Open-access Genetic characteristics of camels bred in the Atyrau region based on microsatellite DNA analysis

Características genéticas de camelos criados na região de Atyrau com base na análise de DNA microssatélite

Abstract

In this article, the level of genetic diversity was assessed, and the degree of heterozygosity was determined for different populations of camels. The studied camel populations are characterized in terms of F-statistics, specifically by the degree of inbreeding and the levels of inter-population and intra-population diversity within each of the studied camel populations. For the first time in Kazakhstan, genotyping of dairy camels of breeding populations in the Atyrau region using DNA technologies was carried out, which makes it possible to reliably assess the genetic profile of high-yielding individuals by microsatellite loci for the development of the dairy industry in different regions of camel breeding. For genetic analysis using ISSR-PCR markers, 30 heads of one- and two-humped camels from each of the Dastan Ata camel breeding populations of the Atyrau region were selected as research materials. Genomic DNA was isolated from camel blood samples using a set of reagents in a commercial kit for cleaning genomic DNA. We evaluated the quality of genomic DNA using agarose gel electrophoresis and a concentration spectrophotometer. During the experiment, seven ISSR primers were tested, of which two primers were selected, as they showed high-quality results: AG-ISSR, i.e. 5' -AGA GAG AGA GAG AGA GAG C3, and GA-ISSR-5' - GAG AGA GAG AGA C-3 '. PCR was performed in a classic format in a special commercial PCR Master Mix (Thermo Scientific, USA) with the enzyme tag polymerase. PCR was performed on the Mastercycler Nexus Gradient Amplifier (Eppendorf, Germany). The PCR cycle was as follows: initial denaturation 5 min 95 °C; denaturation 95 °C – 40 sec, adhesion 55 °C – 30 sec, synthesis 72 °C – 1 min (35 cycles); final synthesis 72 °C, 2 min. By the number of alleles obtained, a base was created in Microsoft Excel. Population and genetic parameters were evaluated in the TFPGA program. Fragment frequencies, proportions of polymorphic loci, genetic diversity, and genetic distance indices were calculated using the PopGene 1.32 program. The results obtained using Gis SR and GA-ISSR markers to determine the genetic heterogeneity of camel species in PopGene v. 1.32 and Microsoft Excel programs made it possible to determine the frequency of DNA fragments, the proportion of polymorphic loci, and the genetic diversity index for the studied populations using ISSR-PCR markers.

Keywords:
allele; homozygote; heterozygote; genotype; genepool; microsatellite; locus; marker; primer

Resumo

Neste artigo, avaliou-se o nível de diversidade genética e determinou-se o grau de heterozigosidade em diferentes populações de camelos. As populações de camelos estudadas foram caracterizadas em termos de estatísticas F, especificamente pelo grau de consanguinidade e pelos níveis de diversidade inter e intrapopulacional em cada uma das populações estudadas. Pela primeira vez no Cazaquistão, realizou-se a genotipagem de camelos leiteiros de populações reprodutoras na região de Atyrau utilizando tecnologias de DNA, possibilitando avaliar de forma confiável o perfil genético de indivíduos de alta produção por meio de loci microssatélites para o desenvolvimento da indústria leiteira em diferentes regiões de criação de camelos. Para a análise genética utilizando marcadores ISSR-PCR, foram selecionados 30 camelos de uma e duas corcovas de cada uma das populações reprodutoras de camelos Dastan Ata da região de Atyrau. O DNA genômico foi isolado de amostras de sangue de camelos utilizando um conjunto de reagentes em um kit comercial para purificação de DNA genômico. A qualidade do DNA genômico foi avaliada por eletroforese em gel de agarose e espectrofotometria de concentração. Durante o experimento, sete primers ISSR foram testados, dos quais dois foram selecionados por apresentarem resultados de alta qualidade: AG-ISSR (5'-AGA GAG AGA GAG AGA GAG C3') e GA-ISSR (5'-GAG AGA GAG AGA C3'). A PCR foi realizada em formato clássico, utilizando um Master Mix comercial específico para PCR (Thermo Scientific, EUA) com a enzima tag polimerase. A PCR foi realizada no Mastercycler Nexus Gradient Amplifier (Eppendorf, Alemanha). O ciclo de PCR foi o seguinte: desnaturação inicial a 95 °C por 5 min; desnaturação a 95 °C por 40 s, adesão a 55 °C por 30 s, síntese a 72 °C por 1 min (35 ciclos); síntese final a 72 °C por 2 min. Os alelos obtidos foram organizados em base de dados no Microsoft Excel. Os parâmetros populacionais e genéticos foram avaliados no programa TFPGA. As frequências de fragmentos, as proporções de loci polimórficos, a diversidade genética e os índices de distância genética foram calculados utilizando o programa PopGene 1.32. Os resultados obtidos com os marcadores ISSR e GA-ISSR permitiram determinar a heterogeneidade genética de espécies de camelos nos programas PopGene v. 1.32 e Microsoft Excel permitiram determinar a frequência de fragmentos de DNA, a proporção de loci polimórficos e o índice de diversidade genética das populações estudadas, utilizando marcadores ISSR-PCR.

Palavras-chave:
alelo; homozigoto; heterozigoto; genótipo; conjunto gênico; microssatélite; locus; marcador; primer

1. Introduction

Camel breeding in Kazakhstan is a traditional branch of agricultural production, which is based on the sustainable, dynamic development of the agro-industrial complex in arid regions, effectively using desert and semi-desert regions (Alibaev et al., 2020; Baimukanov et al., 2018).

In the desert and semi-desert regions of Kazakhstan, which occupy 25% of the region, the main source of milk production is dairy camel breeding due to the difficulty of breeding other types of dairy cattle.

The priority direction of the modern stage of development of camel farming is the production of dairy products, and this production requires a transition from an extensive pedestal to an intensive stage.

Camel milk and its processed products are in high demand both in the domestic and foreign markets (the customs union, the European Union, and the Asia-Pacific region). In the south-western region of Kazakhstan, dairy camel breeding has the potential to reach a higher level in production, that is, camel milk and shubat, which are distinguished by dietary, environmental, and medicinal properties, are among Kazakhstan's branded products.

Currently, domestic agricultural producers are interested in breeding high-yielding camels, and the genotypes of camels with high milk yield are in great demand in the domestic and foreign markets in the development of the dairy industry (Baimukanov et al., 2020).

In camel breeding, in order to monitor genetic resources, that is, to identify, systematize, and document genotypes of high value for effective introduction into agricultural production, the genodiagnostics of camels of different populations has not been developed using modern biotechnological methods – DNA technologies.

Currently, domestic camel breeding does not have a genetic description of camels from different regions, created on the basis of DNA technology.

In this regard, genotyping of the gene pool of camels in different regions of Kazakhstan using DNA technology and its introduction into the field of agricultural production for the development of the dairy industry is an urgent direction of research work in the biotechnology of farm animals.

The natural and climatic conditions of the Atyrau region provide unique opportunities for the development of camel breeding. Camels are an important part of animal husbandry, especially in desert and semi-desert regions. However, studies of the genetic diversity and adaptation mechanisms of camel populations have not been adequately conducted at the moment.

In addition, genetic studies with the camel population of the Atyrau region will help determine the adaptation of these animals to local environmental conditions, the effectiveness of breeding processes, and resistance to genetic diseases. These studies are important for increasing the sustainability of agriculture, the development of animal husbandry, and improving the economic situation of the local population.

The history of the discovery of microsatellites began in the 1980s. Initially, they were discovered when, as a result of DNA sequence analysis, scientists noticed that there were repeating sequences in some sections of DNA. In the 1980s: the first microsatellites were described in works devoted to the study of the structure of genomes. A study conducted in 1985 by Alan Winston and his colleagues revealed tandem repeats in genomes for the first time (Shaltenbay et al., 2024).

Microsatellite DNA markers are an effective tool for studying genetic diversity, population structure, and evolutionary processes. This method allows obtaining important information for determining the genetic characteristics of camel populations, preserving and effectively using their genetic resources (Piro, 2021).

The study of their genetic diversity and population structure, especially through the use of microsatellite DNA markers, is important for the development of camel breeding, the preservation of genetic resources, and the improvement of the breeding process. The genetic diversity of camels is closely related to their ability to adapt to environmental conditions. The genetic structure of camels bred in different geographical regions is formed in response to their breeding history and environmental factors (Gui et al., 2007).

The genetic diversity of camels can be determined through many parameters, such as allelic diversity: the number of different alleles present in a population. The more alleles, the higher the genetic diversity. Heterozygous: the percentage of heterozygous individuals compared to the total number of individuals. High heterozygosity indicates high genetic diversity (Zinovieva and Gladyr, 2011).

The last century was characterized by the development of quantitative theory and methodology in the direction of accurate selection of economically important genetic traits in animal husbandry, as well as the prediction of genetic reactions to biotic and abiotic stresses. However, the development of molecular biological methods in recent decades has created interesting new tools for studying animal genetics and animal husbandry. However, genetic studies on camels are scarce, and the degree of genetic differentiation of Dromedary populations in Saudi Arabia is poorly documented. Local methods of controlling the selection of different ethnic groups can contribute to genetic differentiation, but on the other hand, there may also be gene flow between populations. Thus, this study is carried out with the aim of identifying the genetic diversity of four populations of Saudi camels and determining the relationship between them. The assessment of genetic variability in camels is important for the development of future breeding programs to preserve genetic resources and increase the productivity of camels (Evanno et al., 2005).

In Egypt, the camel ecotype is not well defined, and there is very little information about its genetic origin. Therefore, this study was carried out in part using the mitochondrial 16s region to determine the phylogenetic relationship and genetic variation of the three camel populations raised in Egypt (Baladi, Sudan, and Magrabi). The purpose of this study is to determine the genetic preservation of three camel breeds bred in Egypt using the mtDNA 16s gene and the phylogenetic relationships between our tested camels and other camel breeds in the world, to select high-quality animals for breeding (Amandykova et al., 2023).

The use of microsatellites is considered a powerful tool for monitoring alleles in a population and assessing genetic variation within and between breeds. TheGenes 2023, 14, 1373 of the 13 international panels on Animal Genetic Diversity (FAO, 2004) presented a list of 25 microsatellite markers to assess genetic diversity in camels; 16 of them are considered the most polymorphic and thus highly recommended for the genetic description of Dromedary camels. The genetic diversity of four groups of Moroccan camels was studied on the basis of these 16 microsatellite markers, which showed high informativeness and a high level of diversification of the studied genetic resources of camels (Al-Shorepy, 2011).

Other studies also describe the distribution, lineage, evolutionary history, domestication, and genetic diversity of various camel populations based on mtDNA, nuclear DNA, and holistic genomic sequencing, such as identifying the Association of polymorphisms in growth hormone, insulin-like growth factor, and other genes with some physical characteristics of camels (Yousif et al., 2019).

Recently, camel breeding has been developing rapidly in Kazakhstan, in particular, in 2022, about 272 thousand camels were registered there. The successful development of animal husbandry was largely due to the genetic characteristics of agricultural breeds. Mitochondrial DNA is the optimal molecular marker to trace the evolutionary history of matrilins due to their high rate of mutation, as well as to determine the speciation process (Al-Ajmi and Abdel Rahman, 2001).

The results obtained made it possible to determine the relationship of replication and hybridization, since camels in each population were classified into several subclasses. The results obtained using Gis SR and GA-ISSR markers to determine the genetic heterogeneity of camel species in PopGene and Microsoft Excel made it possible to determine the frequency of DNA fragments, the proportion of polymorphic loci, and the genetic diversity index for the studied populations using ISSR-PCR markers (Romanov et al., 2023).

The publication of the first draft of the genome of Dromedary camels in 2014 revealed several gene ontologies present in adaptive evolution, such as fat and water metabolism, heat stress response, and salt metabolism. Dromedary from Sudan studied the genome of camels and, using genotyping data, looked for selection signatures, where they found signals of natural selection in genes related to energy homeostasis, chondrogenesis, milk composition, and immune response. A recent study by Khalkhali-Evrig R. found that genes related to energy metabolism, reproduction, and long-term memory in Iranian Dromedary camels are also subject to natural positive selection (Khalkhali-Evrigh et al., 2022).

2. Purpose of the Work

Study of the genetic characteristics of camels bred in the Atyrau region using microsatellite DNA markers.

2.1. Research objectives

  1. extraction of DNA molecules from the blood of camels from the farm "Dastan Ata" of Atyrau region and analysis of their qualitative structure;

  2. determination of alleles in the SeqStudio genetic analysis apparatus to obtain amplicons of microsatellite loci and evaluate genetic polymorphisms by polymerase chain reaction (PCR) method;

  3. analysis of synthesized fragments using primers used in DNA synthesis.

2.2. Research materials and methods

In total, 10-15 ml of blood was taken from 30 camels from the farm "Dastan-Ata" of Atyrau region. And the resulting blood was stored in a special bag with test tubes in the refrigerator and delivered to the "Kazakh Research Institute of Animal Husbandry and Feed Production" in Almaty. Further research was carried out, separating DNA from the camel's blood.

Preparation of research samples, extraction of microsatelic DNA from clinical material, GeneJET™ complete blood genomic DNA purification, fragment reading by SeqStudio genetic analyzer.

The object of the study was the population of camels bred in Atyrau region, including genetic material (microsatellite DNA) of camels from the farm "Dastan Ata" located in Zhylyoi district.

The research work was carried out in the molecular genetic laboratory of the Kazakh Research Institute of Animal Husbandry and Feed Production in Almaty.

Research materials and devices: microcentrifuge, test tubes, vortex, medical gloves and dressing gown, dispenser, mini test tubes and tripods, pipettes and tips for them, thermomixer capable of heating up to 56 °C, shaking water bath or rocking platform, set "GeneJET™" for separating DNA from clinical material.

3. Results and Discussion

3.1. Measurement of isolated microsatellite DNA concentrations, purity testing

In order to carry out research work, DNA was isolated from the blood plasma of 30 different camels and 30 primers were taken to determine the purity of the extraction parts.

  1. DNA was isolated from camel blood by protocol;

  2. DNA, trimers and Master Mix were combined and placed in a thermocycle, setting the temperature on the SimpliAmp machine;

  3. Tested by electrophoresis;

  4. Passed PCR product cleaning;

  5. Inserted into the SeqStudio apparatus and determined the result with Samples Plot (Figure 1).

    Figure 1
    Installation in a thermocycle with temperature setting on the SimpliAmp machine.

    1. 1

      At 96 °C, only 1 cycle takes place; the DNA denaturation temperature takes 2 minutes;

    2. 2

      The temperature of 96 °C is included in 40 cycles. It is repeated every cycle;

    3. 3

      At 55 °C, the DNA binding temperature of the primer is 45 seconds;

    4. 4

      At a temperature of 72 °C, it is repeated every 35-40 cycles and occurs for 45 seconds.

The primer synthesizes the chain we need further after binding (elongation).

  1. After the completion of 40 cycles, the synthesis of the remaining chains of the total sequence at 72 °C takes place;

  2. The temperature of 4 °C is the temperature at which the work is completed, and everything is saved. After the process is completed, the DNA is stored in a cool 4 °C to prevent destruction.

The observed homozygosity and inbreeding coefficient (Fis) was calculated for different populations of Dromedary camels using the hom function of the GenABLE package in version 4.1.0 (44) of the R software. The Mann-Whitney U test in the two samples was used to test statistically significant differences in homozygous and Fis values between different dromedary populations. The Mann-Whitney U test in one sample was used to test whether the Fis values of each of the Dromedary populations differed significantly from zero. To determine the genetic relationship between dromedary populations, a primary component analysis (PCA) was performed based on filtered SNP data. The Prcomp function implemented in the R software was used to determine the different basic components and the amount of variation interpreted by each component. Ancestral cluster (K) values from 1 to 3 were taken to represent the total number of populations in the data set. A total of 200 iterations of the bootstrap were performed for each K analysis. A cluster K with the lowest cross-validation error (cv) was considered as the optimal number of clusters corresponding to the data set.

3.2. Analysis of research results

Inserted into the SeqStudio apparatus and reviewed the result from Samples Plot. As can be seen from Figure 1, all samples are valid and the process is set correctly (Figure 2).

Figure 2
Genetic structure of camel breeds by microsatellite DNA loci.

Bars and values of quality values:

  • − Pure base with QV 320;

  • − Pure base with QV 15-19;

  • − Pure base with QV <15.

Mixed base bells are highlighted in red (if they exceed the mixed base limit specified in the analysis settings).

We prepared sequencing reactions according to the instructions of the kit and cleaned the extension products with ethanol sprinkling and spinning columns or with the BigDye XTerminator™ cleaning kit. It is worth noting that if ethanol sowing or spinning columns are used, the samples should be dried in a vacuum centrifuge without heat or over low heat for 10-15 minutes or until dry. Note: do not over-dry the samples.

  • − We reuse 10-20 µL of Hi-Di™ formamide;

  • − For samples prepared with the BigDye Xterminator cleaning kit, a sample volume of 65 µL or 130 µL was used;

  • − For samples prepared using Hi-Di, a sample volume of 10-20 µL was used;

  • − Made sure Hi-Di formamide is fresh;

  • − Hi-Di Formamide should not exceed two freeze-thaw cycles (one for aliquot, the other for use);

  • − Used on the same day after thawing;

  • − Do not put samples back in water, this may reduce the stability of the sample (Figure 3).

    Figure 3
    Distribution of expected and empirically observed heterozygotes and homozygotes across the loci of the 30 camels studied.

As shown in Table 1, the total number of bases obtained by sequencing ranged between 142.1 bps and 223.22 bps among the 30 camels. Heterozygous at locus CVRL05 – 151.23; 144.48. Heterozygous at locus LCA66 – 209.66; 221.4. Heterozygous at locus VOLP08 – 142.09; 152.62.1. At locus 1, those that show the same fragment are homozygous, and those that show different fragments are heterozygous. The primers were studied by dividing them into 2 by 2 different temperatures. So, according to the results of research work, it was shown that all camels have similar population genetic characteristics. The reason why camels are all similar is that they all graze together in the same barn and are not different because their parents are the same, very closely related camels.

Table 1
Correlation with statistical indicators of genetic diversity for all loci.

Today, such breeding work does not allow us to fully comply with the requirements of the program for an immediate increase in the productivity of animals. This is because it takes many years to increase the productivity of animals through phenotypic traits.

In recent years, the rapid development of Molecular Genetics and Biology has made it possible to select farm animals by genotype.

Breeding animals by genotypes has several advantages over phenotypic approaches. Firstly, it is possible to increase production efficiency by genotyping animals from a young age, without taking into account the influence of the external environment on the signs of effective productivity on the farm.

Secondly, it makes it possible to improve the productivity of populations directly at the DNA level, that is, in an effective direction through the marker of performance traits.

Third, it is possible to create a unique documentary database by identifying and passivating the necessary alleles in the population. Taking into account these conditions, for the first time, we conducted a microsatellite analysis of the population of camels bred in different regions of our country.

A microsatellite is a short sequential repetition of the DNA sequence and is characterized by a high degree of polymorphism. Microsatellites are widely used as criteria for assessing the gene pool, inter-population genetic difference, and population structure (system) of agricultural animals.

From the data of Table 2, it can be seen from the results of the study in the population "Dastan-Ata" that in loci other than the YWLL-08 locus, the number of informative alleles ranged from 0.75% to 1.0%. While alleles with a high level of informativeness were present only at locus LCA-37, in loci YWLL-08 and VOLP10, on the contrary, the frequency of occurrence of these alleles was 0.75 and 1%, respectively. The average number of informative alleles was intermediate at all loci.

Table 2
Frequency of occurrence of informative alleles in the camel population of “Dastan Ata”.

In the course of the study, it was found that the classification of alleles by informative level is of particular importance. This is because, although the number of informative alleles identified in the population was high, their informative level was different. In particular, the number of alleles with a high informative level was small, and the number of alleles with a low level was high.

Therefore, in order to be fully aware of the genome of camels in a population, alleles with a high informative level are needed. Undoubtedly, the results of such a study will be of great importance in the technology of identification and documentation by the animal genomes.

We identified an effective allele that represents genetic diversity and homozygous levels in the studied populations.

4. Conclusion

The population and genetic characteristics of camels bred in the Atyrau region were studied and analyzed. The study was carried out using microsatellite DNA markers.

The frequency of alleles and genotypes according to the selected microsatellite loci in camels was determined. The main genetic population parameters, such as expected heterozygosity, observed heterozygosity, inbreeding coefficient, etc., were calculated, and the genetic diversity and structure of the camel population in the studied area were analyzed.

Thus, the conducted study made it possible to obtain new knowledge about the genetic structure and diversity of the camel population bred in the Atyrau region, which is important for the preservation and sustainable use of these valuable animals.

In the course of achieving the goals and objectives of our study, the following work was done and summarized:

  1. DNA molecules were isolated from the blood of camels from the farm "Dastan Ata" of Zhylyoi district, and their qualitative structure was analyzed;

  2. Alleles were identified in the SeqStudio genetic analysis apparatus to obtain amplicons of microsatellite loci and evaluate genetic polymorphisms using the polymerase chain reaction method;

  3. Primers were studied by dividing them into 2 by 2 different temperatures. So, according to the results of research work, it was shown that all camels have similar population genetic characteristics. The reason why camels are all similar is that they all graze together in the same barn and are not different because their parents are the same, very closely related camels.

Genetic analysis of the camel breed for each studied locus showed that each line differs in its own genetic structure. This is evidence that the main breeds of camels in terms of the loci of DNA microsatellites have a high genetic diversity and a sufficient genetic reserve. The features found make it possible to use individual loci for various purposes of genetic population research.

To study the population and genetic characteristics of camels bred in the Atyrau region, the following methods are used using microsatellite DNA markers:

  • DNA isolation: DNA is extracted from camel tissue or blood samples, which is used as a material for analysis;

  • Strengthening microsatellite loci: With the help of PCR (polymerase chain reaction), certain areas of DNA - microsatellite loci - are amplified (copied). This will allow us to get enough material for further analysis;

  • Electrophoresis: The reinforcement products are separated by gel electrophoresis. This results in bands corresponding to certain alleles of microsatellite loci;

  • Data analysis: The data obtained is analyzed using specialized software. The frequency of alleles and genotypes is determined, and the main genetic-population parameters such as expected heterozygosity, observed heterozygosity, inbreeding coefficient, and others are calculated;

  • Statistical analysis: In order to identify patterns and differences between camel populations, a statistical analysis of the data obtained is carried out;

  • Phylogenetic analysis: Based on the data obtained, a phylogenetic tree is created that allows us to visualize genetic connections between different camel populations.

Data Availability Statement

The entire data set that supports the results of this study will be published in the article itself.

Transparency declaration

The author declares that all his co-workers are informed of this paper and its contents. We confirm that neither the article nor any parts of its content are currently under consideration or published in another journal. All data obtained or analyzed in the course of this research are included in the article for publication. Other or additional data that confirm the findings of this research are available upon request from the corresponding author.

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Editor:

Takako Matsumura Tundisi

Publication Dates

  • Publication in this collection
    17 Aug 2026
  • Date of issue
    2026

History

  • Received
    04 May 2026
  • Accepted
    25 June 2026
Creative Common - by 4.0
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