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Romanov MN, Shakhin AV, Abdelmanova AS, Volkova NA, Efimov DN, Fisinin VI, Korshunova LG, Anshakov DV, Dotsev AV, Griffin DK, Zinovieva NA. 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. Genes (Basel) 2024; 15:524. [PMID: 38674458 PMCID: PMC11050503 DOI: 10.3390/genes15040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
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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Affiliation(s)
- Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Dmitry N. Efimov
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Vladimir I. Fisinin
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Liudmila G. Korshunova
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Arsen V. Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | | | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
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Dementieva NV, Shcherbakov YS, Stanishevskaya OI, Vakhrameev AB, Larkina TA, Dysin AP, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbach NR, Griffin DK, Romanov MN. Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds. J Zhejiang Univ Sci B 2024; 25:324-340. [PMID: 38584094 PMCID: PMC11009443 DOI: 10.1631/jzus.b2300443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/10/2023] [Indexed: 04/09/2024]
Abstract
The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
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Affiliation(s)
- Natalia V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia.
| | - Yuri S Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Tatiana A Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Artem P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga A Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anna E Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Anastasiia I Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Olga V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Grigoriy K Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Natalia R Reinbach
- Russian Research Institute of Farm Animal Genetics and Breeding ‒ Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, St. Petersburg, 196601, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. ,
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. ,
- L K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, 142132, Russia. ,
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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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Yildirim EA, Laptev GY, Tiurina DG, Gorfunkel EP, Ilina LA, Filippova VA, Dubrovin AV, Brazhnik EA, Novikova NI, Melikidi VK, Kalitkina KA, Ponomareva ES, Griffin DK, Romanov MN. Investigating adverse effects of chronic dietary exposure to herbicide glyphosate on zootechnical characteristics and clinical, biochemical and immunological blood parameters in broiler chickens. Vet Res Commun 2024; 48:153-164. [PMID: 37594698 PMCID: PMC10810961 DOI: 10.1007/s11259-023-10195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023]
Abstract
Although the herbicide glyphosate is widely used globally and considered safe, more evidence of its adverse effects on animals and humans is accumulating. The present investigation was aimed at evaluating the impact of different glyphosate concentrations on zootechnical characteristics and clinical, biochemical and immunological blood parameters in Ross 308 broiler chickens. Four groups were employed, including untreated control and three experimental groups fed diets enriched with glyphosate at doses of 10, 20 and 100 ppm that conformed to 0.5, 1 and 5 maximum residue limits, respectively. The results showed that glyphosate is a stress factor triggering a multifaceted effect on important blood parameters (e.g., white blood cell and phagocytic counts), which was shown for the first time in the experiments involving productive meat-type poultry. It was first revealed that glyphosate-induced changes in blood parameters may be related to a negative impact on the zootechnical characteristics including the digestive tract organ development and body weight gain. The study findings suggested that exposure to glyphosate in the feedstuffs can adversely affect the physiological condition and productivity of broilers.
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Affiliation(s)
- Elena A Yildirim
- BIOTROF+ Ltd, Pushkin, St. Petersburg, Russia
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg, Russia
| | - Georgi Yu Laptev
- BIOTROF+ Ltd, Pushkin, St. Petersburg, Russia
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg, Russia
| | | | | | - Larisa A Ilina
- BIOTROF+ Ltd, Pushkin, St. Petersburg, Russia
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg, Russia
| | - Valentina A Filippova
- BIOTROF+ Ltd, Pushkin, St. Petersburg, Russia
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg, Russia
| | | | | | | | | | - Kseniya A Kalitkina
- BIOTROF+ Ltd, Pushkin, St. Petersburg, Russia
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg, Russia
| | | | | | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, UK.
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, Russia.
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Narushin VG, Volkova NA, Vetokh AN, Dzhagaev AY, Volkova LA, Griffin DK, Romanov MN, Zinovieva NA. Metabolic Rate and Egg Production in Japanese Quails Can Be Predicted by Assessing Growth Parameters of Laying Hens. Animals (Basel) 2024; 14:258. [PMID: 38254427 PMCID: PMC10812541 DOI: 10.3390/ani14020258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
The aim of the current study was to assess the female metabolic rate and test the hypothesis that there is a relationship between the egg productivity of Japanese quails from eight breeds and their morphometric, or growth, parameters. Parameters measured were body weight (B), volume (V), and surface area (S), as well as the metabolism level expressed by the ratio S/V. The collected egg performance traits were as follows: the number of eggs produced (N), the average egg weight (W), and the total egg mass (M) (i.e., N multiplied by W). To measure the S and V values, a novel technique was developed that takes into account the similarity of the quail's body to an ellipsoid. An analysis of the relationships between productivity indicators allowed us to introduce a new index called the metabolic index, B·S/V, based on all three main growth parameters in quails. Using the values of this index, we were then able to judge indirectly the level of quails' egg productivity. We went on to assess the N, W, and M values, not only depending on the size of the bird's growth parameters but also according to the degree of their changes during quail growth. These changes were expressed as the slope angles of trend lines describing the growth process data. This approach produced more accurate results for predicting the egg productivity in terms of W and M.
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Affiliation(s)
- Valeriy G. Narushin
- Research Institute for Environment Treatment, 69035 Zaporizhya, Ukraine;
- Vita-Market Ltd., 69035 Zaporizhya, Ukraine
| | - Natalia A. Volkova
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.N.V.); (A.Y.D.); (L.A.V.); (N.A.Z.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.N.V.); (A.Y.D.); (L.A.V.); (N.A.Z.)
| | - Alan Yu. Dzhagaev
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.N.V.); (A.Y.D.); (L.A.V.); (N.A.Z.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.N.V.); (A.Y.D.); (L.A.V.); (N.A.Z.)
| | | | - Michael N. Romanov
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.N.V.); (A.Y.D.); (L.A.V.); (N.A.Z.)
- School of Biosciences, University of Kent, Canterbury CT2 7NZ, UK;
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.N.V.); (A.Y.D.); (L.A.V.); (N.A.Z.)
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Dementieva NV, Dysin AP, Shcherbakov YS, Nikitkina EV, Musidray AA, Petrova AV, Mitrofanova OV, Plemyashov KV, Azovtseva AI, Griffin DK, Romanov MN. Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study. Animals (Basel) 2024; 14:251. [PMID: 38254422 PMCID: PMC10812825 DOI: 10.3390/ani14020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Elena V. Nikitkina
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Artem A. Musidray
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Anna V. Petrova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Kirill V. Plemyashov
- Federal State Budgetary Educational Institution of Higher Education “St. Petersburg State University of Veterinary Medicine”, 196084 St. Petersburg, Russia;
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
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Tarasova EI, Frolov AN, Lebedev SV, Romanov MN. Landmark native breed of the Orenburg goats: progress in its breeding and genetics and future prospects. Anim Biotechnol 2023; 34:5139-5154. [PMID: 36495096 DOI: 10.1080/10495398.2022.2154221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This paper reviews information about a unique and iconic breed of the Orenburg Oblast, the homeland and the only place where the best herds of Orenburg down-hair goats in Russia are concentrated. Three types of these small ruminant animals are widespread on the territory of the region: Orenburg purebred gray goats, Orenburg purebred white goats, as well as crossbred white goats of F1 White Don × White Orenburg. Currently, at the farms of the Orenburg region, animals are selected according to their phenotype, with selected traits being color, weight and length of down hair. In recent years, the Orenburg goat breed has become an object of genetic research using various marker systems including immunogenetic, microsatellite, mtDNA and SNP markers. Overall, these studies evidence about the uniqueness of the allele pool in the landmark native breed of the Orenburg goats, which is a complex dynamic genetic system, prioritizing its further in-depth genome research and breeding applications.
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Affiliation(s)
- Ekaterina I Tarasova
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
| | - Alexey N Frolov
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
| | - Svyatoslav V Lebedev
- Federal Research Center for Biological Systems and Agrotechnologies, Orenburg, Russia
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8
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail ( Coturnix japonica) Breeds. Animals (Basel) 2023; 13:3439. [PMID: 38003057 PMCID: PMC10668688 DOI: 10.3390/ani13223439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
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 indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center Zagorsk Experimental Breeding Farm—Branch of the Federal Research Centre, All-Russian Poultry Research and Technological Institute, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Valeriy G. Narushin
- Research Institute for Environment Treatment, 69032 Zaporizhya, Ukraine;
- Vita-Market Co., Ltd., 69032 Zaporizhya, Ukraine
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
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Narushin VG, Orszulik ST, Romanov MN, Griffin DK. A novel approach to egg and math: Improved geometrical standardization of any avian egg profile. Ann N Y Acad Sci 2023; 1529:61-71. [PMID: 37642389 DOI: 10.1111/nyas.15059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Developing a geometric formulation of any biological object has a number of justifications and applications. Recently, we developed a universal geometric figure for describing a bird's egg in any of the possible basic shapes: spherical, ellipsoidal, ovoid, and pyriform. The formulation proved widely applicable but had a number of drawbacks, including a very obvious join between two parts of the egg. To correct this, we developed the Main Axiom of the universal mathematical formula. This essentially involved making the ordinate of the extremum of the function correspond to half the maximum egg breadth (B), and the abscissa to the reciprocal of the parameter w that reflects the shift of the vertical axis to its coincidence with B. This, in turn, helped us develop a new, simplified mathematical model without a nonbiological join. Experimental verification was performed to confirm the adequacy of the new geometric figure. It accurately described actual avian eggs of various shapes more closely than our previous model. To the best of our knowledge, our new, simplified equation can be applied as a standard for any bird egg that exists in nature. As a rather simple equation, it can be used in a broad range of applications.
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Affiliation(s)
- Valeriy G Narushin
- Research Institute for Environment Treatment, Zaporozhye, Ukraine
- Vita-Market Ltd, Zaporozhye, Ukraine
| | | | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, UK
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, Russia
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Grozina AA, Ilina LA, Laptev GY, Yildirim EA, Ponomareva ES, Filippova VA, Tyurina DG, Fisinin VI, Kochish II, Griffin DK, Surai PF, Romanov MN. Probiotics as an alternative to antibiotics in modulating the intestinal microbiota and performance of broiler chickens. J Appl Microbiol 2023; 134:lxad213. [PMID: 37715326 DOI: 10.1093/jambio/lxad213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023]
Abstract
AIMS Gut bacteria play an important role in poultry nutrition and the immune defense system. Changes in the intestinal microbiome affect the physiological state, metabolism, and innate immunity of poultry. The present study aimed to characterize age-related changes in the gastrointestinal tract microflora in broiler chickens, depending on supplementation of the diet with the in-feed antibiotic Stafac® 110 and a Bacillus subtilis strain-based probiotic. METHODS AND RESULTS In this regard, a comprehensive analysis of the taxonomic structure of the microbial community in the gastrointestinal tract (GIT) of broiler chickens was carried out using a molecular genetic technique of the terminal-restriction fragment length polymorphism analysis and taking into account age dynamics and feeding treatment. A beneficial effect on the microbiological composition and body weight of broilers was observed when using the antibiotic and probiotic in compound feeds. Different bacterial communities were revealed in the duodenum and cecum, and their positive impact on broiler growth was established. The results obtained shed light on the formation of GIT microflora of broiler chickens during the growing period and its changes in response to the use of the antibiotic and the probiotic. CONCLUSIONS We suggest that the implementation of the tested in-feed antibiotic and probiotic can be beneficial in regulating the intestinal microflora microbiological processes in the GIT and improving the feeding efficiency and productivity of broiler chickens.
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Affiliation(s)
- Alena A Grozina
- Federal Scientific Center "All-Russia Research and Technological Poultry Institute", Russian Academy of Sciences, Sergiev Posad, Moscow Oblast 141311, Russia
| | - Larisa A Ilina
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg 196601, Russia
- BIOTROF LLC, Pushkin, St. Petersburg 196602, Russia
| | - Georgiy Yu Laptev
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg 196601, Russia
- BIOTROF LLC, Pushkin, St. Petersburg 196602, Russia
| | - Elena A Yildirim
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg 196601, Russia
- BIOTROF LLC, Pushkin, St. Petersburg 196602, Russia
| | | | - Valentina A Filippova
- Federal State Budgetary Educational Institution of Higher Education "St. Petersburg State Agrarian University", Pushkin, St. Petersburg 196601, Russia
- BIOTROF LLC, Pushkin, St. Petersburg 196602, Russia
| | | | - Vladimir I Fisinin
- Federal Scientific Center "All-Russia Research and Technological Poultry Institute", Russian Academy of Sciences, Sergiev Posad, Moscow Oblast 141311, Russia
| | - Ivan I Kochish
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow 109472, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Peter F Surai
- Vitagene and Health Research Centre, Bristol BS4 2RS, United Kingdom
- Department of Microbiology and Biochemistry, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
- Department of Animal Nutrition, Faculty of Agricultural and Environmental Sciences, Szent Istvan University, H-2103 Gödöllo, Hungary
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast 142132, Russia
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, Zinovieva NA. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. Biology (Basel) 2023; 12:979. [PMID: 37508409 PMCID: PMC10376169 DOI: 10.3390/biology12070979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
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.
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Affiliation(s)
- Michael N Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Alexandra S Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Vladimir I Fisinin
- Center "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Elena A Gladyr
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Dmitry V Anshakov
- Breeding and Genetic Center "Zagorsk Experimental Breeding Farm"-Branch of the Federal Research Centre "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Arsen V Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Natalia A Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
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Sazanov AA, Sazanova AL, Nefedov MD, Griffin DK, Romanov MN. A pair of gametologous genes provides further insights into avian comparative cytogenomics. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
AbstractExploration of avian gametologous genes, i.e., homologous genes located on both the Z and W chromosomes, provides a crucial information about the underlying mechanism pertaining to the evolution of these chromosomes. The domestic chicken (Gallus gallus (Linnaeus 1758); GGA) traditionally serves as the primary reference subject of these comparative cytogenomic studies. Using bioinformatic, molecular (overgo BAC library scanning), and cytogenetic (BAC-based FISH) techniques, we have investigated in detail a pair of UBE2R2/UBE2R2L gametologs. By screening a gridded genomic jungle fowl BAC library, CHORI-261, with a short labeled UBE2R2L gene fragment called overgo probe, we detected seven specific clones. For three of them, CH261-019I23, CH261-105E16, and CH261-114G22, we identified their precise cytogenetic location on the Gallus gallus W chromosome (GGAW). They also co-localized with the UBAP2L2 gene on the, as was shown previously, along with the CH261-053P09 BAC clone also containing the GGAW-specific UBE2R2L DNA sequence. The fine mapping of the UBE2R2/UBE2R2L homologs in the chicken genome also shed the light on comparative cytogenetic aspects in birds. Our findings provided further evidence that bird genomes moderately changed only during evolution and are suitable for successful use of interspecies hybridization using both overgo-based BAC library screen and BAC-based FISH.
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Koshkina OA, Rodionov AN, Vetokh AN, Gusev IV, Anshakov DV, Stanishevskaya OI, Dotsev AV, Griffin DK, Zinovieva NA. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. J Anim Sci Biotechnol 2023; 14:35. [PMID: 36829208 PMCID: PMC9951459 DOI: 10.1186/s40104-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/27/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.
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Affiliation(s)
- Michael N. Romanov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia ,grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Vladimir I. Fisinin
- grid.4886.20000 0001 2192 9124Federal State Budget Scientific Institution Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Olga A. Koshkina
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Igor V. Gusev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Dmitry V. Anshakov
- grid.4886.20000 0001 2192 9124Breeding and Genetic Centre “Zagorsk Experimental Breeding Farm” – Branch of the Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Olga I. Stanishevskaya
- grid.473314.6Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, St. Petersburg, Russia
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Darren K. Griffin
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
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Kochish II, Brazhnik EA, Vorobyov NI, Nikonov IN, Korenyuga MV, Myasnikova OV, Griffin DK, Surai PF, Romanov MN. Features of Fractal Conformity and Bioconsolidation in the Early Myogenesis Gene Expression and Their Relationship to the Genetic Diversity of Chicken Breeds. Animals (Basel) 2023; 13:521. [PMID: 36766410 PMCID: PMC9913260 DOI: 10.3390/ani13030521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Elements of fractal analysis are widely used in scientific research, including several biological disciplines. In this study, we hypothesized that chicken breed biodiversity manifests not only at the phenotypic level, but also at the genetic-system level in terms of different profiles of fractal conformity and bioconsolidation in the early myogenesis gene expression. To demonstrate this effect, we developed two mathematical models that describe the fractal nature of the expression of seven key genes in the embryonic breast and thigh muscles in eight breeds of meat, dual purpose, egg and game types. In the first model, we produced breed-specific coefficients of gene expression conformity in each muscle type using the slopes of regression dependencies, as well as an integral myogenesis gene expression index (MGEI). Additionally, breed fractal dimensions and integral myogenesis gene expression fractal dimension index (MGEFDI) were determined. The second gene expression model was based on plotting fractal portraits and calculating indices of fractal bioconsolidation. The bioconsolidation index of myogenesis gene expression correlated with the chick growth rate and nitric oxide (NO) oxidation rate. The proposed fractal models were instrumental in interpreting the genetic diversity of chickens at the level of gene expression for early myogenesis, NO metabolism and the postnatal growth of chicks.
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Affiliation(s)
- Ivan I. Kochish
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
| | | | - Nikolai I. Vorobyov
- All-Russia Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia
| | - Ilya N. Nikonov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
| | - Maxim V. Korenyuga
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
| | - Olga V. Myasnikova
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
| | | | - Peter F. Surai
- Vitagene and Health Research Centre, Bristol BS4 2RS, UK
- Department of Microbiology and Biochemistry, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
- Department of Animal Nutrition, Faculty of Agricultural and Environmental Sciences, Szent Istvan University, H-2103 Gödöllő, Hungary
| | - Michael N. Romanov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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Kochish II, Titov VY, Nikonov IN, Brazhnik EA, Vorobyov NI, Korenyuga MV, Myasnikova OV, Dolgorukova AM, Griffin DK, Romanov MN. Unraveling signatures of chicken genetic diversity and divergent selection in breed-specific patterns of early myogenesis, nitric oxide metabolism and post-hatch growth. Front Genet 2023; 13:1092242. [PMID: 36712856 PMCID: PMC9874007 DOI: 10.3389/fgene.2022.1092242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction: Due to long-term domestication, breeding and divergent selection, a vast genetic diversity in poultry currently exists, with various breeds being characterized by unique phenotypic and genetic features. Assuming that differences between chicken breeds divergently selected for economically and culturally important traits manifest as early as possible in development and growth stages, we aimed to explore breed-specific patterns and interrelations of embryo myogenesis, nitric oxide (NO) metabolism and post-hatch growth rate (GR). Methods: These characteristics were explored in eight breeds of different utility types (meat-type, dual purpose, egg-type, game, and fancy) by incubating 70 fertile eggs per breed. To screen the differential expression of seven key myogenesis associated genes (MSTN, GHR, MEF2C, MYOD1, MYOG, MYH1, and MYF5), quantitative real-time PCR was used. Results: We found that myogenesis associated genes expressed in the breast and thigh muscles in a coordinated manner showing breed specificity as a genetic diversity signature among the breeds studied. Notably, coordinated ("accord") expression patterns of MSTN, GHR, and MEFC2 were observed both in the breast and thigh muscles. Also, associated expression vectors were identified for MYOG and MYOD1 in the breast muscles and for MYOG and MYF5 genes in the thigh muscles. Indices of NO oxidation and post-hatch growth were generally concordant with utility types of breeds, with meat-types breeds demonstrating higher NO oxidation levels and greater GR values as compared to egg-type, dual purpose, game and fancy breeds. Discussion: The results of this study suggest that differences in early myogenesis, NO metabolism and post-hatch growth are breed-specific; they appropriately reflect genetic diversity and accurately capture the evolutionary history of divergently selected chicken breeds.
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Affiliation(s)
- Ivan I. Kochish
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Vladimir Yu. Titov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia,Federal Scientific Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Oblast, Russia
| | - Ilya N. Nikonov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | | | - Nikolai I. Vorobyov
- All-Russia Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Maxim V. Korenyuga
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Olga V. Myasnikova
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Anna M. Dolgorukova
- Federal Scientific Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Michael N. Romanov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia,School of Biosciences, University of Kent, Canterbury, United Kingdom,*Correspondence: Michael N. Romanov,
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Romanov MN, Sölkner J, Zinovieva NA, Wimmers K, Weigend S. Editorial: Traditional and up-to-date genomic insights into domestic animal diversity. Front Genet 2023; 13:1117708. [PMID: 36685846 PMCID: PMC9846024 DOI: 10.3389/fgene.2022.1117708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, United Kingdom,*Correspondence: Michael N. Romanov,
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | | | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Steffen Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt, Germany
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Narushin VG, Romanov MN, Griffin DK. A novel model for eggs like pears: How to quantify them geometrically with a mathematical formula of two parameters? J Biosci 2023; 48:35. [PMID: 37731257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Of the variety of bird egg shapes, perhaps the most fascinating and unusual are pyriform (pear-shaped, or conical) eggs. Among oologists, there is still no consensus on what exactly caused this evolutionary and ecological adaptation. To address this, our research was aimed to develop a minimalistic mathematical model for an accurate description of the pyriform egg contour, using the minimum number of measurements. As such, egg length (L) and its maximum breadth (B) were found to be an optimal set of parameters that were easy enough to measure with the required accuracy. We tested four analytical premises that can be used for successful pyriform egg shape modelling. To validate these four model premises, images of pyriform eggs characteristic of 32 species were used. As a result, we derived a novel mathematical dependence that we called the 'pyriform model with two parameters'. Based on this model, it is feasible to geometrically reconstruct any pyriform egg profile under study using only two egg measurements, i.e., L and B. Since pyriform eggs are characteristic of wild bird species that are most often investigated in the field, the measurement of only two parameters minimizes the time spent and, accordingly, the stress factor on the animals. The least error estimate for the new model was 3.9%, which turned out to be even more accurate than that of the previously developed model with three parameters.
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Griffin DK, Larkin DM, O’Connor RE, Romanov MN. Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants. Animals (Basel) 2022; 13:ani13010106. [PMID: 36611715 PMCID: PMC9817885 DOI: 10.3390/ani13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species. The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine-Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
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Affiliation(s)
- Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence:
| | - Denis M. Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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Romanov MN, Da Y, Chemnick LG, Thomas SM, Dandekar SS, Papp JC, Ryder OA. Towards a Genetic Linkage Map of the California Condor, an Endangered New World Vulture Species. Animals (Basel) 2022; 12:ani12233266. [PMID: 36496789 PMCID: PMC9739316 DOI: 10.3390/ani12233266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Abstract
The development of a linkage map is an important component for promoting genetic and genomic studies in California condors, an endangered New World vulture species. Using a set of designed anonymous microsatellite markers, we genotyped a reference condor population involving 121 individuals. After marker validation and genotype filtering, the genetic linkage analysis was performed using 123 microsatellite loci. This resulted in the identification of 15 linkage groups/subgroups that formed a first-generation condor genetic map, while no markers linked to a lethal chondrodystrophy mutation were found. A panel of polymorphic markers that is instrumental in molecular parentage diagnostics and other genetic studies in the California condor was selected. Further condor conservation genomics research will be focused on updating the linkage map and integrating it with cytogenetic and BAC-based physical maps and ultimately with the genome sequence assembly.
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Affiliation(s)
- Michael N. Romanov
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Correspondence:
| | - Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Leona G. Chemnick
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Steven M. Thomas
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Sugandha S. Dandekar
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Jeanette C. Papp
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Oliver A. Ryder
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
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Narushin VG, Griffin AW, Romanov MN, Griffin DK. Measurement of the neutral axis in avian eggshells reveals which species conform to the golden ratio. Ann N Y Acad Sci 2022; 1517:143-153. [PMID: 36052445 PMCID: PMC9826523 DOI: 10.1111/nyas.14895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Avian eggs represent a striking evolutionary adaptation for which shell thickness is crucial. An understudied eggshell property includes the neutral axis, a line that is drawn through any bent structure and whose precise location is characterized by the k-factor. Previous studies have established that, for chicken eggs, mean k corresponds to the golden ratio (Φ = 1.618, or 0.618 in its reciprocal form). We hypothesized whether such an arrangement of the neutral axis conforms to the eggshell of any bird or only to eggshells with a certain set of geometric parameters. Implementing a suite of innovative methodological approaches, we investigated variations in k of 435 avian species, exploring which correspond to Φ. We found that mean k is highly variable among birds and does not always conform to Φ, being much lower in spherical and ellipsoid eggs and higher in pyriform eggs. While 21 species had k values within 0.618 ± 0.02 (including four falcon species) and the Falconinae subfamily (six species) revealed a mean of 0.618, it is predominantly domesticated species (chicken, ducks, and geese) that lay eggs whose neutral axis corresponds to the golden ratio. Thus, the study of the mathematical secrets of the eggshell related to the golden ratio of its neutral axis suggests its species-specific signatures in birds.
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Affiliation(s)
- Valeriy G. Narushin
- Research Institute for Environment TreatmentZaporozhyeUkraine,Vita‐Market LtdZaporozhyeUkraine
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21
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Dementieva NV, Shcherbakov YS, Tyshchenko VI, Terletsky VP, Vakhrameev AB, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbah NR, Griffin DK, Romanov MN. Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds. Genes (Basel) 2022; 13:genes13101876. [PMID: 36292761 PMCID: PMC9601448 DOI: 10.3390/genes13101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence: (N.V.D.); (M.N.R.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Anatoly B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anna E. Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Grigoriy K. Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia R. Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence: (N.V.D.); (M.N.R.)
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22
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Vakhrameev AB, Narushin VG, Larkina TA, Barkova OY, Peglivanyan GK, Dysin AP, Dementieva NV, Makarova AV, Shcherbakov YS, Pozovnikova MV, Bondarenko YV, Griffin DK, Romanov MN. Selection-driven chicken phenome and phenomenon of pectoral angle variation across different chicken phenotypes. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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23
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Narushin VG, Romanov MN, Griffin DK. Egg-inspired engineering in the design of thin-walled shelled vessels: a theoretical approach for shell strength. Front Bioeng Biotechnol 2022; 10:995817. [PMID: 36185460 PMCID: PMC9516309 DOI: 10.3389/fbioe.2022.995817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/10/2022] [Indexed: 12/01/2022] Open
Abstract
A novel subdiscipline of bionics is emerging in the form of ‘egg-inspired engineering’ through the use of egg-shaped ovoids as thin-walled tanks and building structures. Hügelschäffer’s and Narushin’s models of egg geometry are highly applicable within this proposed subdiscipline. Here we conducted a comparative analysis between the two models with respect to some of the most important egg parameters. These included contents volume, shell volume, and the location of the neutral axis along the shell thickness. As a first step, theoretical studies using the Narushin’s model were carried out due to the lack (or limited amount) of data on the geometric relationships of parameters and available calculation formulae. Considering experimental data accumulated in the engineering and construction industries, we postulate a hypothesis that there is a correlation between location of the neutral axis and the strength of the walls in the egg-shaped structure. We suggest that the use of Narushin’s model is preferable to Hügelschäffer’s model for designing thin-walled shelled vessels and egg-shaped building structures. This is due to its relative simplicity (because of the requirement for only two initial parameters in the basic equation), optimal geometry in terms of material costs per unit of internal capacity, and effective prerequisites for shell strength characteristics.
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Affiliation(s)
- Valeriy G. Narushin
- Research Institute for Environment Treatment, Zaporozhye, Ukraine
- Vita-Market Ltd Zaporozhye, Zaporozhye, Ukraine
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, United Kingdom
- *Correspondence: Michael N. Romanov, ; Darren K. Griffin,
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
- *Correspondence: Michael N. Romanov, ; Darren K. Griffin,
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Narushin VG, Romanov MN, Mishra B, Griffin DK. Mathematical progression of avian egg shape with associated area and volume determinations. Ann N Y Acad Sci 2022; 1513:65-78. [PMID: 35333376 PMCID: PMC9545997 DOI: 10.1111/nyas.14771] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/25/2022] [Indexed: 01/10/2023]
Abstract
Development of nondestructive techniques for estimating egg parameters requires a comprehensive approach based on mathematical theory. Basic properties used to solve theoretical and applied problems in this respect are volume (V) and surface area (S). There are respective formulae for calculating V and S of spherical, ellipsoidal, and ovoid eggs in classical egg geometry; however, the mathematical description and calculation of these parameters for pyriform eggs have remained elusive. In the present study, we derived the appropriate formulae and established that this would be not only applicable and valid for the category of pyriform eggs, but also universal and explicit for all other naturally occurring avian egg shapes. Thus, we have demonstrated "mathematical progression" of this natural object, considering the egg as a sequence of geometric figures that transform from one to another in the following sequence of shapes: sphere → ellipsoid → ovoid (whose profile corresponds to Hügelschäffer's model) → pyriform ovoid.
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Affiliation(s)
- Valeriy G Narushin
- Research Institute for Environment Treatment, Zaporozhye, Ukraine.,Vita-Market Ltd, Zaporozhye, Ukraine
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Birendra Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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25
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Nikitkina EV, Dementieva NV, Shcherbakov YS, Atroshchenko MM, Kudinov AA, Samoylov OI, Pozovnikova MV, Dysin AP, Krutikova AA, Musidray AA, Mitrofanova OV, Plemyashov KV, Griffin DK, Romanov MN. Genome-wide association study for frozen-thawed sperm motility in stallions across various horse breeds. Anim Biosci 2022; 35:1827-1838. [PMID: 35240017 DOI: 10.5713/ab.21.0504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/23/2022] [Indexed: 11/27/2022] Open
Abstract
Objective The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds. Methods Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), progressive motility after freezing (FPM), and the difference between PM and FPM. The respective DNA samples from these stallions were genotyped using Axiom™ Equine Genotyping Array. Results We performed a GWAS search for single nucleotide polymorphism (SNP) markers and potential genes related to motility properties of frozen-thawed semen in the stallions of various breeds. As a result of the GWAS analysis, two SNP markers, rs1141327473 and rs1149048772, were identified that were associated with preservation of the frozen-thawed stallion sperm motility, the relevant putative candidate genes being NME8, OR2AP1 and OR6C4. Potential implications of effects of these genes on sperm motility are herein discussed. Conclusion The GWAS results enabled us to localize novel SNPs and candidate genes for sperm motility in stallions. Implications of the study for horse breeding and genetics are a better understanding of genomic regions and candidate genes underlying stallion sperm quality, and improvement in horse reproduction and breeding techniques. The identified markers and genes for sperm cryotolerance and the respective genomic regions are promising candidates for further studying the biological processes in the formation and function of the stallion reproductive system.
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Affiliation(s)
- Elena V Nikitkina
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Natalia V Dementieva
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Yuri S Shcherbakov
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Mikhail M Atroshchenko
- All-Russian Research Institute for Horse Breeding, Rybnovsky District, Ryazan Oblast, 391105, Russia
| | - Andrei A Kudinov
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Oleg I Samoylov
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Marina V Pozovnikova
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Artem P Dysin
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Anna A Krutikova
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Artem A Musidray
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Olga V Mitrofanova
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Kirill V Plemyashov
- Russian Research Institute for Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, Pushkin, St. Petersburg, 196625, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.,L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast, 142132, Russia
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26
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Ryder OA, Thomas S, Judson JM, Romanov MN, Dandekar S, Papp JC, Sidak-Loftis LC, Walker K, Stalis IH, Mace M, Steiner CC, Chemnick LG. Corrigendum to: Facultative Parthenogenesis in California Condors. J Hered 2021; 113:217. [PMID: 35575084 PMCID: PMC9113412 DOI: 10.1093/jhered/esab074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Oliver A Ryder
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Steven Thomas
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Jessica Martin Judson
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Michael N Romanov
- San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA.,School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK and L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Oblast 142132, Russia
| | - Sugandha Dandekar
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Lindsay C Sidak-Loftis
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | | | - Ilse H Stalis
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA
| | - Michael Mace
- San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA
| | - Cynthia C Steiner
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Leona G Chemnick
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
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27
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Ryder OA, Thomas S, Judson JM, Romanov MN, Dandekar S, Papp JC, Sidak-Loftis LC, Walker K, Stalis IH, Mace M, Steiner CC, Chemnick LG. Facultative Parthenogenesis in California Condors. J Hered 2021; 112:569-574. [PMID: 34718632 PMCID: PMC8683835 DOI: 10.1093/jhered/esab052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022] Open
Abstract
Parthenogenesis is a relatively rare event in birds, documented in unfertilized eggs from columbid, galliform, and passerine females with no access to males. In the critically endangered California condor, parentage analysis conducted utilizing polymorphic microsatellite loci has identified two instances of parthenogenetic development from the eggs of two females in the captive breeding program, each continuously housed with a reproductively capable male with whom they had produced offspring. Paternal genetic contribution to the two chicks was excluded. Both parthenotes possessed the expected male ZZ sex chromosomes and were homozygous for all evaluated markers inherited from their dams. These findings represent the first molecular marker-based identification of facultative parthenogenesis in an avian species, notably of females in regular contact with fertile males, and add to the phylogenetic breadth of vertebrate taxa documented to have reproduced via asexual reproduction.
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Affiliation(s)
- Oliver A Ryder
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Steven Thomas
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,SGI-DNA, La Jolla, CA 92037, USA
| | - Jessica Martin Judson
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA
| | - Michael N Romanov
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Sugandha Dandekar
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Human Genetics Department, GenoSeq Core, University of California, Los Angeles, CA 90095, USA
| | - Lindsay C Sidak-Loftis
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA.,Department of Veterinary Microbiology and Pathology, Program in Vector-borne Diseases, Washington State University, Pullman, WA, USA
| | | | - Ilse H Stalis
- Disease Investigations, San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA
| | - Michael Mace
- San Diego Zoo Wildlife Alliance, San Diego, CA 92101, USA
| | - Cynthia C Steiner
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Leona G Chemnick
- Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
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Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens. Biology (Basel) 2021; 10:biology10090876. [PMID: 34571753 PMCID: PMC8469556 DOI: 10.3390/biology10090876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023]
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 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.
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Affiliation(s)
- Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
| | - Olga I. Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Elena S. Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Igor V. Gusev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
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Narushin VG, Romanov MN, Griffin DK. Egg and math: introducing a universal formula for egg shape. Ann N Y Acad Sci 2021; 1505:169-177. [PMID: 34426991 DOI: 10.1111/nyas.14680] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/01/2022]
Abstract
The egg, as one of the most traditional food products, has long attracted the attention of mathematicians, engineers, and biologists from an analytical point of view. As a main parameter in oomorphology, the shape of a bird's egg has, to date, escaped a universally applicable mathematical formulation. Analysis of all egg shapes can be done using four geometric figures: sphere, ellipsoid, ovoid, and pyriform (conical or pear-shaped). The first three have a clear mathematical definition, each derived from the expression of the previous, but a formula for the pyriform profile has yet to be derived. To rectify this, we introduce an additional function into the ovoid formula. The subsequent mathematical model fits a completely novel geometric shape that can be characterized as the last stage in the evolution of the sphere-ellipsoid-Hügelschäffer's ovoid transformation, and it is applicable to any egg geometry. The required measurements are the egg length, maximum breadth, and diameter at the terminus from the pointed end. This mathematical analysis and description represents the sought-for universal formula and is a significant step in understanding not only the egg shape itself, but also how and why it evolved, thus making widespread biological and technological applications theoretically possible.
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Affiliation(s)
- Valeriy G Narushin
- Research Institute for Environment Treatment, Zaporozhye, Ukraine.,Vita-Market Ltd, Zaporozhye, Ukraine
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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Kretschmer R, de Souza MS, Furo IDO, Romanov MN, Gunski RJ, Garnero ADV, de Freitas TRO, de Oliveira EHC, O’Connor RE, Griffin DK. Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds. Cells 2021; 10:cells10040826. [PMID: 33916942 PMCID: PMC8067558 DOI: 10.3390/cells10040826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/18/2023] Open
Abstract
Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.
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Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91509-900 Rio Grande do Sul, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Ivanete de Oliveira Furo
- Laboratório de Reprodução Animal, LABRAC, Universidade Federal Rural da Amazônia, UFRA, Parauapebas, 68515-000 Pará, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | - Analía del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel, 97300-162 Rio Grande do Sul, Brazil; (M.S.d.S.); (R.J.G.); (A.d.V.G.)
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, 67030-000 Pará, Brazil;
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, 66075-110 Pará, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (M.N.R.); (R.E.O.)
- Correspondence: ; Tel.: +44-1227-823022
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Dementieva NV, Mitrofanova OV, Dysin AP, Kudinov AA, Stanishevskaya OI, Larkina TA, Plemyashov KV, Griffin DK, Romanov MN, Smaragdov MG. Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations. Animal 2021; 15:100171. [PMID: 33563558 DOI: 10.1016/j.animal.2021.100171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD<0.5 and LD<0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the Russian White RG population, pruning was substantial for Dataset I, and FST values were only positive when LD<0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the Russian White RG population with the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates.
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Affiliation(s)
- N V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - O V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - A P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - A A Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - O I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - T A Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - K V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
| | - D K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - M N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent, UK.
| | - M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, Russia
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Narushin VG, Laptev GY, Yildirim EA, Ilina LA, Filippova VA, Kochish II, Gorfunkel EP, Dubrovin AV, Novikova NI, Novikova OB, Dunyashev TP, Smolensky VI, Surai PF, Bondarenko YV, Griffin DK, Romanov MN. Modelling effects of phytobiotic administration on coherent responses to Salmonella infection in laying hens. Italian Journal of Animal Science 2020. [DOI: 10.1080/1828051x.2020.1733445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | | | | | | | - Ivan I. Kochish
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | | | | | | | - Oksana B. Novikova
- All-Russian Veterinary Research Institute of Poultry Science – Branch of the Federal State Budget Scientific Institution Federal Scientific Centre ‘All-Russian Poultry Research and Technological Institute’ of the Russian Academy of Sciences, St Petersburg, Russia
| | | | - Vladimir I. Smolensky
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - Peter F. Surai
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
- Department of Microbiology and Biochemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
- Department of Animal Nutrition, Faculty of Agricultural and Environmental Sciences, Szent Istvan University, Gödöllo, Hungary
| | - Yuri V. Bondarenko
- Department of Feed and Animal Feeding Technologies, Faculty of Biology and Technology, Sumy National Agrarian University, Sumy, Ukraine
| | | | - Michael N. Romanov
- K. I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
- School of Biosciences, University of Kent, Canterbury, UK
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Dementieva NV, Kudinov AA, Larkina TA, Mitrofanova OV, Dysin AP, Terletsky VP, Tyshchenko VI, Griffin DK, Romanov MN. Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity. Animals (Basel) 2020; 10:ani10101887. [PMID: 33076516 PMCID: PMC7602725 DOI: 10.3390/ani10101887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary To maintain the uniqueness of conserved chicken populations of local and imported breeds is of great importance. In this study, we genotyped small populations belonging to 14 breeds and 7 crossbreds using an Illumina Chicken 60K SNP (Single Nucleotide Polymorphisms) BeadChip and looked for appropriate methods to characterize their purity/variability. It was not straightforward to identify crossbred individuals, and the best approach was based on calculating the length and number of homozygous regions, or runs of homozygosity (ROH), in the populations studied. The latter enabled most accurate identification of crossbreds and can be served as an effective tool in testing genome-wide purity of chicken breeds. Abstract Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Andrei A. Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Tatiana A. Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Artyom P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Valeriy P. Terletsky
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
- Correspondence:
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Surai PF, Kochish II, Romanov MN, Griffin DK. Nutritional modulation of the antioxidant capacities in poultry: the case of vitamin E. Poult Sci 2019; 98:4030-4041. [DOI: 10.3382/ps/pez072] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/30/2019] [Indexed: 12/12/2022] Open
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Kudinov AA, Dementieva NV, Mitrofanova OV, Stanishevskaya OI, Fedorova ES, Larkina TA, Mishina AI, Plemyashov KV, Griffin DK, Romanov MN. Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens. BMC Genomics 2019; 20:270. [PMID: 30947682 PMCID: PMC6449956 DOI: 10.1186/s12864-019-5605-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/13/2019] [Indexed: 01/09/2023] Open
Abstract
Background The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great potential in meeting demands of local food producers, commercial farmers and biotechnology sector of specific pathogen-free (SPF) eggs, the former valuing the breed for its egg weight (EW), EL, age at first egg (AFE), body weight (BW), and the latter for its yield of extraembryonic fluid (YEF) in 12.5-day embryos, ratio of extraembryonic fluid to egg weight, and embryo mass. Moreover, its cold tolerance has been presumably associated with day-old chick down colour (DOCDC) – white rather than yellow, the genetic basis of these traits being however poorly understood. Results We undertook genome-wide association studies (GWASs) for eight performance traits using single nucleotide polymorphism (SNP) genotyping of 146 birds and an Illumina 60KBeadChip. Several suggestive associations (p < 5.16*10− 5) were found for YEF, AFE, BW and EW. Moreover, on chromosome 2, an association with the white DOCDC was found where there is an linkage disequilibrium block of SNPs including genes that are responsible not for colour, but for immune resistance. Conclusions The obtained GWAS data can be used to explore the genetics of immunity and carry out selection for increasing YEF for SPF eggs production. Electronic supplementary material The online version of this article (10.1186/s12864-019-5605-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrei A Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia.,University of Helsinki, FI-00014, Helsinki, Finland
| | - Natalia V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Olga V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Elena S Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Tatiana A Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Arina I Mishina
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Kirill V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
| | - Michael N Romanov
- Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia.,School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
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O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat Commun 2018; 9:1883. [PMID: 29784931 PMCID: PMC5962605 DOI: 10.1038/s41467-018-04267-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 01/07/2023] Open
Abstract
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning. Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.
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Affiliation(s)
- Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Paul M Barrett
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | | | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, IA, 50011, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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39
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Lee MO, Romanov MN, Plemyashov KV, Dementieva NV, Mitrofanova OV, Barkova OY, Womack JE. Haplotype structure and copy number polymorphism of the beta-defensin 7 genes in diverse chicken breeds. Anim Genet 2017; 48:490-492. [PMID: 28378952 DOI: 10.1111/age.12552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2017] [Indexed: 12/27/2022]
Abstract
Beta-defensins is a family of avian peptides related to the innate immune system. Copy number variation was recently reported for the avian beta-defensin 7 gene (AvBD7) between the highly inbred Leghorn and Fayoumi lines. Here, we examined copy number variants in 35 different chicken breeds and found that 31 of them have at least the same representation of the duplicated AvBD7 allele. We also found haplotypes upstream of the AvBD6 regions that are strongly linked to the AvBD7 duplication. We observed a strong linkage disequilibrium spanning of the upstream region of the AvBD6 gene, with two SNPs being flanking markers to detect duplication of the AvBD7.
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Affiliation(s)
- M O Lee
- Department of Veterinary Pathobiology, Texas A & M University, College Station, 77843, TX, USA
| | - M N Romanov
- School of Biosciences, University of Kent, CT2 7NJ, Canterbury, UK
| | - K V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB), Pushkin, 196601, St. Petersburg, Russia
| | - N V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB), Pushkin, 196601, St. Petersburg, Russia
| | - O V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB), Pushkin, 196601, St. Petersburg, Russia
| | - O Y Barkova
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB), Pushkin, 196601, St. Petersburg, Russia
| | - J E Womack
- Department of Veterinary Pathobiology, Texas A & M University, College Station, 77843, TX, USA
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40
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Sazanov AA, Kiselyova EV, Zakharenko AA, Romanov MN, Zaraysky MI. Plasma and saliva miR-21 expression in colorectal cancer patients. J Appl Genet 2016; 58:231-237. [PMID: 27910062 DOI: 10.1007/s13353-016-0379-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/23/2022]
Abstract
MicroRNA-21 (miR-21) expression was quantified by real-time qRT-PCR in peripheral blood and saliva samples obtained from patients diagnosed with colorectal cancer (CRC) of varying degrees of malignancy and healthy volunteers. All patients had adenocarcinoma located in the distal colon at different stages. Significant differences were detected between the control group and the total experimental group of CRC patients (plasma, P = 0.0001; saliva, P = 5e-12). MiR-21 expression was also significantly different in certain subgroups of patients with CRC disease stages II-IV as compared to the control group. No correlation of miR-21 expression was found with regard to gender and age of patents. Also, there were no significant individual correlations and linear regression of miR-21 expression in the plasma and saliva. The estimated diagnostic sensitivity and specificity of miR-21 expression were respectively 65 and 85% in the plasma, and 97 and 91% in the saliva. Our data suggest that miR-21 in both the saliva and plasma could be a proper biomarker for CRC screening, although the saliva miR-21 expression test looks preferable due to its higher sensitivity, specificity, and technical simplicity.
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Affiliation(s)
- A A Sazanov
- Department of Clinical Laboratory Diagnostics with a course of Molecular Medicine, First Pavlov State Medical University of St. Petersburg, 6/8 Lev Tolstoy Street, St. Petersburg, 197022, Russia. .,Department of the Molecular Biotechnology, Saint-Petersburg State Technological Institute (Technical University), St. Petersburg, Russia.
| | - E V Kiselyova
- Department of Surgery and Emergency Medicine, First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia
| | - A A Zakharenko
- Department of Surgery and Emergency Medicine, First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russia
| | - M N Romanov
- School of Biosciences, University of Kent, Canterbury, UK
| | - M I Zaraysky
- Department of Clinical Laboratory Diagnostics with a course of Molecular Medicine, First Pavlov State Medical University of St. Petersburg, 6/8 Lev Tolstoy Street, St. Petersburg, 197022, Russia
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41
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MTP, Wang J. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 2014; 346:1311-20. [PMID: 25504712 DOI: 10.1126/science.1251385] [Citation(s) in RCA: 647] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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Affiliation(s)
- Guojie Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Cai Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Qiye Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bo Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, UK
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Agostinho Antunes
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Matthew J Greenwold
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Anders Ödeen
- Department of Animal Ecology, Uppsala University, Norbyvägen 18D, S-752 36 Uppsala, Sweden
| | - Jie Cui
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia. Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Qi Zhou
- Department of Integrative Biology University of California, Berkeley, CA 94720, USA
| | - Luohao Xu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hailin Pan
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zongji Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Lijun Jin
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Pei Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Haofu Hu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Wei Yang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jiang Hu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jin Xiao
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zhikai Yang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yang Liu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Qiaolin Xie
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Hao Yu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jinmin Lian
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Ping Wen
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Fang Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Hui Li
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yongli Zeng
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zijun Xiong
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Shiping Liu
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Long Zhou
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Zhiyong Huang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Na An
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jie Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. BGI Education Center,University of Chinese Academy of Sciences,Shenzhen, 518083, China
| | - Qiumei Zheng
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yingqi Xiong
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Guangbiao Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Bo Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jingjing Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ganeshkumar Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Andreas Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Miriam V Rivas
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Erina Hara
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Julia Smith
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Marta Farré
- Royal Veterinary College, University of London, London, UK
| | - Jitendra Narayan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gancho Slavov
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Rui Borges
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - João Paulo Machado
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Imran Khan
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)/Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Mark S Springer
- Department of Biology, University of California Riverside, Riverside, CA 92521, USA
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Olle Håstad
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden
| | - Roger H Sawyer
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Kyu-Won Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyeon Jeong Kim
- Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea
| | - Seoae Cho
- Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Elizabeth Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA. Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Wesley Warren
- The Genome Institute at Washington University, St. Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute at Washington University, St. Louis, MO 63108, USA
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - David A Ray
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia. Nova Southeastern University Oceanographic Center 8000 N Ocean Drive, Dania, FL 33004, USA
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA. Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark
| | - David P Mindell
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David W Burt
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Peter Houde
- Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA
| | - Yong Zhang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Huanming Yang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China
| | - Jian Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | | | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia.
| | - Jun Wang
- China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong.
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Moiseeva IG, Romanov MN, Nikiforov AA, Avrutskaia TB. [Studies in chicken genetics: commemorating the 120th anniversary of the outstanding Soviet geneticist A. S. Serebrovsky (1892-1948)]. Genetika 2012; 48:1021-1038. [PMID: 23113330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The paper highlights the research of A. S. Serebrovsky in chicken genetics, including gene mapping and inheritance of morphological traits. Genetic formulas for several breeds are presented. The data of genetic surveys for local chicken populations from 23 regions of the former Soviet Union are also reviewed. The personal data of the authors on the morphotypological characteristics of different chicken breeds are given and discussed.
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Romanov MN, Dodgson JB, Gonser RA, Tuttle EM. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization. BMC Res Notes 2011; 4:211. [PMID: 21693052 PMCID: PMC3155834 DOI: 10.1186/1756-0500-4-211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Accepted: 06/21/2011] [Indexed: 12/23/2022] Open
Abstract
Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.
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Affiliation(s)
- Michael N Romanov
- Dept, of Biology, Indiana State University, Terre Haute, Indiana 47809, USA.
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Blagoveshchenskiĭ II, Sazanova AL, Stekol'nikova VA, Fomichev KA, Barkova OI, Romanov MN, Sazanov AA. [Investigation of pseudoautosomal and bordering regions in avian Z and W chromosomes with the use of large insert genomic BAC clones]. Genetika 2011; 47:312-319. [PMID: 21542301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
To study pseudoautosomal and bordering regions in the avian Z and W chromosomes, we used seven BAC clones from genomic libraries as DNA probes of fragments of different gametologs of the ATP5A1 gene located close to the proximal border of the pseudoautosomal region (PAR) of sex chromosomes of domestic chicken and Japanese quail. Localization of BAC clones TAM31-b100C09, TAM31-b99N01, TAM31-b27P16, and TAM31-b95L18 in the short arm of Z chromosomes of domestic chicken and Japanese quail (region Zp23-p22) and localization of the BAC clones CHORI-261-CH46G16, CHORI-261-CH33F10, and CHORI-261-CH64F22 on W chromosomes of these species and in the short arm of Z chromosomes (region Zp23-p22) were determined by fluorescence in situ hybridization with the use of W-specific probes. The difference in the localization of the BAC clones on the Z and W chromosomes is probably explained by divergence of the nucleotide sequences of different sex chromosomes located beyond the pseudoautosomal region.
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MohammadabadiM R, Nikbakhti M, Mirzaee HR, Shandi MA, Saghi DA, Romanov MN, Moiseyeva IG. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Genetika 2010; 46:572-576. [PMID: 20536031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This paper represents the results of a study on the genetic diversity in three native chicken populations (Barred, Brown and Black) of Khorasan, a province in northeastern Iran, by using four microsatellite markers (MCW0005, MCW0016, MCW0018 and MCW0034). Average number of alleles was found to be 5.25 per locus across all populations. The examined populations were characterized by a high level of genetic variability as assessed by computing the expected and observed heterozygosities, and polymorphism information content. The authors consider the results of this investigation as an accumulation of data in a research program concerning genetic characteristics of the native chicken populations of Iran that have not been surveyed yet.
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Affiliation(s)
- R MohammadabadiM
- Department of Animal Sciences, Shahid Bahonar University of Kerman, Kerman, 7616914111 Iran.
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47
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Romanov MN, Tuttle EM, Houck ML, Modi WS, Chemnick LG, Korody ML, Mork EMS, Otten CA, Renner T, Jones KC, Dandekar S, Papp JC, Da Y, Green ED, Magrini V, Hickenbotham MT, Glasscock J, McGrath S, Mardis ER, Ryder OA. The value of avian genomics to the conservation of wildlife. BMC Genomics 2009; 10 Suppl 2:S10. [PMID: 19607652 PMCID: PMC2966331 DOI: 10.1186/1471-2164-10-s2-s10] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution. Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care). In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes. Results Genotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology. Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2m and 3a are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2m existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2m form, originally thought to be the derived condition, might actually be the ancestral one. Conclusion Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease. In the white-throated sparrow, genomic studies, combined with ecological data, will help elucidate the basis of genic selection in a natural population. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate yet linked evolutionary trajectories. Such results can transform our understanding of evolutionary and conservation biology.
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Affiliation(s)
- Michael N Romanov
- Genetics Division, San Diego Zoo's Institute for Conservation Research, Zoological Society of San Diego, Arnold and Mabel Beckman Center for Conservation Research, 15600 San Pasqual Valley Rd., Escondido, CA 92027, USA.
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Dehghanzadeh H, Mirhoseini SZ, Romanov MN, Ghorbani A. Evaluation of genetic variability and distances among five Iranian native chicken populations using RAPD markers. Pak J Biol Sci 2009; 12:866-71. [PMID: 19803121 DOI: 10.3923/pjbs.2009.866.871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Genetic variability was studied on five Iranian native chicken populations using Random Amplified Polymorphism DNA (RAPD) markers. The purpose of this study was for the analysis of variation within and between Iranian native chicken populations and for the reconstruction of a phylogenetic tree for these populations using the RAPD marker assay. The populations surveyed were from five provinces including Mazandaran (MZD), Isfahan (ISF), Yazd (YZD), Fars (FRS) and West Azerbaijan (WAZ). On the base of results of this study, the FRS and MZD populations had the highest genetic distance (0.182) and the FRS and ISF populations the lowest one (0.066). The YZD and MZD populations had the highest (0.208) and lowest (0.156) within-population genetic diversity. The phylogenetic tree was reconstructed on UPGMA method and showed two main separated groups. The ISF and FRS populations were first clustered into one group and, then, were clustered into a larger group with YZD and WAZ. Another consists MZD population was clustered separately from this group. This study showed that RAPD technique is an useful tool for evaluation of genetic variation among domesticated animals.
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Affiliation(s)
- H Dehghanzadeh
- Agricultural and Natural Resources Research Center of Guilan, Department of Animal Science, Ministry of Jihad-e-Agriculture, Iran
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Abstract
Iranian chicken genetic resources are characterized by a long history and a vast diversity. This study represents the first results from the selection and evaluation of five polymorphic microsatellite markers for the genetic assessment of five native chicken populations located in the northwestern (West Azerbaijan), northern (Mazandaran), central (Isfahan, Yazd), and southern (Fars) provinces of Iran. The number of alleles ranged from three to six per microsatellite locus. All populations were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the Isfahan population (62%) and the greatest in the populations from West Azerbaijan and Mazandaran (79%). The largest Nei's unbiased genetic distance was found between the Isfahan and Fars populations (0.696) and the smallest between the Mazandaran and Yazd populations (0.097). The Isfahan population was found to be the most genetically distant among all populations studied. These results serve as an initial step in the plan for genetic characterization and conservation of Iranian native chickens.
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Affiliation(s)
- Saleh Shahbazi
- Education Division, Iranian Academic Centre for Education, Culture and Research, PO Box 56135-696, Ardabil, Iran
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Soller M, Weigend S, Romanov MN, Dekkers JCM, Lamont SJ. Strategies to Assess Structural Variation in the Chicken Genome and its Associations with Biodiversity and Biological Performance. Poult Sci 2006; 85:2061-78. [PMID: 17135660 DOI: 10.1093/ps/85.12.2061] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A primary goal in the assessment of structural variation in the avian genome is to understand the relationship of this variation with biodiversity and with biological performance. To develop such knowledge, certain essential tools are needed. One set of tools includes the laboratory techniques used to assess molecular genetic variation. The current time is a transitional one for this field, in that the recently sequenced chicken genome will add significantly to the portfolio of existing methods used to identify molecular markers. To most efficiently discover marker-trait associations, the experimental mapping populations must be appropriately designed and the relevant statistical analyses applied. This paper reviews methods for assessment of molecular markers in poultry and their use in the characterization of avian biodiversity and in studies to identify marker associations with biological traits, including important considerations of population structure and statistical analysis.
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Affiliation(s)
- M Soller
- Hebrew University of Jerusalem, 91904, Israel
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