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Romanets E, Bakoev S, Romanets T, Kolosova M, Kolosov A, Bakoev F, Tretiakova O, Usatov A, Getmantseva L. Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs. Anim Biosci 2024; 37:832-838. [PMID: 38271973 PMCID: PMC11065708 DOI: 10.5713/ab.23.0297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The use of molecular genetic methods in pig breeding can significantly increase the efficiency of breeding and breeding work. We applied the Fst (fixsacion index) method, the main focus of the work was on the search for common options related to the number of born piglets and the weight of born piglets, since today the urgent task is to prevent a decrease in the weight of piglets at birth while maintaining high fertility of sows. METHODS One approach is to scan the genome, followed by an assessment of Fst and identification of selectively selected regions. We chose Large White sows (n = 237) with the same conditions of keeping and feeding. The data were collected from the sows across three farrowing. For genotyping, we used GeneSeek GGP Porcine HD Genomic Profiler v1, which included 68,516 single nucleotide polymorphisms evenly distributed with an average spacing of 25 kb (Illumina Inc, San Diego, CA, USA). RESULTS Based on the results of the Fst analysis, 724 variants representing selection signals for the signs BALWT, BALWT1, NBA, and TNB (weight of piglets born alive, average weight of the 1st piglets born alive, total number born alive, total number born). At the same time, 18 common variants have been identified that are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive characteristics in sows. CONCLUSION Оur work resulted in identification of variants associated with the reproductive characteristics of pigs. Moreover, we identified, variants which are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive performance in sows.
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Affiliation(s)
- Elena Romanets
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Siroj Bakoev
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
- Academy of Biology and Biotechnology named after. DI. Ivanovsky, Southern Federal University, 344090, Rostov region, Rostov-on-Don,
Russia
| | - Timofey Romanets
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Maria Kolosova
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Anatoly Kolosov
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Faridun Bakoev
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Olga Tretiakova
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Alexander Usatov
- Academy of Biology and Biotechnology named after. DI. Ivanovsky, Southern Federal University, 344090, Rostov region, Rostov-on-Don,
Russia
| | - Lyubov Getmantseva
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
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Jayarajan RO, Chakraborty S, Raghu KG, Purushothaman J, Veleri S. Joubert syndrome causing mutation in C2 domain of CC2D2A affects structural integrity of cilia and cellular signaling molecules. Exp Brain Res 2024; 242:619-637. [PMID: 38231387 DOI: 10.1007/s00221-023-06762-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024]
Abstract
Cilia are organelles extend from cells to sense external signals for tuning intracellular signaling for optimal cellular functioning. They have evolved sensory and motor roles in various cells for tissue organization and homeostasis in development and post-development. More than a thousand genes are required for cilia function. Mutations in them cause multisystem disorders termed ciliopathies. The null mutations in CC2D2A result in Meckel syndrome (MKS), which is embryonic lethal, whereas patients who have missense mutations in the C2 domain of CC2D2A display Joubert syndrome (JBTS). They survive with blindness and mental retardation. How C2 domain defects cause disease conditions is not understood. To answer this question, C2 domain of Cc2d2a (mice gene) was knocked down (KD) in IMCD-3 cells by shRNA. This resulted in defective cilia morphology observed by immunofluorescence analysis. To further probe the cellular signaling alteration in affected cells, gene expression profiling was done by RNAseq and compared with the controls. Bioinformatics analysis revealed that the differentially expressed genes (DEGs) have functions in cilia. Among the 61 cilia DEGs identified, 50 genes were downregulated and 11 genes were upregulated. These cilia genes are involved in cilium assembly, protein trafficking to the cilium, intraflagellar transport (IFT), cellular signaling like polarity patterning, and Hedgehog signaling pathway. This suggests that the C2 domain of CC2D2A plays a critical role in cilia assembly and molecular signaling hosted in cilia for cellular homeostasis. Taken together, the missense mutations in the C2 domain of CC2D2A seen in JBTS might have affected cilia-mediated signaling in neurons of the retina and brain.
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Affiliation(s)
- Roopasree O Jayarajan
- Agro-processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Soura Chakraborty
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Kozhiparambil Gopalan Raghu
- Agro-processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jayamurthy Purushothaman
- Agro-processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shobi Veleri
- Drug Safety Division, National Institute of Nutrition, Indian Council of Medical Research, Department of Health Research, Ministry of Health and Family Welfare, Govt. of India, Hyderabad, 500007, India.
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Wojtczak A. Differentiation Disorders of Chara vulgaris Spermatids following Treatment with Propyzamide. Cells 2023; 12:cells12091268. [PMID: 37174667 PMCID: PMC10177507 DOI: 10.3390/cells12091268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Microtubules are cytoskeletal cell elements that also build flagella and cilia. Moreover, these structures participate in spermatogenesis and form a microtubular manchette during spermiogenesis. The present study aims to assess the influence of propyzamide, a microtubule-disrupting agent, on alga Chara vulgaris spermatids during their differentiation by means of immunofluorescent and electron microscopy methods. Propyzamide blocks the functioning of the β-tubulin microtubule subunit, which results in the creation of a distorted shape of a sperm nucleus at some stages. Present ultrastructural studies confirm these changes. In nuclei, an altered chromatin arrangement and nuclear envelope fragmentation were observed in the research as a result of incorrect nucleus-cytoplasm transport behavior that disturbed the action of proteolytic enzymes and the chromatin remodeling process. In the cytoplasm, large autolytic vacuoles and the dilated endoplasmic reticulum (ER) system, as well as mitochondria, were revealed in the studies. In some spermatids, the arrangement of microtubules present in the manchette was disturbed and the structure was also fragmented. The observations made in the research at present show that, despite some differences in the manchette between Chara and mammals, and probably also in the alga under study, microtubules participate in the intramanchette transport (IMT) process, which is essential during spermatid differentiation. In the present study, the effect of propyzamide on Chara spermiogenesis is also presented for the first time; however, the role of microtubule-associated proteins in this process still needs to be elucidated in the literature.
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Affiliation(s)
- Agnieszka Wojtczak
- Faculty of Biology and Environmental Protection, Department of Cytophysiology, University of Lodz, 141/143 Pomorska, 90-236 Lodz, Poland
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Chen SY, Schenkel FS, Melo ALP, Oliveira HR, Pedrosa VB, Araujo AC, Melka MG, Brito LF. Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. BMC Genomics 2022; 23:331. [PMID: 35484513 PMCID: PMC9052698 DOI: 10.1186/s12864-022-08555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic. Results There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits. Conclusions These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08555-z.
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Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ana L P Melo
- Department of Reproduction and Animal Evaluation, Rural Federal University of Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI, 54022, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA. .,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Summers KM, Bush SJ, Wu C, Hume DA. Generation and network analysis of an RNA-seq transcriptional atlas for the rat. NAR Genom Bioinform 2022; 4:lqac017. [PMID: 35265836 PMCID: PMC8900154 DOI: 10.1093/nargab/lqac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
The laboratory rat is an important model for biomedical research. To generate a comprehensive rat transcriptomic atlas, we curated and downloaded 7700 rat RNA-seq datasets from public repositories, downsampled them to a common depth and quantified expression. Data from 585 rat tissues and cells, averaged from each BioProject, can be visualized and queried at http://biogps.org/ratatlas. Gene co-expression network (GCN) analysis revealed clusters of transcripts that were tissue or cell type restricted and contained transcription factors implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes. Many of these clusters overlap with previous data from analysis of other species, while some (e.g. expressed specifically in immune cells, retina/pineal gland, pituitary and germ cells) are unique to these data. GCN analysis on large subsets of the data related specifically to liver, nervous system, kidney, musculoskeletal system and cardiovascular system enabled deconvolution of cell type-specific signatures. The approach is extensible and the dataset can be used as a point of reference from which to analyse the transcriptomes of cell types and tissues that have not yet been sampled. Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single-cell RNA-seq data.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David A Hume
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
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Teves ME, Roldan ERS. Sperm bauplan and function and underlying processes of sperm formation and selection. Physiol Rev 2022; 102:7-60. [PMID: 33880962 PMCID: PMC8812575 DOI: 10.1152/physrev.00009.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023] Open
Abstract
The spermatozoon is a highly differentiated and polarized cell, with two main structures: the head, containing a haploid nucleus and the acrosomal exocytotic granule, and the flagellum, which generates energy and propels the cell; both structures are connected by the neck. The sperm's main aim is to participate in fertilization, thus activating development. Despite this common bauplan and function, there is an enormous diversity in structure and performance of sperm cells. For example, mammalian spermatozoa may exhibit several head patterns and overall sperm lengths ranging from ∼30 to 350 µm. Mechanisms of transport in the female tract, preparation for fertilization, and recognition of and interaction with the oocyte also show considerable variation. There has been much interest in understanding the origin of this diversity, both in evolutionary terms and in relation to mechanisms underlying sperm differentiation in the testis. Here, relationships between sperm bauplan and function are examined at two levels: first, by analyzing the selective forces that drive changes in sperm structure and physiology to understand the adaptive values of this variation and impact on male reproductive success and second, by examining cellular and molecular mechanisms of sperm formation in the testis that may explain how differentiation can give rise to such a wide array of sperm forms and functions.
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Affiliation(s)
- Maria Eugenia Teves
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Eduardo R S Roldan
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
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Yogo K. Molecular basis of the morphogenesis of sperm head and tail in mice. Reprod Med Biol 2022; 21:e12466. [PMID: 35619659 PMCID: PMC9126569 DOI: 10.1002/rmb2.12466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/26/2022] Open
Abstract
Background The spermatozoon has a complex molecular apparatus necessary for fertilization in its head and flagellum. Recently, numerous genes that are needed to construct the molecular apparatus of spermatozoa have been identified through the analysis of genetically modified mice. Methods Based on the literature information, the molecular basis of the morphogenesis of sperm heads and flagella in mice was summarized. Main findings (Results) The molecular mechanisms of vesicular trafficking and intraflagellar transport in acrosome and flagellum formation were listed. With the development of cryo‐electron tomography and mass spectrometry techniques, the details of the axonemal structure are becoming clearer. The fine structure and the proteins needed to form the central apparatus, outer and inner dynein arms, nexin‐dynein regulatory complex, and radial spokes were described. The important components of the formation of the mitochondrial sheath, fibrous sheath, outer dense fiber, and the annulus were also described. The similarities and differences between sperm flagella and Chlamydomonas flagella/somatic cell cilia were also discussed. Conclusion The molecular mechanism of formation of the sperm head and flagellum has been clarified using the mouse as a model. These studies will help to better understand the diversity of sperm morphology and the causes of male infertility.
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Affiliation(s)
- Keiichiro Yogo
- Department of Applied Life Sciences Faculty of Agriculture Shizuoka University Shizuoka Japan
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Central Apparatus, the Molecular Kickstarter of Ciliary and Flagellar Nanomachines. Int J Mol Sci 2021; 22:ijms22063013. [PMID: 33809498 PMCID: PMC7999657 DOI: 10.3390/ijms22063013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Motile cilia and homologous organelles, the flagella, are an early evolutionarily invention, enabling primitive eukaryotic cells to survive and reproduce. In animals, cilia have undergone functional and structural speciation giving raise to typical motile cilia, motile nodal cilia, and sensory immotile cilia. In contrast to other cilia types, typical motile cilia are able to beat in complex, two-phase movements. Moreover, they contain many additional structures, including central apparatus, composed of two single microtubules connected by a bridge-like structure and assembling numerous complexes called projections. A growing body of evidence supports the important role of the central apparatus in the generation and regulation of the motile cilia movement. Here we review data concerning the central apparatus structure, protein composition, and the significance of its components in ciliary beating regulation.
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