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  • 1
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    PSX-18 High-density genomic description of Russian native sheep breed of the Republic of Tyva
    Oxford University Press (OUP) ; 2020
    In:  Journal of Animal Science Vol. 98, No. Supplement_4 ( 2020-11-30), p. 453-454
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 98, No. Supplement_4 ( 2020-11-30), p. 453-454
    Abstract: Tuva breed is the oldest native sheep breed in Russia with more than 2000 year-history and comes in third place by population size among coarse wool sheep. Tuva sheep produce high-quality meat as well as coarse wool to make traditional clothing in the Republic of Tyva. In present study, we aimed to evaluate genetic diversity and to establish genetic links of the Tuva breed with the other Russian coarse wool sheep to understand the origin and current status of this valuable livestock species. Twenty samples of Tuva were genotyped using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). SNP-data were processed in PLINKv1.9, R package ‘diveRsity’ and SneP software. High-density SNP-genotypes of 10 coarse wool sheep breeds were used as comparison groups. Observed heterozygosity (Ho) and allelic richness (Ar) in Tuva breed were 0.336 and 1.884, respectively, and were practically equal to mean values estimated across all analyzed sheep breeds (Ho=0.335, Ar=1.884). All coarse wool breeds showed moderate heterozygote excess which was the highest in Tuva breed (1.6%). Effective population sizes estimated for three and five generations ago for Tuva breed (Ne3 =118 and Ne5 =179) were less than those in other breeds (Ne3 = 314 and Ne5 = 441 for Edilbai or Ne3 = 300 and Ne5 = 450 for Kalmyk) but not the lowest (Ne3 = 49 and Ne5 = 72 for Buubei). Values of historical effective population size estimated for 60 generations ago for Tuva breed was 1457 that was compatible with those obtained for other breeds (Ne60 from 586 for Buubei to 2634 for Kalmyk). Despite the obvious decrease in effective population size, levels of genetic diversity are not critical that would allow to develop programs to ensure preservation and sustainable development of Tuva breed. The study was funded by RSF No. 19-16-00070.
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skaa278.789
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1490550-4
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  • 2
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    Single- and Bayesian Multi-Marker Genome-Wide Association for Haematological Parameters in Pigs
    Public Library of Science (PLoS) ; 2016
    In:  PLOS ONE Vol. 11, No. 7 ( 2016-7-19), p. e0159212-
    Details
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 7 ( 2016-7-19), p. e0159212-
    Type of Medium: Online Resource
    ISSN: 1932-6203
    URL: Article
    URL: Article
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    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.1371/journal.pone.0159212
    DOI: 10.1371/journal.pone.0159212.g001
    DOI: 10.1371/journal.pone.0159212.g002
    DOI: 10.1371/journal.pone.0159212.t001
    DOI: 10.1371/journal.pone.0159212.t002
    DOI: 10.1371/journal.pone.0159212.t003
    DOI: 10.1371/journal.pone.0159212.s001
    DOI: 10.1371/journal.pone.0159212.s002
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2016
    detail.hit.zdb_id: 2267670-3
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  • 3
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    PSXI-6 Genome-wide SNP analysis of three Azerbaijani sheep breeds
    Oxford University Press (OUP) ; 2021
    In:  Journal of Animal Science Vol. 99, No. Supplement_3 ( 2021-10-08), p. 245-245
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 99, No. Supplement_3 ( 2021-10-08), p. 245-245
    Abstract: Azerbaijani sheep breeds are of particular interest since this region is in close proximity to the Fertile Crescent – the proposed place of domestication. Molecular genetic studies of local breeds will help shed light on the history of sheep breeding. Our work was aimed to identify genetic characteristics of three sheep breeds from Azerbaijan: Bozakh (n = 19), Karabakh (n = 16) and Mazekh (n = 19). For genotyping, we used Illumina OvineHD BeadChip (AgResearch) containing around 600 thousand SNPs. PLINK 1.9 was used to perform quality control. Genetic diversity parameters and pairwise FST distances were calculated in R package diveRsity. After all quality control procedures, including LD pruning, 286663 SNPs were selected for subsequent analyses. PCA revealed that, while all the breeds formed their own clusters, only 1.62% of genetic variability was explained by the first component (PC1). Cluster analysis conducted in Admixture 1.3 showed that Bozakh was derived from Karabakh and Mazekh breeds. However, based on CV error, the number of clusters (K) judged to be one. Pairwise FST distances were quite low, with highest value of 0.017 between Karabakh and Mazekh and lowest (0.006) between Mazekh and Bozakh breeds. The global fixation index (FST) was 0.01, which indicated that 99% of genetic variability was due to within breeds differences. Expected heterozygosity was similar in Bozah and Mazeh (0.363±0.000 and 0.360±0.000, respectively) and a slight lower in Karabakh breed (0.353±0.000). We observed neither heterozygotes excess nor deficiency in all of the studied breeds. The inbreeding coefficient (Fis), ranged from 0.001 in Karabakh to 0.011 in Mazekh sheep. Our results demonstrate that the studied Azerbaijani sheep breeds are genetically close, but carry specific genomic components that allows consider them as valuable genetic resources. The study was funded by the RSF 21-66-00007 (genotyping) and the Russian Ministry of Science and Higher Education 0445-2019-0024 (expedition studies).
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skab235.447
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 4
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    PSVIII-1 Genetic characteristics of Karachaev sheep inferred from genome-wide SNP analysis
    Oxford University Press (OUP) ; 2021
    In:  Journal of Animal Science Vol. 99, No. Supplement_3 ( 2021-10-08), p. 243-243
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 99, No. Supplement_3 ( 2021-10-08), p. 243-243
    Abstract: Karachaev sheep is a fat-tailed breed from North-Caucasus, Russia. It has good adaptability to local environments and excellent meat quality. The aim of our study was to investigate genetic characteristics of Karachaev sheep and its relationship with other fat-tailed breeds. Samples of Karachaev (n = 22), Lezgin (n = 21), Edilbai (n = 21), Karakul (n = 21), Alai (n = 20), and Gissar (n = 20) breeds were genotyped using Ovine HD BeadChip. For phylogenetic analyses, we additionally included 50K genotypes of Afshari, Awassi, Barki, Chios, Cyprus Fat-Tailed, and Red Maasai breeds. PLINK 1.9 was used for quality control and performing PCA. Genetic diversity parameters were calculated in R package diveRsity. Historical effective population size (Ne) was estimated using SNeP 1.1. Cluster analysis was conducted in Admixture 1.3. TreeMix tree was constructed in TreeMix 1.13. Genetic diversity indices (observed and expected heterozygosity, allelic richness) were highest in Karachaev and Lezgin breeds. Karachaev sheep was phylogenetically closer to Lezgin and Edilbai breeds. Trends in historical Ne were very similar for these breeds. We observed the increased decline in Ne around 20–25 generations ago (which corresponds to 1940s) that can be associated with deportation of Karachaev people to Kazakhstan and Kyrgyzstan in 1943, which resulted in lost almost all of its livestock. TreeMix analysis allowing one migration event revealed gene flow from Karakul to Karachaev/Lezgin nod. Admixture analysis showed the presence in Karachaev sheep of Edilbai and Karakul specific genomic components (~80 and ~20%, respectively). Our study allow suggest that Karachaev breed was extinct during World War II and then was restored in 1960s after Karachaev people returned to their land. It originated from the sheep they brought from Central Asia (Edilbai), and was improved by Karakul breed and local sheep. This work was supported by RSF No. 21-46-00001 (genotyping) and the Russian Ministry of Science and Higher Education No. 0445-2019-0024 (expedition studies).
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skab235.443
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 5
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    PSXII-32 Testing of low-density SNP panel in wild and domestic reindeer populations (Rangifer tarandus)
    Oxford University Press (OUP) ; 2020
    In:  Journal of Animal Science Vol. 98, No. Supplement_4 ( 2020-11-30), p. 239-240
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 98, No. Supplement_4 ( 2020-11-30), p. 239-240
    Abstract: A territory of northern Russia covering more than 4,194 square kilometers is the world’s largest dwelling and breeding area of wild and domestic reindeer. Unlocking its complete genome sequences should have promoted design and development of species-specific genotyping arrays, but this process is still in progress. However, evaluation of state of gene pool of reindeer populations cannot be paused to prevent dramatic losses in genetic diversity. Thus, we aimed to select SNPs to create low-density panel to perform genetic assessments without losing biological content. Our study was based on SNP genotypes of wild reindeer (n = 83), and domestic reindeer from the Nenets District (Nenets breed, n = 100), Murmansk Region (Nenets breed, n = 19), Republic of Sakha (Yakutia) (Evenk breed, n = 19) obtained using Illumina BovineHD BeadChip. The data processing performed in PLINK 1.9 revealed 4456 polymorphic SNPs. Using Delta method implemented in the TRES software, 368 informative SNPs were selected from the whole set of polymorphic SNPs for further analysis. To compare the resolution power of low-density SNP panel with a whole set of polymorphic SNPs, we estimated minor allele frequencies (MAF) and performed PCA analysis and Admixture clustering. In case of low-density panel, we observed obvious bias to higher MAF (≥ 0.30), and 4% of SNPs had MAF around 0,1. Among the whole set of polymorphic SNPs, 70% SNPs had MAF ≤ 0.2. PCA obtained with low-density panel and the whole SNP set provided similar pattern of genetic differentiation between studied groups. Wild animals were clearly separated by PC1 from their domestic relatives. Besides Evenk reindeer was distant from two Nenets groups. The Admixture clustering demonstrated the identical patterns for both SNPs sets. The next step of our study will be developing custom DNA array based on 368 selected informative SNPs. The research was funded by RSF № 16-16-10068-P.
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skaa278.437
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
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  • 6
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    Bridging Gaps in the Agricultural Phosphorus Cycle from an Animal Husbandry Perspective—The Case of Pigs and Poultry
    MDPI AG ; 2018
    In:  Sustainability Vol. 10, No. 6 ( 2018-06-01), p. 1825-
    Details
    In: Sustainability, MDPI AG, Vol. 10, No. 6 ( 2018-06-01), p. 1825-
    Type of Medium: Online Resource
    ISSN: 2071-1050
    URL: Article
    DOI: 10.3390/su10061825
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2518383-7
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  • 7
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    Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hens
    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-06-29)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-06-29)
    Abstract: Phosphorus (P) and calcium (Ca) are critical for egg production in laying hens. Most of P in plant-based poultry diet is bound as phytic acid and needs to be hydrolysed before absorption. To increase P bioavailability, exogenous phytases or bioavailable rock phosphate is added in feed. There is growing evidence of the importance of miRNAs as the epicentre of intestinal homeostasis and functional properties. Therefore, we demonstrated the expression of miRNA profiles and the corresponding target genes due to the different levels of P (recommended vs. 20% reduction) and/or Ca (recommended vs. 15% reduction) in feed. Jejunal miRNA profiles of Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens strains were used (n = 80). A total of 34 and 76 miRNAs were differentially expressed (DE) in the different diet groups within LSL and LB strains respectively. In LSL, the DE miRNAs and their targets were involved in calcium signaling pathway, inositol phosphate metabolism, and mitochondrial dysfunction. Similarly, in LB miRNAs targets were enriched in metabolic pathways such as glutathione metabolism, phosphonate metabolism and vitamin B6 metabolism. Our results suggest that both strains employ different intrinsic strategies to cope with modulated P and Ca supply and maintain mineral homeostasis.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-021-92932-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2615211-3
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  • 8
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    Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation
    Springer Science and Business Media LLC ; 2019
    In:  Scientific Reports Vol. 9, No. 1 ( 2019-01-29)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2019-01-29)
    Abstract: Genome wide association study was conducted using a mixed linear model (MLM) approach that accounted for family structure to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with body weight (BW) and feed efficiency (FE) traits in a broiler chicken population. The results of the MLM approach were compared with the results of a general linear model approach that does not take family structure in to account. In total, 11 quantitative trait loci (QTL) and 21 SNPs, were identified to be significantly associated with BW traits and 5 QTL and 5 SNPs were found associated with FE traits using MLM approach. Besides some overlaps between the results of the two GWAS approaches, there are considerable differences in the detected QTL. Even though the genomic inflation factor (λ) values indicate that there is no strong family structure in this population, using models that account for the existing family structure may reduce bias and increase accuracy of the estimated SNP effects in the association analysis. The SNPs and candidate genes identified in this study provide information on the genetic background of BW and FE traits in broiler chickens and might be used as prior information for genomic selection.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-018-37216-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
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  • 9
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    Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
    Springer Science and Business Media LLC ; 2018
    In:  Scientific Reports Vol. 8, No. 1 ( 2018-01-11)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-01-11)
    Abstract: This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern. Four modules, one in liver (with 444 co-expressed genes) and three in duodenum (gathering 37, 126 and 41 co-expressed genes), were significantly associated with FE indicators. Intra-module analyses revealed tissue-specific candidate genes; 12 of these genes were also identified as DE between individuals with high and low RFI. Pathways enriched by the list of genes showing DE and/or belonging to FE co-expressed modules included response to oxidative stress, inflammation, immune response, lipid metabolism and thermoregulation. Low overlapping between genes identified in duodenum and liver tissues was observed but heat shock proteins were associated to FE in both tissues. Our results suggest tissue-specific rather than common transcriptome regulatory processes associated with FE in pigs.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-017-19072-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
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  • 10
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    Mineral Phosphorus Supply in Piglets Impacts the Microbial Composition and Phytate Utilization in the Large Intestine
    MDPI AG ; 2021
    In:  Microorganisms Vol. 9, No. 6 ( 2021-06-01), p. 1197-
    Details
    In: Microorganisms, MDPI AG, Vol. 9, No. 6 ( 2021-06-01), p. 1197-
    Abstract: A sufficient supply of phosphorus (P) to pigs in livestock farming is based on the optimal use of plant-based phytate and mineral P supplements to ensure proper growth processes and bone stability. However, a high P supplementation might bear the risk of higher environmental burden due to the occurrence of excess P and phytate degradation products in manure. In this context, the intestinal microbiota is of central importance to increase P solubility, to employ non-mineral P by the enzymatic degradation of phytate, and to metabolize residual P. A feeding experiment was conducted in which piglets were fed diets with different P levels, resulting in three groups with low, medium (covering requirements), and high concentrations of available P. Samples from caecum and colon digesta were analysed for microbial composition and phytate breakdown to estimate the microbial contribution to metabolize P sources. In terms of identified operational taxonomic units (OTU), caecum and colon digesta under the three feeding schemes mainly overlap in their core microbiome. Nevertheless, different microbial families correlate with increased dietary P supply. Specifically, microbes of Desulfovibrionaceae, Pasteurellaceae, Anaerovoracaceae, and Methanobacteriaceae were found significantly differentially abundant in the large intestine across the dietary treatments. Moreover, members of the families Veillonellaceae, Selenomonadaceae, and Succinivibrionaceae might contribute to the observed phytate degradation in animals fed a low P diet. In this sense, the targeted manipulation of the intestinal microbiota by feeding measures offers possibilities for the optimization of intestinal phytate and P utilization.
    Type of Medium: Online Resource
    ISSN: 2076-2607
    URL: Article
    DOI: 10.3390/microorganisms9061197
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2720891-6
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