Genetic characterization and bottleneck analysis of Maghateer camel population in Saudi Arabia using microsatellite markers

1 Introduction

Camels are unique animals in various aspects and are very difficult to compare with other farm animals based on their adaptation and responses to the environment. Camels are diverse in nature and it is found in Arabian Peninsula, Afghanistan, African deserts and Somalia. Arabian Camels meet the food requirement in various countries than sheep and cattle, which are mainly affected by water scarcity and heat. In Kingdom of Saudi Arabia, Camel population is classified based on morphological characters and area of origin (Al-Hazmi et al., 1994). Generally coat colour is used to classify Camels in Saudi Arabia. Based on coat colour, Saudi Arabian Camels have classified into three types. These include Al-Sofr (brown), Maghateer (white), and Al-Homr and Magaheem (black). In a study, Elamin and Wilcox (1992a,b) classified Camels into four types, including, Omani (used for riding), Al-Hawara (survives in Al-Hawara area), Wadha (survies in Hejaz area) and Najdi or Magaheem. The camels in Saudi Arabia are one humped and dromedaries types. In Saudi Arabia, Camels have various roles in celebrations as the part of Kingdom heritage, and is the typical icon in Kingdom heritage. In Arabian Peninsula, a total of 1.6 million populations are found and this population is about 53% population of entire Saudi Arabia (FAO, 2012). The Camels, Wadha is dominant in Hejaz region and Al-Hawara type camels are predominant in Northern Saudi Arabia. In Najd and AL Dawaser valley, the populations of Maghateer are very high. Maghateer type Camels are white in colour and rigid in nature and is well known to yield milk than other types under range conditions. In Saudi Arabia, studies on genetic variability of Camels are very rare, it is very important to study the Camels using molecular markers to assess the population. This kind of genetic analysis is useful to improve camels and to develop various breeding mechanisms to improve Camels. In Saudi Arabia, the genetic variation of dromedary populations has been poorly documented. In a study, Spencer et al. (2010) studied the genetic variance in Camel population has been studied using the genetic markers like, Randomly Amplified Polymorphic Dimorphism (RAPD) and DNA fingerprinting (DFP). Recently, Musthafa (2015) analyzed genetic diversity in the Camels from Tunisia, Egypt, India, Canary Islands, Saudi Arabia, Kenya and Australia. These Camels from these countries showed range of genetic diversity and analyzed using various microsatellite markers. The microsatellite markers such as, CMS50, CVRL07, CVRL06, CVRL05, CVRL01, LCA66, VOLP67, VOLP32, VOLP10, VOLP08, VOLP03, YWLL59, YWLL44, YWLL38, YWLL09 and YWLL08 were used to analyze the heterozygosity among Camel population. These microsatellite markers have rich of polymorphic information and degree of allelic richness (Musthafa, 2015). It is anticipated that the obtained information from this study can be used in conservation and genetic improvement plans of Maghateer Camel population in Saudi Arabia.

2 Materials and methods

3 Results and discussion

All the microsatellite primer-pairs successfully amplified 19 SSR markers from the selected markers from the selected Camels. The tested markers, CMS25 and VOLP67 did not yield any result after altering various PCR conditions. The other nineteen microsatellite loci were all polymorphic. The tested various genetic parameters for the population of Maghateer Camel have been described in Table 2. In the tested Camel population showed various alleles per locus and it varied from 4 to 16 which is a good indicator of genetic polymorphism. The allele range obtained in the result was similar with previous results (Nolte et al., 2005; Vijh et al., 2007). However, the range was higher than observations made previously by various research groups (Mehta et al., 2007; Nolte et al., 2005; Vijh et al., 2007) in the analyzed Camel population. This range was very much higher than the results reported by Al-Swailem et al. (2009) in Saudi Camel population and in Kachchhi camel population (Mehta et al., 2007). In a study, Schulz et al. (2010) found 2 to 22 alleles per locus in the Canarian Camels. Likewise, Spencer and Woolnough (2010) reported 5 to 23 alleles per locus in Australian dromedary Camels. It was previously reported that the microsatellite loci should have more than four alleles per locus to minimize standard error (SE) of distance estimates (Li et al., 2002). In general, the average of alleles in a particular population is mainly depend on size of the sample (n) and the availability of unique alleles of very low frequencies. The number of alleles increases gradually when the sample size increases. In a study, Al-Swailem et al. (2009) found 61 alleles with a mean number of alleles per locus (3.81) in Saudi Camels. In Australian Dromedary Camels, 224 alleles with mean 13.18 alleles per locus was reported by Spencer et al. (2010). In another study, Schulz et al. (2010) reported 10.7 alleles per locus in 139 alleles. Among Camel population, 10.3 alleles per locus in 224 alleles was reported by Nolte (2003). In our study revealed a mean of 8.158 alleles in 155 alleles and this is in between previous findings. The locus CVRL06 showed only four alleles and is the least polymorphic, in the case of locus CVRL01, about 16 alleles and showed the most polymorphic SSR marker. In the present study, the average number of alleles (Ne) was reported as 3.599 and the mean Shannon index value was reported as 1.442, the maximum value of Ne in YWLL08 locus was 7.764, and the lowest value of Ne was1.392 in locus VOLP32.Australian camels displayed higher effective number of alleles of 3.44 whereas Bikaneri camels displayed 4.40 as the highest average number of alleles (Mehta and Sahani, 2007; Vijh et al., 2007). Also, heterozygosity value of the reported effective number of the alleles also found to be high. There is a positive relationship between number of alleles at a given locus and number of dinucleotide repeats (Bishop et al., 1994). Heterozygosities also represent a good indicator of genetic polymorphism within breeds. The hetrozygosity level of a microsatellite varies from species to species and sometimes between breeds of the same species (Fatima, 2006). In present study, the expected heterozygosity value of Maghateer Camels populations was 0.667 (Table 2). This value was very much comparable to that of observed values (0.604) in the South African camels which was reported by Nolte et al. (2005). It was 0.633 in the case of Arabian camels and 0.680 in Sudanese Camels (Schulz et al., 2010; Nolte et al., 2005). In Kenyan Camels, it was 0.530, however reduced value was reported in the case of United Arab Emirates camels (0.51) (Mburu et al., 2003). It was marginally increased in the case of Camelus dromedaries and the reported value was 0.544 (Spencer et al., 2010; Spencer and Woolnough, 2010). Table 2 shows the mean observed heterozygosity of the present study (0.717). This observed heterozygosity value was found to be higher than in Australian camel (0.455) and Tunisian camel (0.460) (Spencer and woolnough, 2010; Ould Ahmed et al., 2010). Moreover, in an earlier report the heterozygosity value was found to be 0.552 in Arabian Camel (Schulz et al., 2010). In Mewari, Kutchi, Jaisalmeri and Bikaneri populations, the observed heterozygosity values were found to be 0.600, 0.560, 0.570 and 0.580, respectively (Vijh et al., 2007). The observed and expected heterozygosities reported by Evdotchenko et al. (2003) and Mariasegaram et al. (2002) in dromedary are quite similar to those of present findings. These values of heterozygosity clearly show a significant level of variability in genetic level among Camel population from four populations from Saudi Arabia. Hardy-Weinberg Equilibrium (HWE) has been frequently used to analyze the genetic variation. HWE is defined as a breed with constant genotype and gene frequencies (Falconer and Mackay, 1996). The inbreeding estimate within the population of Camel, which basically reflects the deviation from HWE and the nonrandom union of gametes, showed that there were various genotypes with many loci that followed HWE (P < 0.05). In this investigation, the number of HWE was found to be 12 loci (Table 3). These markers critically indicated an excess and deficiency of heterozygotes, this does not show the variation from HWE. It is well known fact that the migration of various natural processes of nonrandom mating, mutation, genetic drift and both natural selection and artificial selection are critical factors that are well known to induce variations from HWE. It is reported that some loci were usually derived from Hardy-Weinberg Equilibrium and showed that the loci 6, 6, 5 and 11 were not in HWE in the case of Mewari, Kutchi, Jaisalmeri and Bikaneri and statistically significant (P < 0.01). However, the loci 17, 17, 18 and 12 were followed JWE in Mewaricamel, Kutchi, Jaisalmeri and Bikaneri and the reported results were statistically significant (Vijh et al., 2007). A previous study in SaudiArabia using 16 microsatellite markers in Saudi Camel population indicated that half of the loci in the threepopulations were in Hardy-Weinberg Equilibrium (Al-Swailem et al., 2009). Statistical analysis was made on microsatellite to test the Maghateer population having undergone recent genetic bottleneck. The level of genetic variation, population size and historical population sizes are well known and this is used to detect bottlenecks in the absence of historical data. Maghateer population shows number of loci with gene potent diversity, which includes three tests, such as, “Wilcoxons sign-rank test”, “standardized differences test” and “sign test”. The microsatellite model evaluation methods such as, Two Phase Model (TPM), Stepwise Mutation Model (SPM) and InfiniteAllele Model (IAM) were used. In this study, no significant heterozygote excel was found in the Maghateer Camel population by using InfiniteAllele Model, Wilcoxon tests (TPM), standardized differences (SMM) along with the normal L shaped (Fig. 1) distribution of mode-shifttest. Moreover, the previous tests showed no bottleneck inrecent past in Maghateer population (Table 4).

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Fig. 1

Proportion of alleles and their frequencies in Maghateer population.

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Structure revealed, for the 50 individuals of Maghateer camel with no prior distribution, that ΔK has a strong peak at K = 4, suggesting that the optimal number of clusters was 4 (Fig. 2a). In the Fig. 2b, the colors represent four clusters. Each bar in the graph represents an animal and its inferred proportion of genome admixture. The proportion of membership in each of the 4 clusters was 20%, 44%, 26% and 10% for the shoun red, green, blue and yellow cluster, respectively. Within the bar plot, the coefficient for each individual indicates clearly unique ancestral genomes for each of the two first cluster. However, the two last ones appear sharing allele frequencies which indicate low of genetic differentiation and extensive gene flow between these two clusters. The values of nucleotide sequences based on frequencies of allele divergence among the selected populations, confirm these observations. In fact, the highest values were recorded between the first cluster and the others (d1-2 = 0.6%, d1-3 = 0.38%, d1-4 = 0.35%). However, the lowest values were recorded between the two last clusters (d3-4 = 0.002%).

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Fig. 2

(a) Plot of two graphical methods allowing detection of the true value for K. Blue represent the mean of LnP(k) over 8 runs for each K value analyzed the increase of the variance associated to LnP(D) across different K values tested. Red represents the values of ΔK calculated, based on the methodology proposed by Evanno et al. (14). (b) Bar plot of estimation of the membership coefficient (Q) for each individual of Maghateer camels. Each individual is represented by a thin vertical line, which is partitioned into K colored segments that represent the individual's estimated membership fractions in K clusters. Black lines separate individuals of different clusters based on structure analysis. Population groups are labeled below the figure, with their geographical affiliations above it. The figure shown for K = 5 is based on the highest probability run at that K.

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4 Conclusion

Nevertheless, these fifteen microsatellite markers proved useful to detect genetic variability in Majaheem camel populations in Saudi Arabia, thus can be effectively used to analyze the diversity in genetic level in Saudi Arabian Camels. Also, very large sampling of all Camels in Kingdom of Saudi Arabia are required to establish a state of art genetic analysis for genotyping and analyzing the Saudi Arabian Camel population.