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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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Dementieva NV, Shcherbakov YS, Ryabova AE, Vakhrameev AB, Makarova AV, Nikolaeva OA, Dysin AP, Azovtseva AI, Reinbah NR, Mitrofanova OV. Comparative peculiarities of genomic diversity in Gallus gallus domesticus chickens with decorative plumage: the muffs and beard phenotype. Vavilovskii Zhurnal Genet Selektsii 2024; 28:108-116. [PMID: 38465249 PMCID: PMC10917671 DOI: 10.18699/vjgb-24-13] [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: 03/28/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 03/12/2024] Open
Abstract
Throughout history, humans have been attempting to develop the ornamental features of domestic animals in addition to their productive qualities. Many chicken breeds have developed tufts of elongated feathers that jut out from the sides and bottom of the beak, leading to the phenotype known as muffs and beard. It is an incomplete autosomal dominant phenotype determined by the Mb locus localised on chromosome GGA27. This project aimed to analyse the genetic diversity of chicken breeds using full genomic genotyping with the Chicken 60K BeadChip. A total of 53,313 Single Nucleotide Polymorphisms were analysed. DNA was obtained from breeds with the muffs and beard as a marker phenotype: Faverolles (n = 20), Ukrainian Muffed (n = 18), Orloff (n = 20), Novopavlov White (n = 20), and Novopavlov Coloured (n = 15). The Russian White (n = 20) was selected as an alternative breed without the muffs and beard phenotype. The chickens are owned by the Centre of Collective Use "Genetic Collection of Rare and Endangered Breeds of Chickens" (St. Petersburg region, Pushkin), and are also included in the Core Shared Research Facility (CSRF) and/or Large-Scale Research Facility (LSRF). Multidimensional scaling revealed that the Novopavlov White and the Novopavlov Coloured populations formed a separate group. The Ukrainian Muffed and the Orloff have also been combined into a separate group. Based on cluster analysis, with the cross-validation error and the most probable number of clusters K = 4 taken into account, the Orloff was singled out as a separate group. The Ukrainian Muffed exhibited a notable similarity with the Orloff under the same conditions. At K = 5, the populations of the Novopavlov White and the Novopavlov Coloured diverged. Only at K = 6, a distinct and separate cluster was formed by the Ukrainian Muffed. The Russian White had the greatest number of short (1-2 Mb) homozygous regions. If the HOXB8 gene is located between 3.402 and 3.404 Mb on chromosome GGA27, homozygous regions are rarely found in the chickens with the muffs and beard phenotype. Scanning the chicken genome with the Chicken 60K BeadChip provided enough information about the genetic diversity of the chicken breeds for the peculiarities of the development of the ornamental muffs and beard phenotypes in them to be understood. For example, Phoenix bantams, whose tail feathers grow throughout their lives, require greater consideration of husbandry conditions.
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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 Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - Y S Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A E Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A V Makarova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - O A Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A I Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - N R Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - O V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
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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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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [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] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- 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
- Correspondence:
| | - Yuri S. Shcherbakov
- 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
| | - Olga A. Nikolaeva
- 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
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- 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
| | - Natalia V. Dementieva
- 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
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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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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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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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