8 results on '"Rodionov, Andrey N"'
Search Results
2. Genetic Diversity in the Orenburg Goat Breed Revealed by Single-Nucleotide Polymorphism (SNP) Analysis: Initial Steps in Saving a Threatened Population.
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Deniskova, Tatiana E., Dotsev, Arsen V., Abdelmanova, Alexandra S., Petrov, Sergey N., Frolov, Alexey N., Platonov, Stanislav A., Gladyr, Elena A., Gusev, Igor V., Selionova, Marina I., Rodionov, Andrey N., Lebedev, Svyatoslav V., Griffin, Darren K., Romanov, Michael N., and Zinovieva, Natalia A. more...
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SINGLE nucleotide polymorphisms ,GENETIC variation ,LIVESTOCK breeds ,OUTCROSSING (Biology) ,ANIMAL breeders ,GOAT breeds - Abstract
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. [ABSTRACT FROM AUTHOR] more...- Published
- 2024
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3. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia.
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Buggiotti, Laura, Yurchenko, Andrey A, Yudin, Nikolay S, Jagt, Christy J Vander, Vorobieva, Nadezhda V, Kusliy, Mariya A, Vasiliev, Sergei K, Rodionov, Andrey N, Boronetskaya, Oksana I, Zinovieva, Natalia A, Graphodatsky, Alexander S, Daetwyler, Hans D, and Larkin, Denis M more...
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CATTLE breeding ,GENETIC variation ,BIOLOGICAL variation ,CLIMATE change ,ANIMAL breeding - Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate. [ABSTRACT FROM AUTHOR] more...
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- 2021
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4. Complete mitochondrial genomes of Karchaev goat (Capra hircus).
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Rodionov, Andrey N., Dotsev, Arsen V., Fomenko, Oleg Y., Bakoev, Neckruz F., Deniskova, Tatiana E., Shakhin, Alexey V., Bagirov, Vugar A., Kunz, Elisabeth, Medugorac, Ivica, Krebs, Stefan, Brem, Gottfried, and Zinovieva, Natalia A. more...
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GOATS ,MITOCHONDRIA ,GENOMES - Abstract
Karachaev goat (Capra hircus) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A. [ABSTRACT FROM AUTHOR] more...
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- 2020
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5. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens.
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Abdelmanova, Alexandra S., Dotsev, Arsen V., Romanov, Michael N., Stanishevskaya, Olga I., Gladyr, Elena A., Rodionov, Andrey N., Vetokh, Anastasia N., Volkova, Natalia A., Fedorova, Elena S., Gusev, Igor V., Griffin, Darren K., Brem, Gottfried, and Zinovieva, Natalia A. more...
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CHICKEN breeds ,POULTRY breeding ,GENES ,CHICKENS ,PHENOTYPES - Abstract
Simple Summary: The search for genomic regions of putative selective signaling is instrumental in obtaining information about selection history in various species and populations. Domestic animals are subject to long-term artificial selection that leaves certain footprints in their genomes one can explore using genome-wide SNP screen. We examined here genomes of two contrasting chicken breeds, the native egg-type Russian White and meat-type White Cornish. Using three statistics, we identified genomic regions under putative selection, both breed-specific and shared between two breeds, that harbor key candidate genes for economically important traits. Our findings will be useful in further understanding selection history and genomic diversity in domestic chickens that would be pivotal in their productive breeding. Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by F
ST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding. [ABSTRACT FROM AUTHOR] more...- Published
- 2021
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6. An Assessment of Applicability of SNP Chip Developed for Domestic Goats in Genetic Studies of Caucasian Tur (Capra caucasica) †.
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Dotsev, Arsen V., Rodionov, Andrey N., Kharzinova, Veronika R., Petrov, Sergey N., Medvedev, Dmitry G., Bagirov, Vugar A., Brem, Gottfried, and Zinovieva, Natalia A.
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GOATS , *CAUCASIAN race , *GENETIC variation , *MICROSATELLITE repeats , *DNA sequencing , *NUCLEAR DNA , *MITOCHONDRIAL DNA - Abstract
Caucasian tur (Capra caucasica) is native to Greater Caucasus Mountain Chain from Azerbaijan and Georgia in the East to Krasnodar region of Russia in the West. This species is divided into two subspecies (by some authors into species)—East-Caucasian tur and West-Caucasian tur and a subpopulation referred to as Mid-Caucasian tur. Up to date most of the genetic studies of Caucasian tur are based on mitochondrial DNA sequences and comprehensive investigation based on nuclear DNA is required for clarification of its genetic diversity and population structure. In our work, we assessed the applicability of Illumina Goat SNP50 BeadChip for genetic studies of Caucasian tur. Total of 15 specimens of Capra caucasica including East-Caucasian tur from Dagestan (E_TUR, n = 5), West-Caucasian tur from Karachay-Cherkessia (W_TUR, n = 5), and Mid-Caucasian tur from Kabardino-Balkaria (M_TUR, n = 5) were genotyped. After quality control, 5544 polymorphic loci, which were distributed all over 29 autosomes, were detected. The lowest number of SNPs was found on the 25th chromosome—68, and the highest on the 1st chromosome—348. It was shown that all the three groups of Caucasian tur clustered separately. A total of 2061 SNPs were common for all the populations, 594 were found only in W_TUR, 689 in E_TUR, and 530 in M_TUR. Individual heterozygosity ranged from 0.273 to 0.282 in W_TUR, from 0.217 to 0.253 in E_TUR, and from 0.255 to 0.283 in M_TUR. A clinal pattern of genetic variation was revealed. It was suggested to consider Caucasian tur a single species with several ecotypes. Thus, in our study we demonstrated that the Illumina Goat SNP50 BeadChip developed for domestic goats can be used as a useful tool for genetic studies of Caucasian tur. [ABSTRACT FROM AUTHOR] more...
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- 2021
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7. Mitochondrial DNA Analysis Clarifies Taxonomic Status of the Northernmost Snow Sheep (Ovis nivicola) Population.
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Dotsev, Arsen V., Kunz, Elisabeth, Kharzinova, Veronika R., Okhlopkov, Innokentiy M., Lv, Feng-Hua, Li, Meng-Hua, Rodionov, Andrey N., Shakhin, Alexey V., Sipko, Taras P., Medvedev, Dmitry G., Gladyr, Elena A., Bagirov, Vugar A., Brem, Gottfried, Medugorac, Ivica, Zinovieva, Natalia A., Luchetti, Andrea, and Plazzi, Federico more...
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MITOCHONDRIAL DNA ,DNA analysis ,SHEEP ,NUCLEAR DNA ,CYTOCHROME b ,SINGLE nucleotide polymorphisms - Abstract
Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies. [ABSTRACT FROM AUTHOR] more...
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- 2021
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8. Complete mitochondrial genomes of Karchaev goat ( Capra hircus ).
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Rodionov AN, Dotsev AV, Fomenko OY, Bakoev NF, Deniskova TE, Shakhin AV, Bagirov VA, Kunz E, Medugorac I, Krebs S, Brem G, and Zinovieva NA
- Abstract
Karachaev goat ( Capra hircus ) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.) more...
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- 2020
- Full Text
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