Bakhytzhan Bekmanov

Understanding the genetic diversity and population structure of farm animals is key to developing effective breeding strategies and conserving genetic resources. The aim of this study was to assess the genetic diversity and population structure of the Auliekol cattle breed based on genotyping using the BovineSNP50 BeadChip. This study included 1440 animals from eight farms. Genetic diversity indices (observed and expected heterozygosity), the inbreeding coefficient (F_IS), and allelic richness were calculated, and population structure was analyzed using PCA, ADMIXTURE, fineSTRUCTURE, and genomic relationship matrix (GRM) methods. The results showed comparable levels of observed and expected heterozygosity across populations (Ho = 0.3478–0.3537; He = 0.3445–0.3492) and negative F_IS values ranging from −0.0211 to −0.0025, suggesting no strong population-level signal of inbreeding. Low F_ST (0.007–0.028) and GRM values indicate weak genetic differentiation between populations. PCA and fineSTRUCTURE analyses showed no clear clustering, while ADMIXTURE identified three main genetic components shared across all populations. TreeMix analysis further suggested genetic connectivity among farms, with the Moskalyevskoe population occupying a central position in the inferred network of genetic relationships and migration events. In general, the Auliekol breed is characterized by a high level of genetic coherence and preserved genetic diversity, which creates favorable conditions for its further selective improvement and the preservation of genetic resources.

The Eurasian Steppe in the first millennium BCE saw the rise of the Scytho-Siberian archaeological horizon, which would come to stretch from the Altai Mountains in the east to the Black Sea in the west. We examined the genetic profiles of Iron Age Scythians to explore how social status shaped biological relatedness and ancestry patterns. We present genome-wide data from 85 individuals (38 elite and 47 non-elite), including 45 newly sequenced individuals and the first genome-wide data for the Scythian “Golden Man.” We identify consanguineous unions, a reduced effective population size, and identity-by-descent links among the elites. Dynastic rule is supported by elite grandparent-grandchild relationships across cemeteries. While ancestries are heterogeneous, elite Iron Age Scythians show lower variation and no detectable patrilocal or matrilocal signal. These findings highlight hereditary status transmission and the emergence of social stratification in ancient nomadic societies.

Бұл зерттеуде Қостанай облысы Әулиекөл ауданы «Тимофеев-Агро» шаруашылығынан алынған 308 бас Әулиекөл ірі қара популяциясының генетикалық құрылымы BovineSNP50 микрочипінің негізінде алынған мәліметтер арқылы талданды. Сапалық бақылаудан кейінгі талдауда 22,865 аутосомалық SNP болды және үлгілердің орташа генотиптеу тазалығы 0.99947 мәнін құрады. Популяциялық құрылымды бағалау мақсатында негізгі компоненттерге талдау (PCA), ADMIXTURE және identity-by-descent (IBD) негізіндегі генетикалық ұқсастық зерттеулері жүргізілді. PCA нәтижелері үлгілердің басым бөлігінің орталық аймақта шоғырланып, айқын популяциялық стратификацияның жоқ болатындығын көрсетті, ал жекелеген үлгілердің орталық кластерден салыстырмалы түрде алшақ орналасуы популяция ішіндегі генетикалық вариацияның бар екенін аңғартты. IBD талдауы нәтижесінде алынған генетикалық ұқсастық қатнастары популяцияның тұтастығын және үлгілер арасындағы генетикалық жақындықтың үздіксіз сипатын көрсетті. ADMIXTURE талдауы (K=2-5) зерттелген популяцияда бір негізгі ата-тектік компоненттің басым болатындығын, ал қосымша компоненттердің әртүрлі пропорцияда көрінуі дербес субпопуляцияның болмайтындығын көрсетті. PCA, ADMIXTURE және IBD нәтижелері бірін-бірі толықтыра отырып, Әулиекөл ірі қара популяциясының генетикалық құрылымы біртекті екенін, айқын субпопуляциялық бөлінудің жоқтығын және популяция ішіндегі генетикалық әртүрліліктің табиғи деңгейде екенін көрсетті. Алынған нәтижелер бұл популяцияның әрі қарай геномдық зерттеулер мен селекциялық бағдарламалар үшін сенімді генетикалық негізге ие екенін айғақтайды.

Honeybee (Apis mellifera L.) populations are a vital resource for pollination and honey production, yet their genetic diversity in Central Asia remains poorly understood. This study provides a comprehensive genetic assessment of 16 honeybee populations from Kazakhstan, with comparative samples from Russia, Georgia and Kyrgyzstan, utilizing mitochondrial COI–COII intergenic region and 12 highly polymorphic nuclear STR markers. Mitochondrial DNA analysis revealed the predominance of the Eastern European C lineage (A. m. carnica), while a few populations from East Kazakhstan and Russia attributed the M lineage (A. m. mellifera), indicating local introgression and the persistence of relict lineages. STR analyses showed high levels of polymorphism and genetic diversity, with variation in heterozygosity and inbreeding across populations. Analyses of population genetic structure delineated four principal genetic clusters shaped by regional differentiation, historical gene flow, and sporadic admixture. Concordance between mitochondrial and nuclear markers confirms the robustness of these findings. Overall, this study highlights the rich genetic diversity of honeybees from Kazakhstan and emphasizes the importance of conserving local populations and implementing selective breeding programs to sustain adaptive potential and long-term apiculture.

Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics remain poorly studied. This raises concerns about the potential loss of unique, breed-specific traits that could be important for the future development and resilience of Kazakh stan’s sheep farming sector. This study aimed to analyze genome-wide genotyping SNP data of local fat-tailed coarse-wooled sheep breeds (Kazakh fat-tailed coarse-wooled, Edilbay, and Gissar) to reveal their genetic diversity, breed characteristics, and phylogenetic relationships with worldwide domestic sheep breeds and wild sheep. Methods: The OvineSNP50 Genotyping BeadChip was used to obtain genome-wide SNP genotyping data from 160 fat-tailed coarse-wooled sheep from Kazakhstan. Population structure analysis, principal component analysis, phylogenetic and the maximum likelihood tree analysis were performed in comparison with foreign domestic sheep breeds and wild sheep populations. Results: Kazakh breeds exhibited high genetic diversity, with Edilbay showing the greatest allelic richness. PCA and Admixture revealed clear differentiation among the three breeds: Edilbay and Gissar formed homogeneous clusters, while Kazakh fat-tailed coarse-wooled sheep displayed admixture and substructure. Evidence of gene flow from Edilbay into other Kazakh populations supports its role as a genetic source for regional breeds. Phylogenetic analysis placed Kazakhstani sheep close to other Central Asian breeds, while clearly distinct from East Asian and European populations. Wild sheep (Argali and Urial) formed separate clades, with Kerman wild sheep clustering closer to Urial. Conclusions: Our results highlight the value of genotyping data for studying genetic diversity and population structure. Developing genetic resources for Kazakhstan’s native sheep breeds will help preserve their unique diversity and ensure it remains available for future use in breeding and adaptation efforts.

Sheep play a central role in Kazakhstan’s pastoral economy, yet the maternal genetic composition of its traditional breeds remains poorly characterized. We analyzed partial mitochondrial D-loop sequences (848 bp) from 115 individuals of three fat-tailed coarse-wooled breeds (Edilbay, Kazakh fat-tailed coarse-wooled, and Gissar) to assess genetic diversity, population structure, and phylogenetic relationships. Ninety-eight haplotypes were identified, indicating high haplotype diversity (Hd = 0.996 ± 0.002) and moderate nucleotide diversity (π = 0.02624 ± 0.00048). Haplotypes clustered into haplogroups A (57.4%) and B (42.6%), with Edilbay dominating the star-like cluster of haplogroup A, consistent with recent expansion. AMOVA revealed that most variation (92.03%) occurred within populations, with no significant differentiation among breeds. Phylogenetic analyses placed Edilbay close to the most recent common ancestor of fat-tailed domestic sheep and the wild Ovis species, suggesting retention of an ancestral lineage. These findings highlight Kazakhstan as a genetic crossroads in sheep history and underscore the conservation value of its maternal diversity.

Camels have been essential to human survival and development across the arid Central Asian steppes, particularly in Kazakhstan, where the breeding of one-humped and two-humped camels is a longstanding tradition supporting the nomadic lifestyle. This study aimed to assess the genetic diversity and population structure of these camels across their distribution range in Kazakhstan. Blood samples from 100 individuals were collected from five locations, Almaty (ALA), Atyrau (ATR), Shymkent (SHK), Kyzylorda (KZL), and Taraz (TRZ), and genotyped using 17 microsatellite markers. All loci were polymorphic, with a mean observed heterozygosity of 0.707 in C. dromedarius and 0.643 in C. bactrianus. The highest expected heterozygosity (He = 0.939) was observed at VOLP67 in C. bactrianus and at VOLP03 in C. dromedarius. Genetic differentiation was low (FST = 0.021), indicating a weak population structure between the two species with substantial gene flow (Nm = 19.972). The hybrid analysis identified 31% hybrids, including F1, F2, and backcrosses, with the highest frequencies in KZL and TRZ, moderate frequencies in ATR, and lowest frequencies in SHK and ALA. These patterns, consistent with STRUCTURE clustering, reflect widespread but regionally variable hybridization. The phylogenetic analysis revealed three clades, separating Bactrian camels (ALA), dromedaries (SHK), and a hybrid group (ATR, KZL, and TRZ). These findings enhance our understanding of the genetic diversity of Kazakhstan’s camels and support effective conservation, breeding strategies, and genotyping applications in camel husbandry.

The Kazakh Tazy is a unique breed of dog characterized by its special morphological features and behavior. In addition to its biological characteristics, the Tazy occupies a special place in the cultural and historical heritage of the Kazakh people and has been officially recognized as part of the national heritage. Historically, it played an important role in the nomadic lifestyle of life of the Kazakhs and was an indispensable companion in traditional hunting. Within the traditional Kazakh value system known as the “Seven Treasures”, the inclusion of the Tazy emphasizes its high socio-cultural status. Previous studies have examined the genetic relationships between the Kazakh Tazy and other sight hound breeds. In this study, analysis was extended to examine the genetic relationship of the Tazy with a wider range of hunting dog breeds. The dataset included whole-genome SNP genotyping results from 39 Kazakh Tazy dogs, 471 dogs representing 16 different hunting dog breeds, and 18 gray wolves (Canis lupus) that served as an outgroup. The results confirmed earlier findings indicating a close genetic relationship between the Kazakh Tazy and the eastern sighthounds, the Arabian Saluki and the Afghan Hound, while also confirming the breed’s genetic distinction from other breeds. In addition, phylogenetic analysis revealed a remarkable genetic relationship between the Tazy and the Basenji, suggesting an ancient origin of this lineage. These results contribute to a deeper understanding of the phylogenetic history of hunting dog breeds and demonstrate once again the importance of the Tazy as a unique cultural and genetic heritage.

The aim of the study is to assess the impact of radiation pollution on the stability of the genome and human health, taking into account the long-term genetic consequences. Measurements of gamma activity showed that the radiation level of the surveyed territory of the landfill and adjacent settlements is in the range of 0.06-0.014 mSv/h. Of particular importance in this regard is the study of the mechanisms of individual sensitivity to radiation and the role of the DNA repair system [1,36]. Molecular genetic studies of the DNA of blood cells and cytogenetic analyses of people living in the zone of influence of the radioactive waste landfill revealed the spread of several mutant genotypes, which indicates the likelihood of an increased risk of environmental diseases in persons with pronounced genome instability. The radiation level on the territory of the landfill and adjacent settlements is in the range of 0.06-0.014 mSv/h. By genotyping the XRCC1 Arg399Gln DNA repair gene, it was found: homozygous Arg/Arg (89+159), heterozygous Arg/Gln (248+159+89 ), homozygous Gln/Gln (248). The genotype distribution is as follows: XRCC1 Arg/Arg - 15 people, XRCC1 Arg/Gln - 14 people, XRCC1 Gln/Gln - 1 person. Key words: mutagens, radiation, environment, genes, hereditary diseases, genome

Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10⁻⁶) and MGAT5 gene (p = 8.4 × 10⁻⁶). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10⁻⁴). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction.