Decoding a highly mixed Kazakh genome

Whole-genome sequencing reveals genetic architecture and selection signatures of Kazakh cattle

Local cattle breeds play a critical role in breeding programs due to their genetic adaptations to diverse environmental conditions. However, the genomic architecture of local cattle breeds in Kazakhstan remains largely unexplored. This study utilized whole-genome sequencing data from Kazakh cattle to elucidate their genetic composition, uncovering three primary ancestral components: European, Eurasian, and East Asian taurine. The East Asian taurine lineage likely represents the earliest genetic contribution to Kazakh cattle but was largely replaced by subsequent waves of cattle migrations across Eurasia, leaving only a minor genetic signature in the current cattle population. In contrast, Eurasian taurine ancestry predominated in the Alatau and Kazakh local breeds, while the European taurine component was most prevalent in Kazakh white-headed cattle, consistent with their documented breeding history. Kazakh cattle exhibited higher genetic diversity and lower inbreeding coefficients compared to European commercial breeds, reflecting reduced exposure to intense artificial selection. A strong selection signal was identified on chromosome 6 at a locus encompassing PDGFRA, KIT, and KDR, which may be associated with the white-headed pigmentation characteristic of Kazakh white-headed cattle. Additional genes under selection were linked to lipid metabolism ( IRS1, PRKG1, and ADCY8), meat production traits ( KCNMA1, PDGFRA, HIF1A, and ANTXR1), and dairy production ( ATP2B1, DHX15, FUK, NEGR1, CCDC91, COG4, and PTK2B). This study represents the first comprehensive analysis of nuclear genome data from local Kazakh cattle. It highlights the impact of historical cattle migrations across Eurasia on their genetic landscape and identifies key genomic regions under selection. These findings advance our understanding of the evolutionary history of cattle and offer valuable genetic resources for future breeding strategies.

Gene pool preservation across time and space In Mongolian-speaking Oirats

The Oirats are a group of Mongolian-speaking peoples residing in Russia, China, and Mongolia, who speak Oirat dialects of the Mongolian language. Migrations of nomadic ethnopolitical formations of the Oirats across the Eurasian Steppe during the Late Middle Ages/early Modern times resulted in a wide geographic spread of Oirat ethnic groups from present-day northwestern China in East Asia to the Lower Volga region in Eastern Europe. In this study, we generate new genome-wide and mitochondrial DNA data for present-day Oirat-speaking populations from Kalmykia in Eastern Europe, Western Mongolia, and the Xinjiang region of China, as well as Issyk-Kul Sart-Kalmaks from Central Asia, and historically related ethnic groups from Altai, Tuva, and Northern Mongolia to study the genetic structure and history of the Oirats. Despite their spatial and temporal separation, small current population census, both the Kalmyks of Eastern Europe and the Oirats of Western Mongolia in East Asia are characterized by strong genetic similarity, high effective population size, and low levels of interpopulation structure. This contrasts the fine genetic structure observed today at a smaller geographic scale in traditionally sedentary populations, and is conditioned by high mobility and marriage practices (traditional strict exogamy) in nomadic groups. Conversely, the genetic profile of the Issyk-Kul Sart-Kalmaks suggests a distinct source(s) of genetic ancestry, along with indications of isolation and genetic drift compared to other Oirats. Our results also show that there was limited gene flow between the ancestors of the Oirats and the Altaians during the late Middle Ages. Source of the yurt image: https://www.vecteezy.com/free-vector/yurt .

Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals

Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the genomes of five ethnic Kazakhs at high coverage using the Illumina HiSeq2000 next-generation sequencing platform. The five Kazakhs yielded a total number of base pairs ranging from 87,308,581,400 to 107,526,741,301. On average, 99.06% were properly mapped. Based on the Het/Hom and Ti/Tv ratios, the quality of the genomic data ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Genetic variants were identified and annotated. Functional analysis of the genetic variants identified several variants that were associated with higher risks of metabolic and neurogenerative diseases. The present study showed high levels of genetic admixture of Kazakhs that were comparable to those of other Central Asians. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype–phenotype relations at the population level.

North Asian population relationships in a global context

Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.

The Heart of Silk Road "Xinjiang," Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy-Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.