Ecological genetics

BACKGROUND: One approach to identify the “traces” of selection is to search for extended homozygous (ROH) and heterozygous-enriched (HRR) regions in the animal genome. ROH islands are thought to result from directional selection, while HRR islands are thought to result from balanced selection.

AIM: This study aimed to perfrom a genome-wide SNP analysis of the genotype of cross-selected Cornish chickens to identify ROH and HRR islands on their chromosomes and to annotate the genes within them.

METHODS: For this study, biological materials of the Cornish Hubbard cross were obtained from the biobank of the RRIFAGB institute. The chickens were genotyped with a 60K SNP array.

RESULTS: The HRR segments were an order of magnitude shorter than the ROH segments. The data indicate the removal of monomorphic SNPs from the chicken genome, since SNPs with a minor allele frequency (MAF) < 0.01 were removed. The localization of the ROH islands was completely altered by the removal of SNPs with a MAF < 0.01, whereas the localization of the HRR islands was only partially altered. Genes in the ROH islands identified while retaining SNPs with a MAF < 0.01 are responsible for chicken weight and their feed consumption. Removal of SNPs with a MAF < 0.01 identified ROH islands containing genes associated with the regulation of intramuscular fat content and the number of eggs laid. The HRR islands that were found contain genes responsible for chicken body weight, feed intake, and embryonic development.

CONCLUSIONS: Genes located in ROH islands are responsible for the consumer traits of the Cornish meat breed bred by directional selection, while genes located in HRR islands are most likely not targets of balanced selection.

BACKGROUND: Despite compelling evidence of convergent evolution in the EGLN1 and SPRTN genes in indigenous populations of the Andes and Tibet, the role of these adaptive variants in inhabitants of other high-altitude regions, particularly the Caucasus, remains unexplored. This study will determine whether the identified genetic pattern is universal or Caucasian populations exhibit unique pathways of genetic adaptation to high altitudes.

AIM: This study is aimed identify differences in the distribution of allele and genotype frequencies of genetic variants rs479200 (in EGLN1) and rs2437150 (in SPRTN) between the highland population of Balkars and the lowland population of Kabardians inhabiting the plains and foothills of the Central Caucasus, in order to assess the contribution of these variants to the formation of adaptive traits to hypoxia.

METHODS: Samples of Balkars (n = 132) and Kabardins (n = 131) were collected from representatives of these ethnic groups living in the highland and lowland zones of the Kabardino-Balkarian Republic, respectively. Genotyping was performed using the KASP method.

RESULTS: Population genetic analysis revealed significant differences in the distribution of genotypes and alleles of the hypoxia genes EGLN1 and SPRTN between Balkars and Kabardians. In the Balkar population, signs of selection were detected, including increased heterozygosity for the rs479200 locus of EGLN1 and a higher frequency of the adaptive allele rs2437150 of SPRTN. These differences likely reflect local adaptation to high-altitude conditions, despite the overall genetic similarity of the Caucasus populations.

CONCLUSION: A study of the role of EGLN1 and SPRTN in the Balkars’ adaptation to high altitude revealed a complex picture: EGLN1 exhibits a unique, balanced selection favoring heterozygotes, whereas SPRTN exhibits universal, positive selection. This demonstrates a combination of unique and universal evolutionary pathways for adaptation to hypobaric hypoxia.

Cystinuria is an inherited disorder caused by impaired reabsorption of cystine and dibasic amino acids—ornithine, lysine, and arginine—in the proximal renal tubules. Ornithine, arginine, and lysine are highly soluble in urine, but the solubility of cystine depends on pH and is low under physiological conditions. The genetic basis of cystinuria involves mutations in the SLC3A1 gene (encoding the heavy subunit rBAT of the Na⁺-independent amino acid transporter (rBAT-b^0,+AT) and the SLC7A9 gene (encoding the light subunit b^0,+AT). Dysfunction of the rBAT-b^0,+AT transporter leads to excessive cystine excretion, promoting urine supersaturation, crystallization, and the formation of cystine stones. Mutations in SLC7A9 exhibit a broad inheritance spectrum, ranging from recessive to dominant. Mutations in SLC3A1 are usually considered autosomal recessive; heterozygous carriers of these mutations mostly have a normal urinary amino acid profile, whereas homozygotes exhibit various symptoms of cystinuria. Accumulating clinical evidence reveals genotypic–phenotypic discordance that challenges this classical model. This review systematizes atypical cases where heterozygous carriers of pathogenic SLC3A1 mutations manifest recurrent cystine stones and hypercystinuria, whereas family members with identical mutations remain asymptomatic. Notably, approximately 10% of patients lack detectable mutations in the coding regions of these genes, suggesting the potential involvement of non-coding regulatory regions or modifier genes, including but not limited to SLC7A10 (ASC1), SLC1A5 (ASCT2), and SLC7A13 (AGT1). The review concludes that additional methods, such as whole-genome sequencing of well-characterized families, are necessary to identify these hidden genetic factors, improve diagnostic accuracy, and better understand the molecular mechanisms underlying cystinuria.

BACKGROUND: Sourdough is an important semi-finished product in bakery production, largely determining the quality of baked goods. Studying the taxonomic composition of the microbiome of sourdoughs from different regions of the Russian Federation and the Republic of Belarus will ultimately enable the selection of lactic acid bacteria and yeast strains with high biotechnological properties for the development of new microbial consortia that will standardize the fermentation process and control the quality of baked goods, thereby ensuring sustainable development and import independence of the country’s bakery enterprises.

AIM: To study the taxonomic diversity of bacteria and yeasts in sourdoughs from different regions of the Russian Federation and the Republic of Belarus.

METHODS: The study included 27 bakery sourdoughs, including rye, wheat, and gluten-free varieties, collected in 2025 from various regions of the Russian Federation and the Republic of Belarus. The sourdoughs were used in industrial and artisanal production. The taxonomic structure of the bacterial and fungal microbiome was determined using nanopore sequencing (Oxford Nanopore Technologies).

RESULTS: Using standard microbiological methods, it was found that the lactic acid bacteria content in the starters varied from 7.7 to 9.4 lg CFU/g, while yeast ranged from < 4 to 7.8 lg CFU/g. Acetic acid bacteria were detected in six starters (from 4.2 to 7.5 lg CFU/g). In 59% of the samples, the lactobacilli Fructilactobacillus sanfranciscensis predominated in the bacterial communities (accounting for 93.3%–100% of the metagenome). Yeasts of the species Kazachstania humilis and/or Saccharomyces cerevisiae predominated in the sourdoughs. Yeasts of the species K. barnettii, K. kunashirensis, K. spencerorum, K. piceae, K. bulderi, K. unispora, K. jinghongensis, and K. exigua were identified, which had not previously been detected in Russian bakery sourdoughs.

CONCLUSION: Sourdough production conditions (industrial production / bakery / home conditions), as well as the raw materials used, have a statistically significant effect on the alpha diversity of sourdough bacterial communities.

BACKGROUND: Retrotransposons are mobile genetic elements that replicate via reverse transcription and constitute substantial fractions of eukaryotic genomes; they are also considered evolutionary precursors of retroviruses, and can affect host fitness. Intriguingly, some retrotransposon proteins share motifs with amyloids—fibrous protein aggregates with cross-β architecture that readily self-assemble into polymeric structures and can, in some cases, self-propagate in an infectious manner (prions).

AIM: To identify and characterize potential amyloid-forming regions within the integrase of Saccharomyces cerevisiae Ty1 retrotransposon, which mediates integration of transposon copies into the host genome.

METHODS: Computational analysis of the Ty1 integrase sequence was performed with the ArchCandy algorithm to identify putative amyloidogenic motifs. To evaluate the amyloidogenic potential of candidate regions, we employed a yeast-based nucleation assay. Aggregation was visualized by expressing Ty1Int(AD)-GFP fusion constructs. Colocalization of Ty1 amyloidogenic domain with full length in yeast cells was evaluated by confocal microscopy.

RESULTS: We identified and experimentally validated an amyloidogenic region within the Ty1 integrase, designated Ty1Int(AD). ArchCandy predicted the region with amyloidogenic potential, and these predictions were confirmed in a yeast prion-nucleation assay and by expression of the Ty1Int(AD)-GFP fragment, which formed detergent-resistant aggregates. Confocal microscopy showed co-localization of these aggregates with native Ty1 integrase fused with YFP, indicating recruitment of the full-length protein into inclusions.

CONCLUSION: Together, these results identify a previously unrecognized amyloidogenic region within Ty1 integrase, possessing amyloid-like properties, and suggest that aggregation of this domain may regulate retrotransposon activity by altering integrase availability and/or function. This is therefore important for the design, optimization, and biosafety assessment of retrotransposon based vectors and other GMO constructs.