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Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data

Published online by Cambridge University Press:  18 June 2018

N. Boushaba ,
I. Boujenane ,
K. Moazami-Goudarzi ,
L. Flori ,
N. Saïdi-Mehtar ,
N. Tabet-Aoul  and
D. Laloë
N. Boushaba*
Affiliation:
Département de Génétique Moléculaire Appliquée, Laboratoire de LGMC, Université des Sciences et de la Technologie d’Oran ‘Mohamed Boudiaf’, B.P 1505 El M’Naouar, 31000 Oran, Algeria
I. Boujenane
Affiliation:
Département de Productions et de Biotechnologies Animales, Institut Agronomique et Vétérinaire Hassan II, 10101 Rabat, Morocco
K. Moazami-Goudarzi
Affiliation:
GABI INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
L. Flori
Affiliation:
SELMET, INRA, CIRAD, Montpellier Supagro, F34398 Montpellier, France
N. Saïdi-Mehtar
Affiliation:
Département de Génétique Moléculaire Appliquée, Laboratoire de LGMC, Université des Sciences et de la Technologie d’Oran ‘Mohamed Boudiaf’, B.P 1505 El M’Naouar, 31000 Oran, Algeria
N. Tabet-Aoul
Affiliation:
Département de Génétique Moléculaire Appliquée, Laboratoire de LGMC, Université des Sciences et de la Technologie d’Oran ‘Mohamed Boudiaf’, B.P 1505 El M’Naouar, 31000 Oran, Algeria Département de Biotechnologie, Université d’Oran 1 Ahmed Ben Bella, 31000 Oran, Algeria
D. Laloë
Affiliation:
GABI INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
*
†E-mail: [email protected]
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Abstract

The local cattle populations belonging to the ‘Brune de l’Atlas’ cattle in Algeria and Morocco are potential resources in terms of genetic diversity and socioeconomic prevalence and their characterization is an essential step in any program designed to conserve genetic diversity. Our objectives were to assess the genetic diversity, the population structure and relationships among four Algerian cattle breeds, the Biskra, Cheurfa, Chelifienne and Guelmoise and of two Moroccan, the Oulmès-Zaër and Tidili by genotyping 50 309 single nucleotide polymorphism in 203 unrelated animals. A low population structure was observed across breeds with pairwise FST values ranging from 0.008 to 0.043, suggesting a high level of gene flow. These data were combined with the available data on cattle populations representative of Europe (EUT), West African taurine (WAT) and zebu (ZEB). Principle Components Analysis was carried out which revealed that the Maghrebin populations are closer to the EUT/ZEB population than to the WAT. Structure analysis confirmed this mixed origin of the Maghrebin cattle populations. We also detected the influence of zebu breeds in Cheurfa and Guelmoise populations. This study provides the first information about genetic diversity within and between Algerian and Moroccan cattle populations and gives a detailed description of their genetic structure and relationships according to their historical origins. This study revealed that several combined effects contributed to shape the genetic diversity of the six Maghrebin populations studied: (i) gene flow among local breeds, (ii) the recent introgression of European breeds in local Algerian breeds and (iii) the traditional management systems. The results of this study will primarily assist policy makers and livestock keepers to make useful decisions for improvement of genetic resources while ensuring the preservation and conservation of local breeds in Algeria and Morocco.

Keywords

genetic diversityMaghrebin cattlehistorical originpopulation structuregenetic resources
Type
Research Article
Information
animal , Volume 13 , Issue 1 , January 2019 , pp. 8 - 14
Copyright
© The Animal Consortium 2018 

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References

Alexander, DH, Novembre, J and Lange, K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19, 1655–1664.Google Scholar
Animal Genetic Resources (AnGR) 2003. Rapport National sur les Ressources Génétique Animales. Ministère de l’Agriculture et du Développement Rural, Algérie. 46p.Retrieved on 16 September 2017, from ftp://ftp.fao.org/docrep/fao/010/a1250e/annexes/CountryReports/Algeria.pdf.Google Scholar
Association pour le Développement du Pastoralisme (ADP) 1961. Perspectives d’amélioration des productions fourragères et animales. Tome II, Edition CAEES. p. 52. Alger.Google Scholar
Bedrani, S and Bouaita, A 1998. Consommation et production du lait en Algérie: éléments de bilan et perspectives. Cahiers duCentre de Recherche en Economie Appliquée pour le Développement 44, 45–70.Google Scholar
Benjamini, Y and Hochberg, Y 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 5, 289–300.Google Scholar
Boujenane, I, Ghoddane, A and Benidir, M 2004. Effets de l’environnement sur la quantité de lait et les poids corporels des bovins de race Tidili au Maroc. Revue d’élevage et de médecine vétérinaire des pays tropicaux 57, 101–105.Google Scholar
Chakraborty, R and Jin, L 1993. A unified approach to study hypervariable polymorphisms: Statistical considerations of determining relatedness and population distances. In DNA fingerprinting: state of the science (ed. SDJ Pena, R Chakraborty, JT Epplen and AJ Jeffreys), pp. 153–175. Basel, Birkhäuser. https://doi.org/10.1007/978-3-0348-8583-6_14.Google Scholar
Chessel, D, Dufour, AB and Thioulouse, J 2004. The ade4 package-I-One-table methods. R News 4, 5–10.Google Scholar
Epstein, H 1971. The origin of the domestic animals of Africa.Volume 1, Edition Leipzig, Africana Publishing Corporation, NK, USA, 573p.Google Scholar
Ezzahiri, A, Ouchtou, M and Dahbar, M 1984. La vache laitière Tidili. La vache laitière Tidili (rapport). Ormva, Ouarzazate, Maroc.Google Scholar
Felius, M 1995. Cattle breeds – an Encylopedia, Edition. Misset Uitgeverij, Doetinchem, the Netherlands. p. 512.Google Scholar
Gautier, M, Flori, L, Riebler, A, Jaffrézic, F, Laloë, D, Gut, I, Moazami-Goudarzi, K and Foulley, JL 2009. A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BioMed Central Genomics 10, 550.Google Scholar
Gautier, M, Laloë, D and Moazami-Goudarzi, K 2010. Insights into the genetic history of French cattle from dense SNP Data on 47 worldwide breeds. PLoS One 5, e13038.Google Scholar
Hoffmann, I 2010. Climate change and the characterization, breeding and conservation of animal genetic resources. Animal Genetics 41, 32–46.Google Scholar
Jordana, J, Alexandrino, P, Beja-Pereira, A, Bessa, I, Canon, J, Carretero, Y, Dunner, S, Laloë, D, Moazami-Goudarzi, K, Sanchez, A and Ferrand, N 2003. Genetic structure of eighteen local south European beef cattle breeds by comparative F-statistics analysis. Journal of Animal Breeding and Genetics 120, 73–87.Google Scholar
Leroy, G, Baumung, R, Boettcher, P, Scherf, B and Hoffmann, I 2016. Review: sustainability of crossbreeding in developing countries; definitely not like crossing a meadow. Animal 10, 262–273.Google Scholar
Loftus, RT, MacHugh, DE, Bradley, DG, Sharp, PM and Cunningham, P 1994. Evidence for two independent domestications of cattle. Proceedings of the National Academy of Sciences 91, 2757–2761.Google Scholar
Matukumalli, LK, Lawley, CT, Schnabel, RD, Taylor, JF, Allan, MF, Heaton, PM, O’Connell, J, Moore, SS, Smith, TPL, Sonstegard, TS and Van Tassellet, CP 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4, e5350.Google Scholar
Maudet, C, Luikart, G and Taberlet, P 2002. Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. Journal of Animal Science Abstract 80, 942–950.Google Scholar
Ministère de l’Agriculture, de l’Agroalimentaire et de la Forêt (MAAF) 2012. Les politiques agricoles à travers le monde: quelques exemples. Sources : MAAF, SE Alger, MAE, Ministère Algérien de l'Agriculture et du Développement Rural, Commission Européenne, Banque Mondiale, CIHEAM. FAO, Douanes françaises citées par Ubifrance, IGN.Google Scholar
Muzzolini, A 1982. Une "relecture" de la littérature archéologique relative au Bosibericus. Bulletin de la Société méridionale de Spéléologie et de Préhistoire 22, 11–29.Google Scholar
Paradis, E, Claude, J and Strimmer, K 2004. Ape: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290.Google Scholar
Payne, WJA and Hodges, J 1997. Tropical cattle. Origins, breeds and breeding policies Blackwell Science, Oxford, UK 328. p.Google Scholar
Ramos, AM, Megens, HJ, Crooijmans, RPMA, Schook, LB and Groenen, MAM 2011. Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing. Stichting International Foundation for Animal Genetics 42, 613–620.Google Scholar
R Core Team 2016. R: a language and environment for Statistics and Computing. R foundation for Statistical Computing, Vienna, Austria.Google Scholar
Sempéré, G, Moazami-Goudarzi, K, Eggen, A, Laloë, D, Gautier, M and Flori, L 2015. WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle. BioMed Central Genomics 16, 940.Google Scholar
Sraïri, MT, Benyoucef, MT and Kraiem, K 2013. The dairy chains in North Africa (Algeria, Morocco and Tunisia): from self sufficiency options to food dependency? SpringerPlus 2, 1–13.Google Scholar
Wigginton, JE, Cutler, DJ and Abecasis, GR 2005. A note on exact tests of Hardy-Weinberg equilibrium. The American Journal of Human Genetics 76, 887–893.Google Scholar
Yakhlef, H 1989. La production extensive de lait en Algérie. Options Méditerranéennes – Série A. Séminaires Méditerranéens 6, 135–139.Google Scholar