the occurrence of population substructure. The high
values of allelic and gene diversity showed that Senegalese native
cattle breeds represented an important reservoir of genetic
variation. The genetic distances and clustering trees concluded
that the N’Dama cattle were most distinct among the investigated
cattle populations. So, the principal component analyses showed
qualitatively that there was an intensive genetic admixture
between the Gobra zebu and Maure zebu breeds.
Conclusions: The broad genetic diversity in Senegalese cattle
breeds will allow for greater opportunities for improvement of
productivity and adaptation relative to global changes. For the
development of sustainable breeding and crossbreeding programs of
Senegalese local breeds, effective management is needed towards
genetic selection and transhumance to ensure their long-term
survival.
Keywords: cattle, genetic diversity, microsatellite markers,
phylogenetic analysis, Senegal.
References
|
1. Gueye, M. (2011). The future of the African livestock:
salvation by the value chain. SOS Faim, défis sud., 98 :
26-28. |
|
|
|
2. Diawara, I. (1984). Evolution of cattle farming in the
sylvo-pastoral area of Senegal. Thesis of Veterinary Medicine.
Dakar: EISMV, p 103. |
|
|
|
3. Cissé, M. (1992). Current situation of dairy production in
Senegal. Dakar : LNERV, p13. |
|
|
|
4. Broutin, C., Sokona, K., Tandia, A., Ba, M. (2000).
Business landscape and environment of milk spinneret in
Senegal: Study of spinneret. Dakar: GRET and Network TPA, p
56. |
|
|
5. Courtin, F.S.L., Rouamba, J., Jammoneau, V., Gouro, A. and
Solano, P. (2009). Population growth and global warming:
Impacts on tsetse and trypanosomiasis in West Africa.
Parasite, 16: 3-10.
http://dx.doi.org/10.1051/parasite/2009161003
PMid:19353946 |
|
|
6. Touré, S.M. (1977). Trypanotolerance: Review of knowledge.
Rev. Elev. Méd. Vét. Pays Trop., 30: 157-174.
PMid:337422 |
|
|
7. Lhoste, P.H. (1978). The West African taurine breeds:
situation and conservation Communication to Study Day of
Ethnozootechnie (ORSTOM), May 1978. Zootechnical Research
Center. Côte d'Ivoire: INRA, 26 : 126-128.
PMCid:PMC393075 |
|
|
8. Chandler, R.L.J. (1958). Studies on the tolerance N'Dama
cattle to trypanosomiasis. J. Comp. Pathol., 68:253.
http://dx.doi.org/10.1016/S0368-1742(58)80025-9 |
|
|
|
9. Meyer, C., ed. sc. (2013). Dictionary of Animal Science.
[Online]. Montpellier, France, CIRAD. Available from:
http://www.dico-sciences-animales.cirad.fr. Accessed on
03-12-2013. |
|
|
|
10. Dia, D., Broutin, C., Duteurtre, G. (2009). The systems of
milk collection in West Africa: failure or hope? Grain de
Sel., 46-47: 18-19. |
|
|
|
11. FAO. (2012). Transhumance - Cross-border in West Africa:
Proposal for a plan of action. FAO report, p 146. |
|
|
|
12. Ndiaye, N.P., Sow, A., Sawadogo, G.J. and Sembène, M.
(2012). Biochemical and genetic identification of Senegalese
cattle breeds (Artiodactyla: Bovidae). E3 J. Biotechnol.
Pharm. Res., 3: 149-160. |
|
|
|
13. FAO. (2011). Molecular Genetic Characterization of Animal
Genetic Resources. FAO Animal Production and Health
Guidelines. No. 9. Rome. p85. |
|
|
14. Boettcher, P.J., Hoffmann, I., Baumung, R., Drucker, A.G.,
McManus, C., Berg, P., Stella, A., Nilsen, L.B., Moran, D.,
Naves, M. and Thompson, M.C. (2015). Genetics resources and
genomics for adaptation of livestock to climate change. Front.
Genet., doi: 10.3389/fgene.2014.00461.
http://dx.doi.org/10.3389/fgene.2014.00461 |
|
|
15. MacHugh, D.E., Shriver, M.D., Loftus, R.T., Cunningham,
P., Bradley, D.G. (1997). Microsatellites DNA Variation and
the Evolution, Domestication and Phylogeography of Taurine and
Zebu cattle (Bos taurus and Bos indicus). Genetics, 146:
1071-1086.
PMid:9215909 PMCid:PMC1208036 |
|
|
16. Hanotte, O., Tawah, C.L, Bradley, D.G., Okomo, M., Verjee,
Y. and Ochieng, J., and Rege, J.E. (2000). Geographic
distribution and frequency of a taurine Bos Taurus and an
indicine Bos indicus Y specific allele amongst sub-Saharan
African cattle breeds. Mol. Ecol., 9: 387-396.
http://dx.doi.org/10.1046/j.1365-294x.2000.00858.x
PMid:10736042 |
|
|
17. Freeman, A.R., Meghen, C.M., MacHugh, D.E., Loftus, R.T.,
Achukwi, M.D., Bado, A., Sauveroche, B. and Bradley, D.G.
(2004). Admixture and diversity in West African cattle
populations. Mol. Ecol., 13: 3477-3487.
http://dx.doi.org/10.1111/j.1365-294X.2004.02311.x
PMid:15488005 |
|
|
18. Oosterhout, C.V., William, F.H., Wills, D.P. and Shipley,
P. (2004). Program Note: Microchecker: Softaware for
identififying and correcting genotyping errors in
microsatellite data. Mol. Ecol. Notes., 4: 535-538.
http://dx.doi.org/10.1111/j.1471-8286.2004.00684.x |
|
|
|
19. Nei, M. (1978). Estimation of average heterozygosity and
genetic distance from a small number of individuals. Genetics,
89: 853-590. |
|
|
|
20. Nei, M. (1987). Molecular Evolutionnary Genetics. Columbia
University Press, New York. p506. |
|
|
21. Weir, C.A. and Cockerham, C.C. (1984). Estimating
F-statistics for the analysis of population structure.
Evolution, 38: 1358-1370.
http://dx.doi.org/10.2307/2408641 |
|
|
|
22. Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N.,
Bonhomme, F. (2004). GENETIX 4.05, Software under Windows TM
for population genetics. Laboratory of Genome, Populations,
Interactions, CNRS UMR 5171, University of Montpellier II,
Montpellier, France. Available from:
http://www.Kimura.univ-montp2.fr/genetix/constr.htm#download.
Accessed on 14-08-2014. |
|
|
|
23. Goudet, J. (2002). FSTAT, a program to estimate and test
gene diversities and fixation indices (version 2.9.3.2).
Available from: http://www.unil.ch/izea/softwares/fstat.html.
Updated from Goudet (1995). Accessed on 14-08-2014. |
|
|
24. El-Mousadik, A. and Petit, R.J. (1996). High level of
genetic differentiation for allelic richness among populations
of the argan tree [Argania spinosa (L.) Skeels] endemic to
Morocco. Theor. Appl. Genet., 92: 832-839.
http://dx.doi.org/10.1007/BF00221895
PMid:24166548 |
|
|
25. Peakall, R. and Smouse, P.E. (2012). GenAlEx 6.5: Genetic
analysis in Excel. Population genetic software for teaching
and research – An update. Bioinformatics, 28: 2537-2539.
http://dx.doi.org/10.1093/bioinformatics/bts460
PMid:22820204 PMCid:PMC3463245 |
|
|
26. Botstein, D., White, R.L., Skolnick, M., and Davies, R.W.
(1980). Construction of a genetic linkage map in man using
restriction fragment length polymorphisms. Am. J. Human.
Genet., 32:314-331.
PMid:6247908 PMCid:PMC1686077 |
|
|
27. Kalinnowski, S.T., Taper, M.L., and Marshall, T.C. (2007).
Revising how the computer program CERVUS accommodates
genotyping error increases success in paternity assignment.
Mol. Ecol., 16: 1099-1106.
http://dx.doi.org/10.1111/j.1365-294X.2007.03089.x
PMid:17305863 |
|
|
|
28. SAS (Statistical Analysis System) Institute Inc. STATVIEW
version 5.0. (1998). Available from:
http://www.statview.software.informer.com/5.0/. Accessed on
11-07-2014. |
|
|
29. Rousset, F. (2008). GENEPOP'007: A complete
re-implementation of the GENEPOP software for windows and
Linux. Mol. Ecol. Res., 8: 103-106.
http://dx.doi.org/10.1111/j.1471-8286.2007.01931.x
PMid:21585727 |
|
|
30. Nei, M., Tadjima, F. and Tateno, Y. (1983). Accuracy of
estimated phylogenetic trees from molecular data. II. Gene
frequency data. J. Mol. Evol., 19: 153-170.
http://dx.doi.org/10.1007/BF02300753
PMid:6571220 |
|
|
|
31. Sneath, P.H.A. and Sokal, R.R. (1973). Numerical Taxonomy:
The Principles and Practice of Numerical Classification.
Feeman, San Francisco, USA. p573. |
|
|
32. Cavalli-Sforza L.L. and Edwards, A.W. (1967). Phylogenetic
analysis: Models and estimation procedures. Evolution, 21:
550-570.
http://dx.doi.org/10.2307/2406616 |
|
|
33. Nguyen, T.T., Genini, S., Bui, L.C., Veogeli, P.,
Stranzinger, G., Renard, J.P., Maillard, J.C. and Nguyen, B.X.
(2007). Genomic conservation of cattle microsatellite loci in
wild gaur (Bos gaurus) and current genetics status of this
species in Vietnam. BMC Genet., 8:77.
http://dx.doi.org/10.1186/1471-2156-8-77
PMid:17986322 PMCid:PMC2190770 |
|
|
|
34. Langella, O. (1999). POPULATIONS version 1.2.28.
Population genetic software (individuals or populations
distances, phylogenetic trees). CNRS, France, Available from:
http://www.pge.cnrs-gif.fr. Accessed on 29-09-2014. |
|
|
|
35. Rambaut, A. (2014). Fig Tree version 1. 4. 2. Available
from: http: //www.tree.bio.ed.ac.uk/. Accessed on 29-09-2014. |
|
|
36. Dayo, G.K., Thevenon, S., Berthier, D., Moazami-Goudarzi,
K., Denis, C., Cuny, G., Eggen, A. and Gautier, M. (2009).
Detection of selection signatures within candidate regions
underlying trypanotolerance in outbred cattle populations.
Mol. Ecol., 18: 1801-1813.
http://dx.doi.org/10.1111/j.1365-294X.2009.04141.x
PMid:19302350 |
|
|
37. Cymbron, T., Freeman, A.R., Malheiro, I.M., Vigne, J.D.
and Bradley, D.G. (2005). Microsatellite diversity suggests
different histories for Mediterranean and Northern European
cattle populations. Proc. R. Soc. B., 272: 1837-1843.
http://dx.doi.org/10.1098/rspb.2005.3138
PMid:16096097 PMCid:PMC1559860 |
|
|
|
38. Moazami-Goudarzi, K., Belemsaga, D.M.A., Ceriotti, G.,
Laloe, D., Fagbohoun, F., Kouagou, N.T., Sidibé, I., Codjia,
V., Crimella, M.C., Grosclaude, F., Touré, S.M. (2001).
Characterization of Somba bovine breed using molecular
markers. Rev. Elev. Méd. Vét. Pays Trop., 54: 129-138. |
|
|
|
39. Ngono Ema, P.J., Manjeli, Y., Meutchieyié, F., Keambou,
C., Wanjala, B., Desta, A.F., Ommeh, S., Skilton, R. and
Djikeng, A. (2014). Genetic diversity of four Cameroonian
indigenous cattle using microsatellite markers. J. Livestock.
Sci., 5: 9-17. |
|
|
|
40. Foulley, J.L. and Ollivier, L. (2006). Genetic diversity
and allelic richness: concepts and application to bovine
breeds. Renc. Rech. Ruminants., 13: 227-230. |
|
|
|
41. Ndiaye, N.P., Sow, A., Ndiaye, S., Sembène, M., Sawadogo
G.J. (2014). Phenotypical Characterization of Senegalese Local
Cattle Breeds Using Multivariate Analysis. J. Anim. Vet. Adv.,
13: 1150-1159. |
|
|
42. Gross, B.L. and Rieseberg, L.H. (2005). The ecological
genetics of homoploid hybrid speciation. J. Hered., 96:
241-252.
http://dx.doi.org/10.1093/jhered/esi026
PMid:15618301 PMCid:PMC2517139 |
|
|
|
43. Bessa, I., Pinhero, I., Matola, M., Dzama, K., Rocha, A.
and Alexandrino, P. (2009). Genetic diversity and
relationships among indigenous Mozambican cattle breeds. S.
Afr. J. Anim. Sci., 39: 61-72. |
|
|
44. Boichard, D., Maignel, L. and Verrier, E. (1997). The
value of using probabilities of gene origin to measure genetic
variability in a population. Genet. Sel. Evol., 19: 5-23.
http://dx.doi.org/10.1186/1297-9686-29-1-5
PMCid:PMC2708199 |
|
|
|
45. De Meeûs, T. (2012). Initiation to the genetic of natural
populations: Application to parasites and their vectors.
Marseille: IRD Editions, Collection Didactiques, p 335. |
|
|
|
46. Sharma, R., Maitra, A., Singh, P.K, Tantia, M.S. (2013).
Genetic diversity and relationship of cattle populations of
East India: distinguishing lesser known cattle populations and
established breeds based on STR markers. SpringerPlus, 2: 359.
Available from:
http://www.springerplus.com/content/2/1/359.Accessed on
15-02-2015. |
|
