Search Results (16)

This article presents the results of a comprehensive study on Rosa acicularis Lindl., Rosa laxa Retz., and Rosa spinosissima L. growing in the sharply continental climate of the Kazakhstan Altai under diverse ecological and phytocenotic conditions. All three wild rose species show notable ecological plasticity, allowing them to thrive in heterogeneous environments. A total of 41 populations were recorded: 12 of R. acicularis, 13 of R. laxa, and 16 of R. spinosissima, with vertical distribution ranging from 404 to 1837 m a.s.l. Nine populations where each species dominates its plant community were selected as model sites to assess ecological, biological, and economic traits. For each population, the floristic composition and structure were described, and morphometric, resource, and physiological indicators were evaluated. Significant phenotypic variation was noted in plant height, bush diameter, leaf traits, and fruit morphology and taste. Under natural conditions, industrial thickets are mainly formed by R. laxa in the Southern Altai and by R. spinosissima in the Southwestern Altai due to their wide distribution and high plant density. Fruit weight ranged from 2.23 to 2.47 g (R. acicularis), 2.28 to 2.68 g (R. laxa), and 2.17 to 2.55 g (R. spinosissima), values generally lower than those previously reported. Based on coefficients of variation for intra-population diversity in morphological and quantitative traits, several promising populations were identified. These populations hold potential for selecting valuable forms for breeding programs and for establishing a regionally adapted gene pool. Full article

In small ruminants, laparotomy for ovarian exploration followed by oocyte collection has been progressively replaced by laparoscopic puncture of follicles, which has become an important method for obtaining oocytes in vivo. However, the superovulation protocols and collection frequency used for laparoscopic ovum pick-up (LOPU) in sheep still require further investigation. This study explored the factors influencing LOPU efficiency in sheep, including Controlled Internal Drug Release (CIDR) for estrus synchronization, FSH source and dose, and recovery intervals. The optimal superovulation protocol (using the CIDR device, a total of 16 mg of long-acting recombinant ovine FSH (LR-FSH) administered in two doses, and a one-month interval between LOPU sessions) was subsequently identified. Ovarian follicles were collected via LOPU from Hu sheep and Altay sheep for transcriptomic and metabolomic sequencing to explore interbreed differences in follicular development. The results indicated that LOPU efficiency was significantly higher in the CIDR group (p < 0.05) and with a 30-day recovery interval (p < 0.05). No significant differences in LOPU efficiency were observed between FSH sources or hormone doses. Furthermore, Hu sheep exhibited significantly higher LOPU efficiency and more antral follicles than Altay sheep. Transcriptomic analysis of follicular contents and metabolomic profiling of follicular fluid revealed that differentially expressed genes and metabolites were primarily enriched in pathways related to steroidogenesis, amino acid metabolism, and fatty acid metabolism. This study provides an optimized treatment protocol to enhance LOPU efficiency and integrates multi-omics analyses to elucidate the molecular mechanisms underlying follicular development differences among various breeds. Full article

This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. F_ST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). F_ST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point F_ST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions. Full article

This study presents a one-step multiplex reverse transcription polymerase chain reaction (RT-PCR) method for the simultaneous detection of multiple viruses affecting melon crops. Viruses such as Watermelon mosaic virus (WMV), Cucumber mosaic virus (CMV), Zucchini yellow mosaic virus (ZYMV), Squash mosaic virus (SqMV), Tobacco mosaic virus (TMV), Papaya ring spot virus (PRSV), and Melon yellow spot virus (MYSV) pose a great threat to melons. The mixed infection of these viruses is the most common observation in the melon-growing fields. In this study, we surveyed northern Xingjiang (Altay, Changji, Wujiaqu, Urumqi, Turpan, and Hami) and southern Xingjiang (Aksu, Bayingolin, Kashgar, and Hotan) locations in Xinjiang province and developed a one-step multiplex RT-PCR to detect these melon viruses. The detection limits of this multiplex PCR were 10³ copies/μL for ZYMV and MYSV and 10² copies/μL for WMV, SqMV, PRSV, CMV, and TMV. The detection results in the field showed 242 samples were infected by one or more viruses. The multiplex RT-PCR protocol demonstrated rapid, simultaneous, and relatively effective detection of viruses such as WMV, CMV, ZYMV, SqMV, TMV, PRSV, and MYSV. The technique is designed to identify these melon viruses in a single reaction, enhancing diagnostic efficiency and reducing costs, thus serving as a reference for muskmelon anti-virus breeding in Xinjiang. Full article

Background/Objectives: Orenburg goats are renowned for their soft down that acts as a substrate for warm clothing, particularly shawls that have an international reputation. As with many local livestock breeds, however, the Orenburg is presently at risk of extinction, an issue that can be addressed by assessing population genetic diversity and, thereafter, encouraging as much outbreeding as possible. Using single-nucleotide polymorphism (SNP)-based data, therefore, we analyzed the genetic diversity and population structure of modern Orenburg goats using samples collected from an expedition to Orenburg Oblast in 2024. Methods: We applied the Goat SNP50 BeadChip (Illumina, San Diego, CA, USA) for the genotyping of Orenburg goats from modern and archived populations. SNP genotypes of three Orenburg populations sampled in 2017 and 2019, Altai Mountain, Altai White, and Soviet Mohair breeds, were added to the dataset. Results: Principal component analysis and network and admixture analyses demonstrated that the genetic background inherent to the archived group of Orenburg goats was maintained in all modern populations. Values of genetic diversity indicators in modern populations were compatible with those obtained in comparison groups. Runs of homozygosity (ROH) were found in all the Orenburg goat populations (with a mean ROH length of 72.6–108.9 Mb and mean ROH number of 28–36). Genomic inbreeding based on ROH was low in all the Orenburg populations (F_ROH = 0.03–0.045). Conclusions: We showed that the ancestral background is retained in present-day Orenburg goats sampled in 2024. We provide the genetic basis through which certain breeder animals may be selected and bred traditionally or ex situ through a conservation program of gamete preservation. Full article

During the last twenty years, minimal white spotting associated with blue eyes was selected by feline breeders to create the Altai, Topaz, and Celestial breeds. Additionally, certain breeders introduced this trait in their lineages of purebred cats. The trait has been called “dominant blue eyes (DBE)” and was confirmed to be autosomal dominant in all lineages. DBE was initially described in outbred cats from Kazakhstan and Russia and in two purebred lineages of British cats from Russia, as well as in Dutch Maine Coon cats, suggesting different founding effects. We have previously identified two variants in the Paired Box 3 (PAX3) gene associated with DBE in Maine Coon and Celestial cats; however, the presence of an underlying variant remains undetermined in other DBE breeding lines. Using a genome-wide association study, we identified a single region on chromosome C1 that was associated with DBE in British cats. Within that region, we identified PAX3 as the strongest candidate gene. Whole-genome sequencing of a DBE cat revealed an RD-114 retrovirus LTR (long terminal repeat) insertion within PAX3 intron 4 (namely NC_018730.3:g.206975776_206975777insN[433]) known to contain regulatory sequences. Using a panel of 117 DBE cats, we showed that this variant was fully associated with DBE in two British lineages, in Altai cats, and in some other DBE lineages. We propose that this NC_018730.3:g.206975776_206975777insN[433] variant represents the DBE^ALT (Altai Dominant Blue Eye) allele in the domestic cat. Finally, we genotyped DBE cats from 14 lineages for the three PAX3 variants and showed that they were not present in four lineages, confirming genetic heterogeneity of the DBE trait in the domestic cat. Full article

In December 2019, a new coronavirus, SARS-CoV-2, was found to in Wuhan, China. Cases of infection were subsequently detected in other countries in a short period of time, resulting in the declaration of the COVID-19 pandemic by the World Health Organization (WHO) on 11 March 2020. Questions about the impact of herd immunity of pre-existing immune reactivity to SARS-CoV-2 on COVID-19 severity, associated with the immunity to seasonal manifestation, are still to be resolved and may be useful for understanding some processes that precede the emergence of a pandemic virus. Perhaps this will contribute to understanding some of the processes that precede the emergence of a pandemic virus. We assessed the specificity and virus-neutralizing capacity of antibodies reacting with the nucleocapsid and spike proteins of SARS-CoV-2 in a set of serum samples collected in October and November 2019, before the first COVID-19 cases were documented in this region. Blood serum samples from 799 residents of several regions of Siberia, Russia, (the Altai Territory, Irkutsk, Kemerovo and Novosibirsk regions, the Republic of Altai, Buryatia, and Khakassia) were analyzed. Sera of non-infected donors were collected within a study of seasonal influenza in the Russian Federation. The sample collection sites were located near the flyways and breeding grounds of wild waterfowl. The performance of enzyme-linked immunosorbent assay (ELISA) for the collected sera included the usage of recombinant SARS-CoV-2 protein antigens: full-length nucleocapsid protein (CoVN), receptor binding domain (RBD) of S-protein and infection fragment of the S protein (S5-6). There were 183 (22.9%) sera reactive to the S5-6, 270 (33.8%) sera corresponding to the full-length N protein and 128 (16.2%) sera simultaneously reactive to both these proteins. Only 5 out of 799 sera had IgG antibodies reactive to the RBD. None of the sera exhibited neutralizing activity against the nCoV/Victoria/1/2020 SARS-CoV-2 strain in Vero E6 cell culture. The data obtained in this study suggest that some of the population of the analyzed regions of Russia had cross-reactive humoral immunity against SARS-CoV-2 before the COVID-19 pandemic started. Moreover, among individuals from relatively isolated regions, there were significantly fewer reliably cross-reactive sera. The possible significance of these data and impact of cross-immunity to SARS-CoV-2 on the prevalence and mortality of COVID-19 needs further assessment. Full article

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age. Full article

Horns, also known as headgear, are a unique structure of ruminants. As ruminants are globally distributed, the study of horn formation is critical not only for increasing our understanding of natural and sexual selection but also for the breeding of polled sheep breeds to facilitate modern sheep farming. Despite this, a significant number of the underlying genetic pathways in sheep horn remain unclear. In this study, to clarify the gene expression profile of horn buds and investigate the key genes in horn bud formation, RNA-sequencing (RNA-seq) technology was utilized to investigate differential gene expression in the horn buds and adjacent forehead skin of Altay sheep fetuses. There were only 68 differentially expressed genes (DEGs) identified, consisting of 58 up-regulated genes and 10 down-regulated genes. RXFP2 was differentially up-regulated in the horn buds and had the highest significance (p-value = 7.42 × 10⁻¹⁴). In addition, 32 DEGs were horn-related genes identified in previous studies, such as RXFP2, FOXL2, SFRP4, SFRP2, KRT1, KRT10, WNT7B, and WNT3. Further, Gene Ontology (GO) analysis showed that the DEGs were mainly enriched with regard to growth, development, and cell differentiation. Pathway analysis revealed that the Wnt signaling pathway may be responsible for horn development. Further, through combining the protein–protein interaction networks of the DEGs, it was found that the top five hub genes, namely, ACAN, SFRP2, SFRP4, WNT3, and WNT7B, were also associated with horn development. Our results suggest that only a few key genes, including RXFP2, are involved in bud formation. This study not only validates the expression of candidate genes identified at the transcriptome level in previous studies but also provides new possible marker genes for horn development, which may promote our understanding of the genetic mechanisms of horn formation. Full article

Food fat content is one of the most controversial factors from a consumer’s point of view. Aim: (1) The trends in consumer attitudes towards pork and the fat and meat compositions in Duroc and Altai meat breeds and Livny and Mangalitsa meat and fat breeds were studied. (2) Methods: Netnographic studies were used to assess Russian consumer purchasing behavior. Protein, moisture, fat, backfat fatty acid content from pigs, longissimus muscles, and backfat from (A) Altai, (L) Livny, and (M) Russian Mangalitsa breeds were compared with those from (D) Russian Duroc. Raman spectroscopy and histology were applied to the backfat analysis. (3) Results: The attitude of Russian consumers to fatty pork is contradictory: consumers note its high fat content as a negative factor, but the presence of fat and intramuscular fat is welcomed because consumers positively associate them with better taste, tenderness, flavor, and juiciness. The fat of the ‘lean’ D pigs did not show a “healthy” fatty acid ratio, while the n-3 PUFA/n-6 PUFA ratio in the fat of the M pigs was the best, with significant amounts of short-chain fatty acids. The highest UFA content, particularly omega 3 and omega 6 PUFA, was found in the backfat of A pigs with a minimum SFA content. The backfat of L pigs was characterized by a larger size of the adipocytes; the highest monounsaturated and medium chain fatty acid contents and the lowest short-chain fatty acid content; the ratio of omega 3 to omega 6 was 0.07, and the atherogenicity index in L backfat was close to that of D, despite the fact that D pigs are a meat type, while L pigs are a meat and fat type. On the contrary, the thrombogenicity index in L backfat was even lower than the D one. (4) Conclusions: Pork from local breeds can be recommended for functional food production. The requirement to change the promotion strategy for local pork consumption from the position of dietary diversity and health is stated. Full article

Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources. Full article

Thermogenesis plays an important role in the survival of sheep exposed to low temperatures; however, little is known about the genetic mechanisms underlying cold adaptation in sheep. We examined 6 Altay (A) and 6 Hu (H) six-month-old ewe lambs. Altay sheep are raised in northern China and are adapted to dry, cold climates, while Hu sheep are raised in southern China and are adapted to warm, humid climates. Each breed was divided into two groups: chronic cold sheep, exposed to −5 °C for 25 days (3 A^c; 3 H^c), and thermo-neutral sheep, maintained at 20 °C (3 A^w; 3 H^w). The transcriptome profiles of hypothalamus, tail-fat and perirenal fat tissues from these four groups were determined using paired-end sequencing for RNA expression analysis. There are differences in cold tolerance between Hu and Altay sheep. Under cold exposure of the lambs: (1) UCP1-dependent thermogenesis and calcium- and cAMP-signaling pathways were activated; and (2) different fat tissues were activated in Hu and Altay lambs. Several candidate genes involved in thermogenesis including UCP1, ADRB3, ADORA2A, ATP2A1, RYR1 and IP6K1 were identified. Molecular mechanisms of thermogenesis in the sheep are discussed and new avenues for research are suggested. Full article

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status. Full article

We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes. Full article

It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep. Full article