30 results on '"Abdelmanova, Alexandra S."'
Search Results
2. Genome-wide association study revealed putative SNPs and candidate genes associated with growth and meat traits in Japanese quail
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Volkova, Natalia A., Romanov, Michael N., Abdelmanova, Alexandra S., Larionova, Polina V., German, Nadezhda Yu., Vetokh, Anastasia N., Shakhin, Alexey V., Volkova, Ludmila A., Anshakov, Dmitry V., Fisinin, Vladimir I., Griffin, Darren K., Sölkner, Johann, Brem, Gottfried, McEwan, John C., Brauning, Rudiger, Zinovieva, Natalia A., Volkova, Natalia A., Romanov, Michael N., Abdelmanova, Alexandra S., Larionova, Polina V., German, Nadezhda Yu., Vetokh, Anastasia N., Shakhin, Alexey V., Volkova, Ludmila A., Anshakov, Dmitry V., Fisinin, Vladimir I., Griffin, Darren K., Sölkner, Johann, Brem, Gottfried, McEwan, John C., Brauning, Rudiger, and Zinovieva, Natalia A.
- Abstract
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F 2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.
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- 2024
3. Dissecting selective signatures and candidate genes in grandparent lines subject to high selection pressure for broiler production and in a local Russian chicken breed of Ushanka
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Romanov, Michael N., Shakhin, Alexey V., Abdelmanova, Alexandra S., Volkova, Natalia A., Efimov, Dmitry N., Fisinin, Vladimir I., Korshunova, Liudmila G., Anshakov, Dmitry V., Dotsev, Arsen V., Griffin, Darren K., Zinovieva, Natalia A., Romanov, Michael N., Shakhin, Alexey V., Abdelmanova, Alexandra S., Volkova, Natalia A., Efimov, Dmitry N., Fisinin, Vladimir I., Korshunova, Liudmila G., Anshakov, Dmitry V., Dotsev, Arsen V., Griffin, Darren K., and Zinovieva, Natalia A.
- Abstract
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.
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- 2024
4. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds
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Volkova, Natalia A., primary, Romanov, Michael N., additional, Abdelmanova, Alexandra S., additional, Larionova, Polina V., additional, German, Nadezhda Yu., additional, Vetokh, Anastasia N., additional, Shakhin, Alexey V., additional, Volkova, Ludmila A., additional, Anshakov, Dmitry V., additional, Fisinin, Vladimir I., additional, Narushin, Valeriy G., additional, Griffin, Darren K., additional, Sölkner, Johann, additional, Brem, Gottfried, additional, McEwan, John C., additional, Brauning, Rudiger, additional, and Zinovieva, Natalia A., additional
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- 2023
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5. Genotyping-by-sequencing strategy for integrating genomic structure, diversity and performance of various Japanese quail (Coturnix japonica) breeds
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Volkova, Natalia A., Romanov, Michael N., Abdelmanova, Alexandra S., Larionova, Polina V., German, Nadezhda Yu., Vetokh, Anastasia N., Shakhin, Alexey V., Volkova, Ludmila A., Anshakov, Dmitry V., Fisinin, Vladimir I., Narushin, Valeriy G., Griffin, Darren K., Sölkner, Johann, Brem, Gottfried, McEwan, John C., Brauning, Rudiger, Zinovieva, Natalia A., Volkova, Natalia A., Romanov, Michael N., Abdelmanova, Alexandra S., Larionova, Polina V., German, Nadezhda Yu., Vetokh, Anastasia N., Shakhin, Alexey V., Volkova, Ludmila A., Anshakov, Dmitry V., Fisinin, Vladimir I., Narushin, Valeriy G., Griffin, Darren K., Sölkner, Johann, Brem, Gottfried, McEwan, John C., Brauning, Rudiger, and Zinovieva, Natalia A.
- Abstract
Simple Summary: Artificial selection has been applied to domesticated birds for many decades. More recently, this selection has made use of so-called single-nucleotide polymorphism (SNP) markers—simple variants in a DNA sequence. These SNPs can be used for whole-genome screening to detect the unique traces of areas of the genome that are subject to selection. Doing this may help to shed light on the evolutionary and family history (phylogeny) of domestic Japanese quails of different breeds and utility types (e.g., egg, meat or dual-purpose breeds). In this study, 99 birds were used, representing eight breeds (11% of the world’s quail gene pool) and various purposes of use to gather genetic (whole-genome) data in the first-ever analysis of its kind performed on domestic quails. We thereby uncovered evolutionary relationships and points of divergence of individual quail breeds, gleaning important insights into the genetic diversity of domestic quail breeds and their future breeding potential. Abstract: Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indica
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- 2023
6. Whole genome screening procures a holistic hold of the Russian chicken gene pool heritage and demographic history
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Romanov, Michael N., Abdelmanova, Alexandra S., Fisinin, Vladimir I., Gladyr, Elena A., Volkova, Natalia A., Anshakov, Dmitry V., Stanishevskaya, Olga I., Vakhrameev, Anatoly B., Dotsev, Arsen V., Griffin, Darren K., Zinovieva, Natalia A., Romanov, Michael N., Abdelmanova, Alexandra S., Fisinin, Vladimir I., Gladyr, Elena A., Volkova, Natalia A., Anshakov, Dmitry V., Stanishevskaya, Olga I., Vakhrameev, Anatoly B., Dotsev, Arsen V., Griffin, Darren K., and Zinovieva, Natalia A.
- Abstract
Simple Summary: A collection of native farm animal breeds can be considered as a gene pool and a national heritage. Long-term artificial selection in domesticated animals has certain effects on their genomes, which can be investigated using genome-wide screens for DNA sequence variation, that is, so-called single nucleotide polymorphism (SNP) screens. Here, we looked at the genomes of 19 Russian chicken gene pool breeds, both native and imported, evaluating the contrasting egg, meat and dual-purpose types. Based on genetic diversity statistics, we identified differences between the breeds using many DNA markers (SNPs) that may represent genomic regions that are being selected for, either within a specific breed or shared between breeds. Our research will be helpful for further understanding the genomic diversity and demographic history of Russian domestic chickens. This would be essential for their successful breeding. Abstract: A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn
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- 2023
7. Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds
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Abdelmanova, Alexandra S., primary, Sermyagin, Alexander A., additional, Dotsev, Arsen V., additional, Bardukov, Nikolay V., additional, Fornara, Margaret S., additional, Brem, Gottfried, additional, and Zinovieva, Natalia A., additional
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- 2022
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8. Investigation of the Genetic Diversity of Dagestan Mountain Cattle Using STR-Markers
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Volkova, Valeria V., primary, Abdelmanova, Alexandra S., additional, Deniskova, Tatiana E., additional, Romanenkova, Olga S., additional, Khozhokov, Abdusalam A., additional, Ozdemirov, Alimsoltan A., additional, Sermyagin, Alexander A., additional, and Zinovieva, Natalia A., additional
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- 2022
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9. PSXV-10 Study of allelic pattern of PLAG1 gene in the historical and modern populations of two oldest Russian dairy cattle breeds
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Abdelmanova, Alexandra S, primary, Kharzinova, Veronika R, additional, Dotsev, Arsen V, additional, Sermyagin, Alexander A, additional, Boronetskaya, Oxana, additional, Chinarov, Roman, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A, additional
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- 2021
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10. PSI-B-25 Assessment of the genetic resources of Russian local cattle breeds by genome-wide SNP analysis
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Abdelmanova, Alexandra S, primary, Dotsev, Arsen V, additional, Sermyagin, Alexander A, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A, additional
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- 2021
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11. PSXIV-26 Selection footprints in Russian red cattle identified by linkage disequilibrium blocks based on SNP data
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Sermyagin, Alexander A, primary, Dotsev, Arsen V, additional, Abdelmanova, Alexandra S, additional, Sölkner, Johann, additional, and Zinovieva, Natalia A, additional
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- 2021
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12. PSXII-1 Tracing the historical genetic components in turano-mongolian cattle breeds based on the microsatellite analysis of modern and museum samples
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Abdelmanova, Alexandra S, primary, Kharzinova, Veronika R, additional, Volkova, Valeria, additional, Dotsev, Arsen V, additional, Sermyagin, Alexander A, additional, Boronetskaya, Oxana, additional, Chinarov, Roman, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A, additional
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- 2021
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13. PSI-B-20 A scan for signatures of selection in Russian Romanov sheep breed based on ROH hot spots analysis
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Deniskova, Tatiana E, primary, Abdelmanova, Alexandra S, additional, Dotsev, Arsen V, additional, Koshkina, Olga, additional, Rodionov, Andrey, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A, additional
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- 2021
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14. PSXVI-17 Estimation of inbreeding in local sheep breeds of west Asian and central Asian origin based on high-density SNP-genotypes
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Deniskova, Tatiana E, primary, Abdelmanova, Alexandra S, additional, Dotsev, Arsen V, additional, Lushihina, Eugenia, additional, Zhunushev, Asankadyr, additional, Reyer, Henry, additional, Selionova, Marina I, additional, Wimmers, Klaus, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A, additional
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- 2021
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15. PSI-B-23 Assessment of genomic inbreeding in Russian local and commercial dairy breeds of cattle
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Mishina, Arina I, primary, Abdelmanova, Alexandra S, additional, Dotsev, Arsen V, additional, Sermyagin, Alexander A, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A, additional
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- 2021
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16. 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., primary, Dotsev, Arsen V., additional, Romanov, Michael N., additional, Stanishevskaya, Olga I., additional, Gladyr, Elena A., additional, Rodionov, Andrey N., additional, Vetokh, Anastasia N., additional, Volkova, Natalia A., additional, Fedorova, Elena S., additional, Gusev, Igor V., additional, Griffin, Darren K., additional, Brem, Gottfried, additional, and Zinovieva, Natalia A., additional
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- 2021
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17. Comparative Study of the Genetic Diversity of Local Steppe Cattle Breeds from Russia, Kazakhstan and Kyrgyzstan by Microsatellite Analysis of Museum and Modern Samples
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Abdelmanova, Alexandra S., primary, Kharzinova, Veronika R., additional, Volkova, Valeria V., additional, Dotsev, Arsen V., additional, Sermyagin, Alexander A., additional, Boronetskaya, Oksana I., additional, Chinarov, Roman Yu., additional, Lutshikhina, Evgeniya M., additional, Sölkner, Johann, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A., additional
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- 2021
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18. 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, Zinovieva, Natalia A., 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.
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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. Abstract: 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 FST 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 carcas
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- 2021
19. Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds †.
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Abdelmanova, Alexandra S., Sermyagin, Alexander A., Dotsev, Arsen V., Bardukov, Nikolay V., Fornara, Margaret S., Brem, Gottfried, and Zinovieva, Natalia A.
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CATTLE breeds , *CATTLE breeding , *STATURE , *SINGLE nucleotide polymorphisms , *SCIENCE education , *GENOME-wide association studies - Abstract
Cattle breeds used in industrial production tend to have a larger size compared to the local cattle, as the increased dairy and beef productivity is closely related to the stature. The aim of our work was to identify single nucleotide polymorphisms (SNPs), which are significantly associated with stature in diverse cattle breeds. Thirteen local and transboundary cattle breeds (n = 670) subjected to our study were divided in two groups according to the stature. The high-stature group included Angus, Ayrshire, Black-and-White, Holstein, Kholmogor, Yaroslavl, Tagil and Istoben breeds. The low-stature group comprised of Jersey, Kalmyk, Kyrgyz, Mongolian and Yakut cattle. The average height at withers was 136.3 ± 1.6 and 121.6 ± 2.8 cm in the high- and low-stature groups, respectively. The samples of 11 breeds were genotyped using high-density DNA arrays (Illumina Inc., USA). The genotypes of two remaining breeds were downloaded from the publicly available WIDDE database. Genome-wide association studies revealed four SNPs, which were strongly associated with the stature, including three SNPs at 77.3–77.8 cM on BTA4 (map53144-ss46525999, p < 7.747 × 10−101; BovineHD0400021479, p < 1.173 × 10−91; ARS-BFGL-NGS-116590, p < 7.665 × 10−105) and one SNPs at 25.2 cM on BTA14 (BovineHD1400007259, p < 1.324 × 10−109). Functional annotation showed the localization within identified regions of genes, which are responsible for growth, exterior characteristics, protein and lipid metabolism, and feed intake. Identified SNPs can be considered as useful DNA markers for marker-assistant cattle breeding aimed at increased stature. The study was funded by the Russian Ministry of Science and Higher Education No. 0445-2019-0024. [ABSTRACT FROM AUTHOR]
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- 2022
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20. Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis
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Abdelmanova, Alexandra S., primary, Kharzinova, Veronika R., additional, Volkova, Valeria V., additional, Mishina, Arina I., additional, Dotsev, Arsen V., additional, Sermyagin, Alexander A., additional, Boronetskaya, Oxana I., additional, Petrikeeva, Lidia V., additional, Chinarov, Roman Yu, additional, Brem, Gottfried, additional, and Zinovieva, Natalia A., additional
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- 2020
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21. Study of allelic pattern of PLAG1 gene in the historical and modern populations of two oldest Russian dairy cattle breeds.
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Abdelmanova, Alexandra S., Kharzinova, Veronika R., Dotsev, Arsen V., Sermyagin, Alexander A., Boronetskaya, Oxana, Chinarov, Roman, Brem, Gottfried, and Zinovieva, Natalia A.
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CATTLE breeding , *DAIRY cattle , *CATTLE breeds , *ANIMAL culture , *STATURE , *GENE frequency - Abstract
Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele's frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst Research Center for Animal Husbandry. The samples were genotyped using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds' representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007. [ABSTRACT FROM AUTHOR]
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- 2021
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22. Tracing the historical genetic components in turano-mongolian cattle breeds based on the microsatellite analysis of modern and museum samples.
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Abdelmanova, Alexandra S., Kharzinova, Veronika R., Volkova, Valeria, Dotsev, Arsen V., Sermyagin, Alexander A., Boronetskaya, Oxana, Chinarov, Roman, Brem, Gottfried, and Zinovieva, Natalia A.
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CATTLE breeding , *CATTLE breeds , *BREEDING , *MICROSATELLITE repeats , *ANIMAL culture , *GERMPLASM , *LOCUS (Genetics) - Abstract
In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turanomongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767-0.776 and 0.653-0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012. [ABSTRACT FROM AUTHOR]
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- 2021
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23. Assessment of genomic inbreeding in Russian local and commercial dairy breeds of cattle.
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Mishina, Arina I., Abdelmanova, Alexandra S., Dotsev, Arsen V., Sermyagin, Alexander A., Brem, Gottfried, and Zinovieva, Natalia A.
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CATTLE breeds , *DAIRY cattle , *CATTLE breeding , *GENETIC variation , *INBREEDING , *SCIENCE education - Abstract
Drastic decline of population size of Russian local cattle breeds observed during last three decades has led to the decrease of genetic diversity. Due to the limited number of bulls used for artificial insemination, inbreeding in herds can be increased, which can lead to the decrease of reproduction capacity and adaptability of animals. Our aim was to assess genomic inbreeding in two Russian local cattle breeds, including Kholmogor (n = 26) and Istoben (n = 21). Two transboundary cattle breeds used for milk production in Russia including Holstein (n = 49) and Simmental (n = 38) were chosen for comparison. SNP genotyping was performed using the Bovine GGP 150K BeadArray (Illumina, CA, USA). After the quality control, 117591 autosomal SNPs were selected for analyzes. The degree of genomic inbreeding was assessed by calculations of inbreeding coefficient based on run of homozygosity (F(ROH)) and multilocus heterozygosity (sMLH). We found the strong negative correlations between the F(ROH) and sMLH values in animals of all of studied breeds (r2 = -0.805). The average F(ROH) values were 0.065 < mo >±">±± 0.003 for Kholmogor, 0.048 < mo >±">±± 0.006 for Istoben, 0.129 < mo >± math >">±± 0.007 for Holstein, and 0.102 < mo >±">±± 0.007 for Simmental breed. The sMLH values in Kholmogor, Istoben, Holstein and Simmental breeds varied from 0,99 to 1,076, from 0,829 to 1,102, from 0,890 to 1,069 and from 0,866 to 1,041, and averaged to 1.030, 1.013, 1.000, and 0.974, respectively. According to our research results, two studied Russian cattle breeds are characterized by lower levels of genomic inbreeding compared to transboundary cattle breeds. Our results will be helpful for developing the conservation programs for Russian Kholmogor and Istoben cattle breeds. The study was funded by the Russian Ministry of Science and Higher Education within theme No. 0445-2019-0024 and RFBR within project 19-316-90017 (the study of Kholmogor cattle). [ABSTRACT FROM AUTHOR]
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- 2021
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24. A scan for signatures of selection in Russian Romanov sheep breed based on ROH hot spots analysis.
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Deniskova, Tatiana E., Abdelmanova, Alexandra S., Dotsev, Arsen V., Koshkina, Olga, Rodionov, Andrey, Brem, Gottfried, and Zinovieva, Natalia A.
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SHEEP breeding , *SHEEP breeds , *EMBRYO implantation , *EMBRYOLOGY , *SINGLE nucleotide polymorphisms , *MEAT quality - Abstract
The world-famous Romanov breed of sheep fits easily into different production systems including private households, smallholders, and large farms. Such a resilience and extraordinary reproduction traits combining with good meat qualities have made the Romanov breed as a choice to produce mutton in the Central Russia regions. However, little is known on genetic mechanisms underlying the complex of specific traits of this breed. In this regard, we performed a scan of signatures of selection by identification of runs of homozygosity (ROH) islands in the Romanov sheep population. Forty-eight samples of the Romanov sheep from the Yaroslavl and Kaluga regions of Russia were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). ROHs were estimated in the R package "detectRUNS" using window-free method for consecutive. The ROH shared in more than 50% of sheep were considered as ROH islands. The genes overlapped with the ROH islands were annotated using Ensembl genome browser 103. Enrichment for functional categories of the identified genes was performed using DAVID Functional Annotation Bioinformatics Microarray Analysis tool. More than 88 SNPs were found in ROH islands located on OAR1, OAR10, OAR11, OAR13, OAR14, OAR15, OAR16, OAR17 and OAR18. We detected a major group of genes related to reproduction traits. The identified candidates included UBE2Q1 (embryo implantation, fertilization, prolactin secretion), RNF17 (spermiogenesis), HSD11B2 (pregnancy, follicle function), FANCA (gonad development), and CUBN (embryonic development). In addition, several identified genes were involved in fatty acid metabolism (ACOX1, HAO2, and EIF6), lipid transport (OSBPL11), and biosynthesis of lipid-binding serum glycoproteins (BPIFB4) as well as in osteoblast differentiation (ADAR). The studies will be continued on a larger sample with further validation of the most promising candidate genes. Genotyping of twenty-four samples was performed within RFBR project No. 20-516-56002. Other twenty-four SNP-genotypes were generated within the theme No. 0445-2019-0024. [ABSTRACT FROM AUTHOR]
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- 2021
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25. Assessment of the genetic resources of Russian local cattle breeds by genome-wide SNP analysis.
- Author
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Abdelmanova, Alexandra S., Dotsev, Arsen V., Sermyagin, Alexander A., Brem, Gottfried, and Zinovieva, Natalia A.
- Subjects
- *
CATTLE breeds , *CATTLE breeding , *GERMPLASM , *CATTLE genetics , *SINGLE nucleotide polymorphisms , *GENETIC variation , *SCIENCE education - Abstract
Russia is reach by local cattle genetic resources, which are well adapted to the different environment. However, the modern cattle husbandry tends to the replacing the local cattle breeds by highly productive commercial breeds, which can lead to the decline of genetic diversity. The aim of our work was to estimate the genetic identity of five Russian local cattle breeds, including Yaroslavl (n = 52), Kholmogor (n = 26), Istoben (n = 21), Tagil (n = 26), and Black-and-White (n = 44). The Holstein breed (n = 49), which is actively used for improvement of above breeds was included in the study for comparison. The genotyping was performed using GGP Bovine 150K Array (Illumina, San Diego, CA, USA) and more than 112000 autosomal SNPs passed through the quality control and were selected for the analysis. We observed the significant excess of heterozygotes in four studied breeds (the values of unbiased inbreeding coefficient were varied from -0.009 to -0.022), except for Black-and-White breed. The effective population size (Ne) for Istoben, Tagil and Kholmogor breeds was declined until present, while Holstein and Black-and-White breeds showed the increase of Ne values starting at 5 generations ago. The Black-and-White breed was the closest to the Holsteins (Fst=0.014), while the Yaroslavl breed was the most distant (Fst=0.115). The highest ratio of Holstein specific genomic components was shown for Tagil (18.79%) and Black-and-White (59.73%) breeds. Our results indicated replacing the part of aboriginal genomic components in several Russian local cattle breeds by Holstein specific components. The comprehensive strategies for conservation of the Russian local cattle breeds are needed to avoid the further decline of genetic diversity of these valuable national animal genetic resources. The study was funded by the Ministry of Science and Higher Education of the Russian Federation within theme 0445-2019-0024. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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26. Estimation of inbreeding in local sheep breeds of west Asian and central Asian origin based on high-density SNP-genotypes.
- Author
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Deniskova, Tatiana E., Abdelmanova, Alexandra S., Dotsev, Arsen V., Lushihina, Eugenia, Zhunushev, Asankadyr, Reyer, Henry, Selionova, Marina I., Wimmers, Klaus, Brem, Gottfried, and Zinovieva, Natalia A.
- Subjects
- *
SHEEP breeding , *GENETIC variation , *INBREEDING , *SHEEP breeds , *SUSTAINABILITY , *SHEEP diseases , *GENE flow - Abstract
Maintaining high levels of genetic diversity is a key factor of successful breeding of resilient, resistant to diseases and productive sheep. Prevention of inbreeding is of special importance in the mountainous hard-to-get habitats where gene flow is limited or absent. An assessment of inbreeding coefficients based only on pedigree information is not always correct. In addition, pedigree information is often missing for flocks of native sheep. In this regard, we performed a genomic assessment of inbreeding in 15 local sheep breeds inhabiting severe environments of Russia and neighboring Asian countries based on estimations of standardized multilocus heterozygosity (sMLH) and runs of homozygosity [F(ROH)]. For this study, we used SNP genotypes of twelve Russian local breeds (n = 316) and three Kyrgyz local breeds (n = 68), which were generated using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). The sMLH values were calculated using R package inbreedR and visualized in R package ggplot2. The F(ROH) values were calculated using the R package detectRUNS by applying the consecutive runs method. Mean sMLH values were varied from 0.962 ± 0.006 in the Andean breed to 1.031 ± 0.002 in the Buryat breed and averaged to 1.001± 0.004. The least mean F(ROH) value was detected in the Mongolian breed (0.0043 ± 0.0009) while the greatest ones were observed in the Alai and Andean breeds (0.0364 ± 0.0049 and 0.0357 ± 0.0061, respectively). The strong negative correlations between sMLH and F(ROH) were detected for all of studied breeds (r2 = -0.8496, CI = -0.8752... -0.8192). The obtained data is relevant for control of inbreeding level in the populations and for future sustainable management of native fat-tailed sheep breeds. The study was funded by RSF No. 19-16-00070. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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27. Selection footprints in Russian red cattle identified by linkage disequilibrium blocks based on SNP data.
- Author
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Sermyagin, Alexander A., Dotsev, Arsen V., Abdelmanova, Alexandra S., Sölkner, Johann, and Zinovieva, Natalia A.
- Subjects
LINKAGE disequilibrium ,FAT content of milk ,CATTLE breeds ,CATTLE breeding ,CATTLE ,BIODIVERSITY conservation - Abstract
Among the variety of cattle breeds in Russia, the Russian red dual-purpose cattle breeds have great importance because of their ability to produce high milk yields as well as to provide excellent milk quality. The low census size of the Russian red cattle breeds requires development of programs for conservation of their biodiversity. Our study aimed to investigate selection footprints in Russian red cattle breeds, using high values of linkage disequilibrium (LD) in SNP haplotype blocks as indicators. For finding such LD blocks, we used the genotypes (?35K SNPs) of Red Gorbatov (RGB, n = 26), Bestuzhev (BST,n = 27), and Suksun (SKS,n = 17) breeds, as well as Red Holstein (RH,n = 16) as an outgroup. Quality control and LD calculations for different distances were performed in Plink 1.90. Top 0.01% SNP pairs by LD value (0.9=r2< 1.0) were selected for further analysis. The effective population size derived from LD patterns was estimated using SNeP tool. Comparison of LD values for 70 kb interval between breeds and chromosomes by MANOVA pairwise testing significantly distinguished RH/RGB and BST/SKS breeds (P < 0.05-0.001). LD values among chromosomes were 0.195-0.287 for RH, 0.194-0.272 for RGB, 0.172-0.237 for BST, and 0.157-0.217 for SKS. The SKS and BST breeds had higher Ne values (84 and 113, respectively) compared to RH (63) and RGB (79). Selection footprints by LD blocks in Russian red cattle genome covered several relevant genes on BTA1 (EPHA6,DGKG), BTA2 (LRP1B,THSD7B,STAT1), BTA5 (CPM,BAIAP2L2), BTA9 (TRDN,UTRN), BTA10 (KCNN2,CAPN3), BTA11 (SH3RF3,RABGAP1,RALGPS1), BTA14 (ZNF16,ARHGAP39,TOX,DGAT1), and BTA19 (MYH10), BTA22 (FHIT). Detected genes were found to be responsible for milk fat and protein contents, fatty acid composition, somatic cells score, fertility, feet and legs, and udder conformation traits. Our results can be useful for developing the breeding and conservation programs of the Russian red cattle genetic resources. The study was funded by RFBR within project No. 20-516-00020. [ABSTRACT FROM AUTHOR]
- Published
- 2021
28. Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka.
- Author
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Romanov MN, Shakhin AV, Abdelmanova AS, Volkova NA, Efimov DN, Fisinin VI, Korshunova LG, Anshakov DV, Dotsev AV, Griffin DK, and Zinovieva NA
- Subjects
- Animals, Quantitative Trait Loci, Breeding, Russia, Whole Genome Sequencing methods, Chickens genetics, Selection, Genetic, Polymorphism, Single Nucleotide
- Abstract
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on Z F
ST , hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.- Published
- 2024
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29. Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail.
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Sermyagin AA, Anshakov DV, Fisinin VI, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, and Zinovieva NA
- Subjects
- Male, Animals, Polymorphism, Single Nucleotide genetics, Meat analysis, Body Weight genetics, Genome-Wide Association Study, Coturnix genetics
- Abstract
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F
2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes ( GNAL , DNAJC6 , LEPR , SPAG9 , and SLC27A4 ) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.- Published
- 2024
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30. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History.
- Author
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, and Zinovieva NA
- Abstract
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
- Published
- 2023
- Full Text
- View/download PDF
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