Genetic analysis of native Moroccan cattle

I Boujenane and L Ouragh*

Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II,
P.O. Box 6202 Rabat-Instituts, 10101 Rabat, Morocco
* Department of Medical and Surgical Pathology, Institut Agronomique et Vétérinaire Hassan II,
P.O. Box 6202 Rabat-Instituts, 10101 Rabat, Morocco
i.boujenane@iav.ac.ma

Abstract

A total of 395 cattle of Oulmès-Zaer and Tidili breeds were genotyped at 8 microsatellite markers with the aim of studying the genetic diversity of these populations and their genetic relationship.

The average number of alleles across all loci in the analysed populations was found to be 11.5. The expected mean heterozygosity per population was 0.751 in Oulmès-Zaer and 0.738 in Tidili. Significant departures from Hardy-Weinberg equilibrium were observed. Population differentiation, analysed by estimation of the F_ST index, showed that the average proportion of genetic variation explained by breed differences was 3.2%. The global heterozygote deficit across populations (F_IT) was 28.5%. The overall deficit of heterozygotes because of inbreeding within populations (F_IS) was 26.2%. Genetic distance between the two populations estimated from allele frequencies was 0.108 suggesting some genetic differentiation.

The results of this study are useful for the implementation of a conservation strategy that should aim to conserve native Moroccan cattle.

Keywords: allele frequency, F-statistics, genetic distance, heterozygosity, microsatellite

Introduction

Native Moroccan cattle population was about 1.34 million head in 2007. It is composed by three principal breeds: Brune de l'Atlas, Oulmès-Zaer and Tidili, which are well adapted to harsh conditions of the country, such as scarcity of feed and diseases. However, their milk production and growth rate are low (Boujenane 2002; Boujenane et al 2004). Therefore, during the last three decades, native breeds have been used in crossbreeding programmes in order to improve their productivity. Consequently, their proportion within the total Moroccan cattle population decreased drastically from 95% in 1975 to 48.2% in 2007. In order to implement improvement and conservation programmes for satisfying the demands of changeable markets, the first step is to characterise population genetic variability. Thus, previous studies to assess genetic variability in Moroccan breeds made use of biochemical markers (Boujenane and Ouragh 2006). However, microsatellites were designed today as the markers of choice for providing useful information on the evolution of breeds, gene pool development and the magnitude of genetic differentiation.

This study was designed to investigate the genetic variability in Oulmès-Zaer and Tidili native Moroccan cattle and the relationship between them. The findings will help characterization of these populations and implementation of sustainable programmes for their improvement and conservation.

Materials and methods 

Breed

Oulmès-Zaer is one of the principal native cattle breeds in Morocco. Its breeding area is located at piedmont of the Middle Atlas mountain at about 100 to 200 km south-east of Rabat, especially in Khémisset, Tiflet and Oulmès regions (Figure 1).

The number of animals is about 80000 head. The herd book of Oulmès-Zaer was created in 1949, and at present some breeders are organized in a breed cooperative. Coat colour of animals is uniformly red. Height at withers ranged from 120 to 135 cm. Adult weights were 300 kg for females and 450 kg for males (Photo 1). Tidili breed is raised in Ouarzazate region, south of Morocco (Figure 1).

The number of animals is about 15000 head. This breed is phenotypically similar to the Brune de l’Atlas breed, with the exception of a voluminous udder. The most dominant coat colour is black with yellow to red on the back, but some animals are also either uniformly red or uniformly black. Height at withers ranged from 110 to 120 cm. Adult weights were 285 kg for females and 330 kg for males (Photo 2).

Both breeds have not been subject of breeding programmes with significant selection pressure (Boujenane 2002). 

Animals

A total of 395 unrelated animals were examined for microsatellite polymorphisms, 216 Oulmès-Zaer and 179 Tidili. Sampling was carried out randomly among cattle of different farms located in the breeding area of each breed, kept under extensive low input management conditions. These populations are mainly composed of small herds (not larger than 10 animals for Oulmès-Zaer and not larger than 5 animals for Tidili), mainly cows, with few bulls, which are shared among neighbours, using exclusively natural mating.

The blood was collected from the jugular vein in EDTA tubes, and kept refrigerated at 4°C until the time of DNA extraction. DNA was isolated by standard protocols. DNA samples were then amplified by PCR employing the “StockMarks genotyping kit for cattle (PE Applied Biosystems, Foster City, Californie, USA)”. Among the 11 microsatellites tested, 8 loci amplified successfully (TGLA227, TGLA126, TGLA122, TGLA53, BM2113, BM1824, ETH3, and ETH225), while three (ETH10, SPS115 and INRA23) did not amplify.  Data obtained were interpreted and translated to alleles by using Genotyper software (PE Applied Biosystems, Foster City, Californie, USA).

Number of alleles, allele frequency, observed and unbiaised average expected heterozygosity were calculated for each breed using GENETIX software (Belkhir et al 1998). Possible deviation from Hardy-Weinberg equilibrium at each locus for each breed was evaluated using the computer program GENPOP version 3.4 (Raymond and Rousset 1995). Population structure was evaluated by the hierarchical F-statistics using the estimators of Weir and Cockerham (1984) implemented in FSTAT (Goudet 2002). Genetic distance between breeds was estimated according to Nei's formula (1972) using GENETIX.

Results and discussion 

A total of 92 alleles were detected among the 395 animals genotyped. The average number of alleles per locus was 10 ranging from 7 to 13 in Oulmès-Zaer cattle, and 10.9 ranging from 6 to 13 in Tidili cattle (Table 1).

The allelic frequencies varied at all loci from 0.002 to 0.643 in Oulmès-Zaer and from 0.003 to 0.620 in Tidili cattle, with about 40% of all the alleles were in low frequency and contributed very little to the whole genetic variability. The most polymorphic microsatellites were MB2113, TGLA122, TGLA126 and TGLA227 with 13 alleles, while the least polymorphic was ETH225 with 6 alleles. The medium to high variability of these populations could be attributed to low selection pressure since animals are usually subject to traditional husbandry management and reared by small breeders following their own breeding schemes and usually using their own bulls. When the 8 microsatellite loci were examined for breed-specific alleles, a total of 5 alleles at loci BM864, ETH225, ETH3, MB2113 and TGLA53 were found to be specific for Oulmès-Zaer population, and 12 alleles at loci BM864, ETH3, MB2113, TGLA122, TGLA126 and TGLA53 for Tidili cattle. The combined frequency of the breed-specific alleles found at each locus varied from 0.003 to 0.044. It may be a little surprising that the Oulmès-Zaer breed is less polymorphic than the Tidili, as the latter is a relatively small population, with a small number of bulls, compared with the Oulmès-Zaer. A possible explanation for this observation may be that the Oulmès-Zaer is a relatively closed population as compared with the Tidili, in which intercrosses with the Brune de l’Atlas may occur (Boujenane 2002). At this point, it should be pointed out that Tidili and Brune de l’Atlas breeds are phenotypically similar. Moreover, the result could be explained also by the heterogeneous nature of Tidili population being represented by animals with three different coat colours.         

The Hardy-Weinberg equilibrium was tested for all breed-locus combination (n=16). Both populations were found to be in Hardy-Weinberg disequilibrium, with a deficiency of heterozygosity. This condition may result from inbreeding in case of Oulmès-Zaer and inbreeding and the presence of population substructure (Wahlund effect) in Tidili as this population is composed by animals of different phenotypes.

Observed and expected heterozygosity per locus in the two populations are presented in Table 2. Observed heterozygosity is always less than the expected.

Moreover, observed and expected heterozygosity was relatively high within the 8 microsatellite loci, ranging from 0.375 to 0.801 and from 0.562 to 0.833, respectively in Oulmès-Zaer, and from 0.223 to 0.771 and from 0.598 to 0.841, respectively in Tidili cattle. Average observed and expected heterozygosity among the 8 microsatellite loci were 0.573 and 0.751, respectively in Oulmès-Zaer, and 0.522 and 0.738, respectively in Tidili cattle. The relatively lower values of heterozygosity detected in Tidili indicated some loss of variability. This could be attributed to its relatively smaller population size when compared to Oulmès-Zaer. Average heterozygosities overall loci were similar to those reported by Arranz et al (1996) in Spanish cattle, but slightly higher than those reported by Canon et al (2001) for 18 European beef cattle breeds and Brenneman et al (2007) in American cattle.

Observed heterozygote deficiency per locus in the two cattle populations is presented in Table 2. Both populations showed a significant heterozygote deficit; 23.7% for Oulmès-Zaer and 29.3% for Tidili. The average F_IS values for each breed and for most of the loci were significantly different (p < 0.05) from zero. Three loci contributed to this deficit in Oulmès-Zaer population while up to five loci significantly affected the F_IS value in the Tidili breed.

Mean estimates of F-statistics obtained from Jackknifing over loci were showed in Table 3.

From global analysis a significant deficit of heterozygotes (F_IS) of 26.2% was observed for each of the analysed breeds, whereas the total population (F_IT) had a 28.5% deficit of heterozygotes. Most loci contributed significantly to the heterozygote deficit within populations (F_IS), while all loci except ETH3 and ETH225 significantly affected the global heterozygote deficit (F_IT). Nei (1987) explained this lack of heterozygotes in a population by number of factors such us inbreeding, locus under selection (genetic hitchhiking), null alleles (non-amplifying alleles), and presence of population substructure (Wahlund effect). The inbreeding that occurred in these populations may result from the use for mating of bulls born in the herd in case of Oulmès-Zaer breed, and from the use of few bulls to mate all cows of the district in case of Tidili breed. The overall genetic differentiation among breeds (F_ST) was moderate (3.2%) but significantly different from zero. All loci except TGLA122 contributed significantly to the overall differentiation. This moderate genetic differentiation (F_ST) among breeds implies that 96.8% of the total genetic variation corresponds to differences among individuals. This result indicates a high genetic diversity among the two populations that may be a consequence of different origins of the cattle. Few reports were made on the origin of native Moroccan cattle. Grimpret (1954) reported that Oulmès-Zaer belongs to the Blond trunk of the Atlantic coast that includes some French (Limousine and Bazadaise), Portuguese (Mirendeza) and Spanish breeds, while Tidili is a variety of the Brune de l’Atlas population which is native of North Africa. This level of differentiation, although rather low, is within the range reported in the literature for F_ST values in cattle. A value of 11.2% was found in seven European cattle breeds (MacHugh et al 1998), 9% in Swiss cattle (Schmid et al 1999), 3.5% in Belgian breeds (Mommens et al 1999), 10.7% in North European cattle breeds (Kantanen et al 2000).

The genetic distance between Oulmès-Zaer and Tidili populations was 0.108, indicating some breed differentiation. Based on four biochemical loci, the genetic distance between Oulmès-Zaer and Tidili was 0.017 (Boujenane and Ouragh 2006). The result of the present study doesn’t support the findings of Joshi et al (1957) who reported that all native Moroccan cattle descended from the Brune de l’Atlas population. Genetic distance estimate reported in the present study was in the range of those among native breeds of various species (Nei 1987). Moreover, although comparative studies of the values obtained in different works may be unreliable since the number of markers used and the loci selected are different, in general, distance found in the present work between Oulmès-Zaer and Tidili is comprised into the intervals reported in studies using microsatellites (MacHugh et al 1998; Arranz et al 1996; Moazami-Goudarzi et al 1997; Martin-Burriel et al 1999). Moreover, 8 microsatellites were used in this study, while 30 microsatellites are probably insufficient to distinguish closely related breeds (Moazami-Goudarzi et al 1997).

Conclusion 

• This study is a contribution to the knowledge of genetic variability of Oulmès-Zaer and Tidili populations. The high variability found in the native Moroccan populations and their good adaptation to very hard conditions make these populations eligible for preservation. Therefore, our findings are important for the establishment of strategic conservation programmes.

Acknowledgements 

This study was supported by the grant PROTARS III n° D54/13 from "Centre National de la Recherche Scientifique".

References 

Arranz J J, Bayon Y and San Primitivo F 1996 Comparison of protein markers and microsatellites in differentiation of cattle populations. Animal Genetics 27: 415-419

Belkhir K, Borsa P, Goudet J, Chikhi L and Bonhomme F 1998 GENETIX, Logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France  http://www.genetix.univ-montp2.fr/genetix/intro.htm

Boujenane I 2002 Cattle breeds in Morocco. Actes Editions, Rabat, Morocco

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 de l’élevage et de médecine vétérinaire des pays tropicaux 57: 101-105 http://remvt.cirad.fr/cd/derniers_num/2004/EMVT04_101_105.pdf

Boujenane I, Ounis O and Aït Taleb H 2000 Effets des facteurs non génétiques sur les performances de croissance des veaux de race Oulmès-Zaer. Actes Institut Agronomique et Vétérinaire (Maroc) 20 : 125-132

Boujenane I and Ouragh L 2006 Genetic analysis of Oulmès-Zaer and Tidili native Moroccan cattle breeds. Proceedings of the 8^th World Congress of Genetics Applied to Livestock Production, Belo Horizonte, MG, Brazil. 33 : 454-1965. http://boujenane.com/phocadownload/8WCGALP_33_454-1965.pdf

Brenneman R A, Chase Jr C C, Olson T A, Riley D G and Coleman S W 2007 Genetic diversity among Angus, American Brahman, Senepol and Romosinuano cattle breeds. Animal Genetics 38: 50-53

Canon J, Alexandrino P, Bessa I, Carleos C, Carretero Y, Dunner S, Ferran N, Garcia D, Jordana J, Laloë D, Pereira A, Sanchez A and Moazami-Goudarzi K 2001 Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genetic Selection Evolution 33: 311-332 http://www.gse-journal.org/index.php?Itemid=129&option=com_article&access=dkey&dkey=10.1051/gse:2001121&lang=en

Goudet J 2002 FSTAT, a computer package that estimates and tests gene diversities and differentiation statistics from codominant genetic markers (version 2.9.3.2). Available from http://www2.unil.ch/popgen/softwares/fstat.htm

Grimpet J 1954 L’élevage bovin au Maroc. Maroc Médical 353: 77-83

Joshi N R, McLaughlin E A and Phillips R W 1957 Les Bovins d’Afrique : types et races.  Agricultural Studies 37, FAO, Rome, Italy

Kantanen J, Olsaker I, Holm L-E, Lien S, Vilkki J, Brusgaard K, Eythorsdottir E, Danell B and Adalsteinsson S 2000 Genetic diversity and population structure of 20 North European cattle breeds. Journal of Heredity 21: 446-457 http://jhered.oxfordjournals.org/cgi/reprint/91/6/446.pdf

MacHugh D E, Loftus R T, Cunningham P and Bradley D G 1998 Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Animal Genetics 29: 333-340.

Martin-Burriel I, Garcia-Muro E and Zaragoza P 1999 Genetic diversity analysis of six Spanish native cattle breeds using microsatellites. Animal Genetics 30: 177-182

Moazami-Goudarzi K, Laloë D, Furet J P and Grosclaude F 1997 Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites. Animal Genetics 28: 338-345

Mommens G, Peelman L J, Van Zeveren A, D’Ieteren G and Wissocq N 1999 Microsatellite variation between an African and five European taurine breeds results in a geographical phylogenetic tree with a bison out group. Journal of Animal Breeding and Genetics 116: 325-330

Nei M 1972 Genetic distance between populations. The American Naturalist 106: 283-292

Nei M 1987 Genetic distance between populations. In: Molecular Evolutionary Genetics (edited by M. Nei), pp. 208-53. Columbia University Press, New York.

Raymond M and Rousset F 1995 GENPOP: population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249

Schmid M, Saitbekova N, Gaillard C and Dolf G 1999 Genetic diversity in Swiss cattle breeds. Journal of Animal Breeding and Genetics 116: 1-8

Weir B S and Cockerham C C 1984 Estimation F-statistics for the analysis of population structure. Evolution 38: 1358-1370

Received 14 June 2010; Accepted 6 July 2010; Published 1 August 2010

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