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Macedo Rafael de Arruda J, da Silva Mendonça M, Maravilha Braga PV, Dos Santos Nascimento L, Burla Dias AJ, Lopes Rios ÁF, Magnelli Mangiavacchi P. Optimizing single-tube nested PCR for enhanced genotyping of single cells and in vitro produced bovine embryos. Gene 2024; 929:148838. [PMID: 39127412 DOI: 10.1016/j.gene.2024.148838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]
Abstract
Single-tube nested PCR (STnPCR) is a technique that improves nested PCR, reducing potential contamination and false-positive results, enhancing the amplification sensitivity. Despite being commonly used for the detection of microorganisms, STnPCR can be a valuable tool for bovine genotyping, encompassing essential targets as ROSA26 and TSPY, pivotal in the fields of animal reproduction, genetic improvement, and transgenic research. The objective of this study was to improve and innovate STnPCR for gene detection in cattle. We aimed to detect the ROSA26 and TSPY genes using low-concentration DNA samples, including single cells, small cell groups (one to five cells), in vitro-produced embryos, and bovine tissue samples. Moreover, we refined STnPCR for gene detection in up to single cells by conducting sensitivity testing with different concentration ratios of internal and external primers. Successful amplification of the ROSA26 and TSPY genes was achieved across all tested primer concentrations, even in single cells, with more consistent results observed at lower primer concentrations. Additionally, simultaneous gene amplification was achieved through STnPCR multiplexing, representing the first study of multiplex STnPCR in cattle. These outcomes not only confirm its effectiveness in detecting genetic markers for animal genetic improvement and transgenic elements but also pave the way for its widespread adoption in reproductive studies in bovines.
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Affiliation(s)
- Jéssica Macedo Rafael de Arruda
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Mariana da Silva Mendonça
- Laboratório da Biologia do Reconhecer, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Paulo Vitor Maravilha Braga
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Leticia Dos Santos Nascimento
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Angelo José Burla Dias
- Laboratório de Reprodução e Melhoramento Genético Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Álvaro Fabrício Lopes Rios
- Laboratório de Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Paula Magnelli Mangiavacchi
- Laboratório de Reprodução e Melhoramento Genético Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602 Campos dos Goytacazes, RJ, Brazil.
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Rho NY, Mogas T, King WA, Favetta LA. Testis-Specific Protein Y-Encoded (TSPY) Is Required for Male Early Embryo Development in Bos taurus. Int J Mol Sci 2023; 24:ijms24043349. [PMID: 36834761 PMCID: PMC9959854 DOI: 10.3390/ijms24043349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/27/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023] Open
Abstract
TSPY is a highly conserved multi-copy gene with copy number variation (CNV) among species, populations, individuals and within families. TSPY has been shown to be involved in male development and fertility. However, information on TSPY in embryonic preimplantation stages is lacking. This study aims to determine whether TSPY CNV plays a role in male early development. Using sex-sorted semen from three different bulls, male embryo groups referred to as 1Y, 2Y and 3Y, were produced by in vitro fertilization (IVF). Developmental competency was assessed by cleavage and blastocyst rates. Embryos at different developmental stages were analyzed for TSPY CN, mRNA and protein levels. Furthermore, TSPY RNA knockdown was performed and embryos were assessed as per above. Development competency was only significantly different at the blastocyst stage, with 3Y being the highest. TSPY CNV and transcripts were detected in the range of 20-75 CN for 1Y, 20-65 CN for 2Y and 20-150 CN for 3Y, with corresponding averages of 30.2 ± 2.5, 33.0 ± 2.4 and 82.3 ± 3.6 copies, respectively. TSPY transcripts exhibited an inverse logarithmic pattern, with 3Y showing significantly higher TSPY. TSPY proteins, detected only in blastocysts, were not significantly different among groups. TSPY knockdown resulted in a significant TSPY depletion (p < 0.05), with no development observed after the eight-cell stage in male embryos, suggesting that TSPY is required for male embryo development.
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Affiliation(s)
- Na-Young Rho
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Teresa Mogas
- Department of Medicine and Animal Surgery, Autonomous University of Barcelona, Cerdanyola del Vallés, 08193 Barcelona, Spain
| | - W. Allan King
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Karyotekk Inc., Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Laura A. Favetta
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
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Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (BETHESDA, MD.) 2022; 12:jkac278. [PMID: 36227030 PMCID: PMC9713435 DOI: 10.1093/g3journal/jkac278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2023]
Abstract
Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.
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Affiliation(s)
- Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Lara Radović
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Sabine Felkel
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources, Vienna 1190, Austria
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Ernest Gus Cothran
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
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Abstract
Mosaic loss of the Y chromosome (LOY) is the most frequent chromosomal aberration in aging men and is strongly correlated with mortality and disease. To date, studies of LOY have only been performed in humans, and so it is unclear whether LOY is a natural consequence of our relatively long lifespan or due to exposure to human-specific external stressors. Here, we explored whether LOY could be detected in rats. We applied a locus-specific PCR and target sequencing approach that we used as a proxy to estimate LOY in 339 samples covering eleven tissues from young and old individuals. We detected LOY in four tissues of older rats. To confirm the results from the PCR screening, we re-sequenced 60 full genomes from old rats, which revealed that the Y chromosome is the sole chromosome with low copy numbers. Finally, our results suggest that LOY is associated with other structural aberrations on the Y chromosome and possibly linked to the mosaic loss of the X chromosome. This is the first report, to our knowledge, demonstrating that the patterns of LOY observed in aging men are also present in a rodent, and conclude that LOY may be a natural process in placental mammals.
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Pei SW, Qin F, Li WH, Li FD, Yue XP. Copy number variation of ZNF280AY across 21 cattle breeds and its association with the reproductive traits of Holstein and Simmental bulls. J Dairy Sci 2019; 102:7226-7236. [PMID: 31202648 DOI: 10.3168/jds.2018-16063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/23/2019] [Indexed: 11/19/2022]
Abstract
The mammalian Y chromosome gene families in the ampliconic region are expressed predominantly or exclusively in the testis, and their copy number variations (CNV) are significantly associated with male reproductive traits, suggesting they have important roles in spermatogenesis and testicular development. ZNF280AY (zinc finger protein 280A, Y-linked) is a member of the zinc finger protein family and has been identified as a bovid-specific Y-chromosome gene. The current study applied a reliable quantitative real-time PCR method to estimate the CNV of ZNF280AY in 715 bulls across 21 cattle breeds and to further investigate the association of the CNV of ZNF280AY with bull reproductive traits and ZNF280AY mRNA expression levels in adult testis. The results revealed that the median copy number of ZNF280AY was 47, and the copy number varied from 11 to 154, showing significant CNV between and within the investigated cattle breeds. In addition, all 715 bulls were classified into Y1, Y2, and Y3 lineage groups based on a rapid genotyping method described previously. Pairwise comparisons indicated that bulls belonging to the Y1 lineage had a significantly lower median copy number (40) than bulls belonging to the Y2 (52) and Y3 lineages (57). Association analysis revealed that the CNV of ZNF280AY was correlated negatively with the percentage of normal sperm and sperm concentration in Holstein bulls, whereas no significant correlation was observed with ejaculation volume, total sperm count, sperm motility, postthaw motility (PTM), and scrotal circumference in Holstein and Simmental bulls. Furthermore, no correlation was observed between ZNF280AY copy number and ZNF280AY mRNA expression levels in the testis. The current study suggests that the CNV of the ZNF280AY gene family is associated with male reproductive traits and may serve as a valuable marker for early bull fertility selection in Holstein breeding programs.
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Affiliation(s)
- S W Pei
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - F Qin
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, P. R. China
| | - W H Li
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - F D Li
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China; Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, P. R. China
| | - X P Yue
- State Key Laboratory of Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China.
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6
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Stojsin-Carter A, Costa NN, De Morais R, De Bem TH, Costa MP, Carter TF, Gillis DJ, Neal MS, Ohashi OM, Miranda MS, Meirelles FV, Favetta LA, King WA. Fetal sex alters maternal anti-Mullerian hormone during pregnancy in cattle. Anim Reprod Sci 2017; 186:85-92. [PMID: 28969874 DOI: 10.1016/j.anireprosci.2017.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/18/2017] [Accepted: 09/21/2017] [Indexed: 01/17/2023]
Abstract
Anti-Mullerian hormone (AMH) is expressed by both male and female fetuses during mammalian development, with males expressing AMH earlier and at significantly higher concentration. The aim of the current study was to explore the potential impact of pregnancy and fetal sex on maternal AMH and to determine if plasma (Pl) AMH or placenta intercotyledonary membrane and cotyledonary AMH receptor 2 (AMHR2) mRNA expression differ in pregnant cows carrying male vs. female fetuses. AMH levels in blood were measured using a bovine optimized ELISA kit. Cows pregnant with a male fetus were observed to have a significantly greater difference in Pl AMH between day 35 and 135 of gestation. Average fetal AMH level between 54 and 220days of gestation was also observed to be significantly higher in male vs. female fetuses. Intercotyledonary membranes and cotyledons were found to express AMHR2 between days 38 and 80 of gestation at similar levels in both fetal sexes. These findings support the hypothesis that fetal sex alters maternal Pl AMH during pregnancy in cattle.
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Affiliation(s)
- Anja Stojsin-Carter
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road, Guelph, ON, N1G 2W1, Canada
| | - Nathalia N Costa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa 1, Belém, PA, 66075-110, Brazil
| | - Rodrigo De Morais
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa 1, Belém, PA, 66075-110, Brazil
| | - Tiago H De Bem
- Departamento de Medicina Veterinaria, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de Sao Paulo, Avenida Duque Caxias Norte 225 - Jardim Elite, Pirassununga, SP, 13635-000, Brazil
| | - Mayra P Costa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa 1, Belém, PA, 66075-110, Brazil
| | - Timothy F Carter
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road, Guelph, ON, N1G 2W1, Canada
| | - Daniel J Gillis
- School of Computer Science, University of Guelph, 50 Stone Road, Guelph, ON, N1G 2W1, Canada
| | - Michael S Neal
- ONE Fertility, 3210 Harvester Rd, Burlington, ON, L7N 3T1, Canada
| | - Otavio M Ohashi
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa 1, Belém, PA, 66075-110, Brazil
| | - Moyses S Miranda
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa 1, Belém, PA, 66075-110, Brazil
| | - Flavio V Meirelles
- Departamento de Medicina Veterinaria, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de Sao Paulo, Avenida Duque Caxias Norte 225 - Jardim Elite, Pirassununga, SP, 13635-000, Brazil
| | - Laura A Favetta
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road, Guelph, ON, N1G 2W1, Canada
| | - W Allan King
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, 50 Stone Road, Guelph, ON, N1G 2W1, Canada.
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