Jul 2026· International Journal of Molecular Sciences· Vol 27· 0 citations· 86 references
Medicine
Abstract
Kazakhstan ruminant genomics is expanding through targeted diagnostic testing, SNP-array studies, whole-genome sequencing, runs of homozygosity, candidate-gene analyses, transcriptomic studies and pathogen molecular diagnostics. However, these evidence types differ substantially in their relevance for breeding decisions. This structured narrative review evaluates molecular evidence for inherited disorders, deleterious alleles, disease-resistance loci, reproductive genes and genomic-health indicators in Kazakhstan cattle, sheep and goats. We define actionable evidence as evidence that can directly inform breeding management because it involves a validated pathogenic variant, risk variant or fertility haplotype detected or excluded in breeding-relevant animals or germplasm. Under this definition, cattle currently provide the strongest immediately actionable evidence, mainly because targeted studies have screened validated defects and fertility-related loci in artificial-insemination bulls, imported germplasm or breed-relevant populations. Evidence includes Kazakhstan-associated screening for BLAD (Bovine leukocyte adhesion deficiency), DUMPS (Deficiency of uridine monophosphate synthase), hypotrichosis, OH1-associated achromatopsia, fertility haplotypes and several beef- or dairy-breed recessive defects. In sheep, evidence is broader but less directly actionable, consisting mainly of prion protein gene preparedness, MHC (Major histocompatibility complex)-related immune hypotheses, reproductive candidate loci, runs of homozygosity, genome wide associated data and pathogen-exposure context. In goats, current evidence is mostly population-genomic and adaptation-oriented, while hereditary-disease surveillance and phenotype-linked resistance studies remain sparse. We propose an author-defined staged genomic-health framework that separates validated carrier-screening evidence from candidate genomic signals and international evidence requiring local validation. Priority actions include carrier-aware management of high-impact cattle germplasm, representative prion protein gene and runs of homozygosity baselines in small ruminants, phenotype-first surveillance, biobanking and national genotype–phenotype databases.
Relevance.
Small Ruminant Lentiviruses (SRLVs), including the Visna-Maedi Virus (VMV) in sheep, induce chronic progressive inflammation primarily targeting the nervous system, lungs, mammary glands, and joints. These viruses exhibit significant genetic variability, leading to a lack of effective therapies or vaccines at an affordable cost. Foreign research has identified breed-specific variations in genetic resistance to these pathogens, but such comparative data remain largely unexplored for Russian sheep breeds. A reliable DNA marker of genetic resistance to VMV infection is the ovine transmembrane protein 154 (TMEM154) gene. This study aimed to evaluate the allelic diversity among different Russian sheep breeds through targeted SNP within the TMEM154 gene linked to genetic resistance.
Methods.
The study utilized biological samples (tissues) of sheep maintained at the Ladozhsky PZ and from the biobank repository titled “Genetic Materials Bank of Domestic and Wild Animals.” To identify specific mutations correlated with resistance to VMV, fragments encompassing the target SNP (OAR17_5388531) within the TMEM154 gene were amplified via RT-PCR.
Results.
Analysis of TMEM154 polymorphisms uncovered two distinct alleles (C and T) along with their corresponding genotypes: TT, CT, and CC. Genotype distributions associated with resistance to the Visna-Maedi virus across eighteen diverse Russian sheep breeds have been documented.
O. S. Yakovleva, T. Deniskova, O. Koshkina et al.· Agrarian science· 0 citations
Recommendations are formulated for building a genetic health management system in beef cattle breeding, based on mandatory DNA testing, inbreeding control, accounting for pleiotropic effects in selection, and the integration of advanced biotechnologies.
N. Bezborodova, O. Sokolova, O. S. Zaitseva et al.· International Journal of Vet...· 0 citations
This narrative review synthesizes major advances in sheep genetic mapping, functional genomics, and GS relevant to economically important traits to provide researchers, breeders, and students with a balanced, evidence-based resource to guide future genomic improvements in sustainable sheep production.
Mostafa Ghaderi-Zefrehei, Effat Nasre Esfahani, Hassan Amini Pozveh et al.· Frontiers in Genetics· 0 citations
Simple Summary Porcine reproductive and respiratory syndrome is a serious infectious disease that causes reproductive problems, breathing illness, and major economic losses in pig production. Vaccines and farm management help control the disease, but they do not always provide enough protection because the virus changes easily. This study aimed to find inherited genetic features that may help identify pigs with better natural resistance to this disease. Pigs were first screened after vaccination and then after exposure to the virus, and animals with clearly different disease-response patterns were selected for detailed genetic analysis. By comparing genetic differences between resistant and susceptible pigs and combining these results with public data showing how genes behave during infection, this study identified several candidate genes and genetic regions related to disease response. A region on chromosome 8, especially around genes named NFXL1 and NIPAL1, was highlighted, and a specific genetic pattern in this region was more common in resistant pigs. These findings provide useful clues for future testing and may support breeding programs aimed at improving disease resistance in pigs.
Genomic signatures of selection can reveal loci underlying adaptation and disease resistance in livestock populations, but such analyses in water buffalo (Bubalus bubalis) have historically been constrained by the absence of a chromosome-level, species-native reference genome for SNP array data. We re-analyzed genotype data from 85 Nili-Ravi buffalo (Axiom Buffalo Genotyping 90K array, originally positioned using bovine (Bos taurus, UMD3.1) proxy coordinates, by performing a full coordinate liftover to the buffalo-native UOA_WB_1 assembly using an independently published SNP remapping resource. Following quality control (51,209 markers retained), haplotype phasing, and genome-wide integrated haplotype score (iHS) and Wright’s Fst (case/control) selection scans, we evaluated 14 classical bovine-tuberculosis (bTB) candidate genes and identified six additional genes with putative immune function through an unbiased genome-wide screen. None of the 14 classical candidates (including SLC11A1, the Toll-like receptors, and IFNG) reached genome-wide significance in either scan. In contrast, six novel loci TNFSF18, IL2RB, TNFRSF19, IRF2, IL15, and CD28 showed significant iHS or Fst signals, four of which (TNFSF18, IL2RB, IL15, CD28) converge functionally on T-cell costimulation and cytokine receptor signaling (KEGG pathways map04660 and map04060, Bos taurus proxy annotation). Using extended haplotype homozygosity (EHH) decay, haplotype furcation structure, and per-marker haplotype counts as three independent lines of corroborating evidence, we classified these six genes into confidence tiers: TNFSF18 and IL2RB showed the strongest, most balanced support, while CD28 and IL15 signals were driven by very few haplotypes (3 and 5 of 30, respectively) and should be interpreted cautiously pending replication. These findings suggest that adaptive, cell-mediated immune signaling rather than the innate/macrophage-centred mechanisms emphasized by existing bTB candidate gene panels may be a more productive avenue for future selection studies in Nili-Ravi buffalo, while underscoring the value of buffalo-native coordinate systems for accurate genomic inference in this species.
Atiq Ahmad, Abu Bakar, Sheikh Muhammad Laeeque et al.· bioRxiv· 0 citations
BACKGROUND
Native Anatolian goat breeds are genetic resources shaped by traditional management, selection, and adaptation to diverse environments.
OBJECTIVES
This study aimed to identify selection signatures in five goat breeds raised in Türkiye: Ankara, Damascus, Honamli, Kil, and Kilis.
METHODS
A total of 192 goats were genotyped using the Axiom Goat Genotyping Array containing 59,795 SNP markers. Genome-wide selection signatures were investigated using three complementary haplotype-based statistics: the integrated haplotype score (iHS), the integrated haplotype homozygosity pooled score (iHH12), and the number of segregating sites by length (nSL).
RESULTS
Across all analyses, 2,960 non-redundant gene-method-breed records were identified, corresponding to 2,385 unique candidate genes. The three methods revealed overlapping but complementary signals. iHS highlighted regions associated with production, pigmentation, growth, reproduction, and immunity; iHH12 identified a smaller set related to pigmentation, epithelial biology, immunity, metabolism, and reproduction; whereas nSL detected the broadest set, including regions linked to growth, lactation, lipid metabolism, pigmentation, immunity, reproduction, and vascular development. Repeatability analysis prioritized 276 core genes, 83 strong core genes, and 23 robust core genes recurrent across methods and breeds. Functional enrichment analysis highlighted melanogenesis, endocytosis, phosphatidylinositol signaling, Hippo signaling, calcium signaling, synaptic processes, and cytoskeletal regulation.
CONCLUSIONS
These findings provide genomic resources for validation, conservation, and sustainable management.
M. Bayraktar, I. Aytekin, Ö. Şahin· Scientific Reports· 0 citations