Lamb meat has become increasingly popular in several nations during the last few decades, especially in Kazakhstan. Due to the rising demand for lamb meat, our sheep breeders developed a new fat-tailed sheep and named the breed Baisary. Animals of the Baisary breed are characterized by a large physique, strong constitution, stretched body, deep and wide chest, medium or large-sized fat tail, long legs (height at the withers of adult rams 85–100 cm, sheep 75–90 cm), long lanceolate ears and strong hooves. Lambs of the Baisary breed surpass their peers of the original parent breeds by 15–20% in live weight at the weaning period. To characterize the genetic structure of Baisary sheep and compare it with the ancestral breeds, we genotyped 247 individuals from five sheep breeds with Ovine SNP50K. The estimated private allelic richness ranged from 0.0030 to 0.0047, with the minimum and maximum provided by the Gissar (Giss1) and Kazakh meat-wool breeds, respectively. The highest and lowest F_IS values, meanwhile, were observed in the Afghan fat-tailed population and Baisary sheep, respectively. The calculated inbreeding coefficient showed that Edilbay and Baisary sheep have excess heterozygosity. According to principal components analysis, Baisary are close to Gissar populations, the Afghan fat-tailed breed and Edilbay sheep. These results were consistent with the Admixture and phylogenetic analysis. Overall, our results indicated that Baisary sheep differ genetically from their progenitors.

Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat–wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat–wool sheep using the Illumina iScan^® system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat–wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH_{1–2 Mb} were much higher than ROH_{2–4 Mb} and ROH_{8–16 Mb} in the three sheep populations. Most of individuals had small number of ROH_{>16 Mb}. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated F_ROH presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (BMP2, BMPR2, BMPRIB, CLOCK, KDM2B, TIAM1, TASP1, MYBPC1, MYOM1, and CACNA2D1), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat–wool sheep breed.

Sheep breeding is an important sector of livestock production in the Republic of Kazakhstan. The Kazakh fat-tailed coarse-wool sheep holds a prominent position among local breeds due to its high meat productivity, resilience to extreme climatic conditions, and efficient use of pasture resources. This study focuses on the analysis of runs of homozygosity (ROH) to evaluate the genetic diversity level, inbreeding and to detect selection signatures in the Kazakh fat-tailed coarse-wool sheep breed. A total of 500 animals were genotyped using the OvineSNP50 BeadChip (Illumina, San Diego, CA, USA). As a result, a total of 41,728 ROH segments were identified, with an average length of 1.59 Mb, distributed across the entire genome. The most prominent homozygous regions were detected on chromosomes OAR10, OAR13, and OAR22, which might be associated with selection signatures. Genomic inbreeding coefficients (F_ROH and F_GRM) showed a strong positive correlation (r = 0.58, p < 0.001), supporting the effectiveness of ROH-based analysis. Several candidate genes were detected, including MYF5, PRDM16, TGM3, SLC26A4 and SMAD5 which are notably involved in muscle formation, wool traits, and fat metabolism. The findings have substantial practical value for breeding programs and for managing genetic diversity in sheep farming enterprises in the Republic of Kazakhstan.

Background: In Kazakhstan, there is a notable demand for fat-tail sheep breeds in both domestic and international markets, which has led to the prioritization of certain breeds for breeding purposes. Among the various sheep breeds raised in the desert and semi-desert regions of Kazakhstan, the Kazakh fat-tailed coarse-wool sheep is particularly valued for its production of high-quality mutton. Objective: This study aimed to identify genomic regions and candidate genes associated with body conformation traits in this breed using a genome-wide association study (GWAS). Methods: A GWAS was performed on 295 Kazakh fat-tailed coarse-wool using OvineSNP50 Genotyping BeadChip (Illumina, San Diego, CA, USA). Results: After quality control, 41,912 single-nucleotide polymorphisms (SNPs) remained for analysis. Several loci showed suggestive associations (p < 1 × 10⁻⁵) with growth traits. These included s23127.1 and OAR6_56152225.1 for live weight; s08490.1 for chest width; s22731.1 for oblique length; OAR10_1168444.1 for cannon bone circumference; and s58409.1 for both rump height and withers height. Candidate genes near these loci encompassed VCAN, NEK1, NRG1, ADAM12, ERBB4, RUNX1T1, and PDGFD. Conclusion: Thus, these genetic variations have the potential to serve as candidate markers for MAS targeting body conformation traits in Kazakh fat-tailed coarse-wool sheep.

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.

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.