1
|
Yang J, Jin S, Zhang S, He S, Chen R, Lei Y, Pan R, Zhang H, Wang Z, Li Z, Yu H, Dong G, Shi C, Li B, Guo S. Pregnancy diagnosis and sex identification with urinary glycopatterns of two mammal species. iScience 2023; 26:108439. [PMID: 38213790 PMCID: PMC10783609 DOI: 10.1016/j.isci.2023.108439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 01/13/2024] Open
Abstract
Glycome in urine could be promising biomarkers for detecting pregnancy diagnosis and sex noninvasively for animals, especially for rare species. We explore the applicability of grouping golden snub-nosed monkeys by sex or diagnosing pregnancy based on their urinary glycopatterns, which are determined via lectin microarray combining mass spectrometry analysis. Sprague-Dawley rats are used to verify whether this approach and whether the glycomic biomarkers can be generalized to other mammalian species. The results show that, for both species, lectin microarray combining mass spectrometry can distinguish individuals' pregnancy status and sex; significant differences are found in the types, amounts, and terminal modification of glycans between pregnant and non-pregnant females and between females and males. This indicates the approach could be generalized to other mammalian species to group sex and detect pregnancy, yet the glycopatterns appear to be species-specific and markers developed from one species may not be directly applicable to another.
Collapse
Affiliation(s)
- Jiayi Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Shiyu Jin
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Simeng Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Shujun He
- Shaanxi Institute of Zoology, Xi’an 710032, China
| | - Rui Chen
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Yinghu Lei
- Qinling Giant Panda Research Center (Shaanxi rare wildlife rescue base), Shaanxi Academy of Forestry, Xi’an 710402, China
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
- School of Human Sciences, The University of Western Australia, Australia and Centre for Evolutionary Biology, College of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - He Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Zhongfu Wang
- College of Food Science and Technology, Northwest University, Xi’an 710069, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Guixin Dong
- Guangdong South China Rare Wild Animal Species Conservation Center, Zhuhai 511430, China
| | - Changhong Shi
- Laboratory Animal Center, The Air Force Medical University, Xi’an 710032, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| |
Collapse
|
2
|
Aucamp J, van der Zwan H, Geldenhuys Z, Abera A, Louw R, van der Sluis R. Diagnostic applications and limitations for the use of cell-free fetal DNA (cffDNA) in animal husbandry and wildlife management. Res Vet Sci 2023; 158:106-116. [PMID: 36989830 DOI: 10.1016/j.rvsc.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/02/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
In animal breeding, a species sex can influence the value of the animal. For example, in the horse breeding industry, mares are preferred as polo horses, while in wildlife breeding males with larger horns are more valuable. Therefore, the economic advantages of knowing the unborn fetus' sex are important to successful animal management. Ultrasonography is used to determine the sex of unborn fetuses, but this method places additional stress on the animal and require specialized equipment and expertise. Conversely, molecular-based sexing techniques require less invasive sampling and can determine sex more reliably. Although in humans, various studies have evaluated the use of cell-free fetal DNA (cffDNA) for prenatal sexing, very few animal studies have been published in this field. Several factors can affect the sensitivity of cffDNA-based sex determination, for example the gestational age. These factors are often not optimized and validated when establishing a protocol for prenatal sexing. In this review, we summarize the current literature on cffDNA in animals. We discuss the diagnostic applications and limitations in the use thereof in animal husbandry and wildlife management. Lastly, the feasibility of implementing diagnostic tests is evaluated and solutions are given to the current drawbacks of the technology.
Collapse
|
3
|
Cabrera AA, Rey-Iglesia A, Louis M, Skovrind M, Westbury MV, Lorenzen ED. How low can you go? Introducing SeXY: sex identification from low-quantity sequencing data despite lacking assembled sex chromosomes. Ecol Evol 2022; 12:e9185. [PMID: 36035270 PMCID: PMC9405501 DOI: 10.1002/ece3.9185] [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: 05/11/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex‐identification pipeline, for very low‐coverage shotgun sequencing data from a single individual. SeXY was designed to utilize low‐effort screening data for sex identification and does not require a conspecific sex‐chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1000 mapped reads and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high‐quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1000 mapped reads. For lower‐quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1000 mapped reads in many cases.
Collapse
Affiliation(s)
| | | | - Marie Louis
- Globe Institute University of Copenhagen Copenhagen K Denmark.,Greenland Institute of Natural Resources Nuuk Greenland
| | - Mikkel Skovrind
- Globe Institute University of Copenhagen Copenhagen K Denmark
| | | | | |
Collapse
|
4
|
Zenke P, Zorkóczy OK, Lehotzky P, Ózsvári L, Pádár Z. Molecular Sexing and Species Detection of Antlered European Hunting Game for Forensic Purposes. Animals (Basel) 2022; 12:ani12030246. [PMID: 35158570 PMCID: PMC8833381 DOI: 10.3390/ani12030246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The reasons behind illegal hunting can be widely different. There are also tricky methods that hunters use in the attempt to legalize their illegally-acquired trophies, specifically, introducing them in later seasons, and registering the eviscerated corpses as hinds. During certain periods of the year, hunters are only able to acquire a license for the shooting of female deer exclusively, with the male-hunting season beginning later. The eviscerated and decapitated carcass of the animal delivered to the wild game processing house cold store can be falsely registered as a female based on phenotype. If the hunting association suspects that the animal’s sex has been falsely reported, a forensic genetic investigation can be proposed. In other criminal events, there are no carcasses at all. When several biological remains left on the crime scene need to be tested, a fast and cost-effective detection of a given species or species-group might be substantial before subsequent analysis. Therefore, sex and species detection can provide an early-stage credibility to the resolution of illegal activities related to trophy animals, and additionally may disclose potential poaching disputes. Abstract Molecular sexing techniques are widely applied in conservation biology, although the range of forensically validated methods is fairly limited. The primary aim of this work was to develop forensically validated assays, using two PCR panels for sex and species assignment for the abundant antlered European game species: red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama). Segments of the SRY and Amelogenin X/Y genes for sex determination, additionally species-specific cytochrome b regions for species detection were targeted and separately amplified in two multiplex reactions. These assays can reliably analyze trace amounts of DNA. The results of both can easily be visualized and interpreted practically, either on agarose gel or by capillary electrophoresis. These simple, fast molecular assays are able to affect the early-stage resolution of disputed or unsolved poaching cases, without the need of individualization or sequencing of forensic samples.
Collapse
Affiliation(s)
- Petra Zenke
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, István u. 2., H-1078 Budapest, Hungary;
- Correspondence:
| | - Orsolya Krisztina Zorkóczy
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, István u. 2., H-1078 Budapest, Hungary;
| | - Pál Lehotzky
- Hungarian Hunters’ National Chamber, Medve u. 34-40., H-1027 Budapest, Hungary;
| | - László Ózsvári
- Department of Veterinary Forensics and Economics, University of Veterinary Medicine Budapest, István u. 2., H-1078 Budapest, Hungary;
| | - Zsolt Pádár
- Department of Forensic Medicine, Medical School, University of Pécs, Szigeti út 12., H-7624 Pecs, Hungary;
| |
Collapse
|
5
|
Sex assignment in a non-model organism in the absence of field records using Diversity Arrays Technology (DArT) data. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01203-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
6
|
Liu X, Zhu Y, Wang Y, Li W, Hong X, Zhu X, Xu H. Comparative transcriptome analysis reveals the sexual dimorphic expression profiles of mRNAs and non-coding RNAs in the Asian yellow pond turtle (Meauremys mutica). Gene 2020; 750:144756. [DOI: 10.1016/j.gene.2020.144756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
|
7
|
Lucas CG, Spate AM, Samuel MS, Spate LD, Warren WC, Prather RS, Wells KD. A novel swine sex-linked marker and its application across different mammalian species. Transgenic Res 2020; 29:395-407. [PMID: 32607872 DOI: 10.1007/s11248-020-00204-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 01/25/2023]
Abstract
Advances in genome editing tools have reduced barriers to the creation of animal models. Due to their anatomical and physiological similarities to humans, there has been a growing need for pig models to study human diseases, for xenotransplantation and translational research. The ability to determine the sex of genetically modified embryos, cells or fetuses is beneficial for every project involving the production of transgenic animals. This strategy can improve the time-efficiency and lower the production costs. Additionally, sex assessment is very useful for wildlife studies to understand population behavior and structure. Thus, we developed a simple and fast PCR-based protocol for sex determination in pigs by using a unique primer set to amplify either the DDX3X or DDX3Y gene. The sex was 100% correctly assigned when tail genomic DNA, Day-35 fetus and hair samples from pigs were used. For both blastocysts and oocytes (84.6% and 96.5% of efficacy, respectively) the unidentified samples were potentially due to a limitation in sample size. Our assay also worked for domestic sheep (Ovis aries), American bison (Bison bison) and European cattle (Bos taurus) samples and by in silico analysis we confirmed X-Y amplicon length polymorphisms for the DDX3 gene in 12 other mammalian species. This PCR protocol for determining sex in pig tissues and cells showed to be simple, specific, highly reproducible and less time consuming as well as an important tool for other livestock species and wildlife studies.
Collapse
Affiliation(s)
- C G Lucas
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - A M Spate
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - M S Samuel
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - L D Spate
- Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - W C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - R S Prather
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.,Division of Animal Science, University of Missouri, Columbia, MO, USA
| | - K D Wells
- National Swine Resource and Research Center, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA. .,Division of Animal Science, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
8
|
Donaldson ME, Jackson K, Rico Y, Sayers JB, Ethier DM, Kyle CJ. Development of a massively parallel, genotyping-by-sequencing assay in American badger (Taxidea taxus) highlights the need for careful validation when working with low template DNA. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01146-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
9
|
Dash HR, Rawat N, Das S. Alternatives to amelogenin markers for sex determination in humans and their forensic relevance. Mol Biol Rep 2020; 47:2347-2360. [DOI: 10.1007/s11033-020-05268-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
|
10
|
Vincze B, Gáspárdy A, Biácsi A, Papp EÁ, Garamvölgyi L, Sós E, Cseh S, Kovács G, Pádár Z, Zenke P. Sex determination using circulating cell-free fetal DNA in small volume of maternal plasma in elephants. Sci Rep 2019; 9:15254. [PMID: 31649290 PMCID: PMC6813297 DOI: 10.1038/s41598-019-51641-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/04/2019] [Indexed: 11/09/2022] Open
Abstract
The genetic sexing of animals having long gestation periods offers significant benefits in regard to breeding management among their populations living in captivity. In our study, a new increased-sensitivity PCR method for fetal sexing was developed and tested successfully on elephants, from only a small volume of maternal plasma. Suitable sensitivity was obtained by using short, reduced amplicon lengths with fluorescent labelling for capillary electrophoresis detection. The fundamental principle for this technique was based on the detection of two Y-specific markers (AmelY and SRY), the presence of which indicates the mother is carrying a male fetus and the absence of these markers designates a female fetus. As a reaction control, the X-chromosomal marker (PlpX) was used. To the best of our knowledge, this is the first report on this topic, confirming the presence of fetal cell-free DNA from the plasma of a pregnant captive elephant, and demonstrating a new opportunity for non-invasive assessment in fetal sex determination.
Collapse
Affiliation(s)
- Boglárka Vincze
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary.
| | - András Gáspárdy
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary
| | | | - Endre Ákos Papp
- Sóstó Zoo, Sóstófürdő, 4431, Sóstói út, Nyíregyháza, Hungary
| | | | - Endre Sós
- Budapest Zoo and Botanic Garden, 1146 Állatkerti krt. 6-12., Budapest, Hungary
| | - Sándor Cseh
- Department of Reproduction and Obstetrics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary
| | - Gábor Kovács
- Research Centre for Forensic Sciences and Criminology, University Széchenyi István, Győr, 9026, Egyetem tér 1., Győr, Hungary
| | - Zsolt Pádár
- Research Centre for Forensic Sciences and Criminology, University Széchenyi István, Győr, 9026, Egyetem tér 1., Győr, Hungary.,Department of Forensic Medicine, Medical School, University of Pécs, 7624, Szigeti út 12., Pécs, Hungary
| | - Petra Zenke
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, 1078, István utca 2., Budapest, Hungary.
| |
Collapse
|
11
|
Strah R, Kunej T. Molecular sexing assays in 114 mammalian species: In silico sequence reanalysis and a unified graphical visualization of diagnostic tests. Ecol Evol 2019; 9:5018-5028. [PMID: 31031962 PMCID: PMC6476764 DOI: 10.1002/ece3.5093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/29/2019] [Accepted: 03/05/2019] [Indexed: 11/11/2022] Open
Abstract
Molecular-based methods for identifying sex in mammals have a wide range of applications, from embryo manipulation to ecological studies. Various sex-specific or homologous genes can be used for this purpose, PCR amplification being a common method. Over the years, the number of reported tests and the range of tested species have increased greatly. The aim of the present analysis was to retrieve PCR-based sexing assays for a range of mammalian species, gathering the gene sequences from either the articles or online databases, and visualize the molecular design in a uniform manner. For nucleotide alignment and diagnostic test visualization, the following genomic databases and tools were used: NCBI, Ensembl Nucleotide BLAST, ClustalW2, and NEBcutter V2.0. In the 45 gathered articles, 59 different diagnostic tests based on eight different PCR-based methods were developed for 114 mammalian species. Most commonly used genes for the analysis were ZFX, ZFY, AMELX, and AMELY. The tests were most commonly based on sex-specific insertions and deletions (SSIndels) and sex-specific sequence polymorphisms (SSSP). This review provides an overview of PCR-based sexing methods developed for mammals. This information will facilitate more efficient development of novel molecular sexing assays and reuse of previously developed tests. Development of many novel and improvement of previously developed tests is also expected with the rapid increase in the quantity and quality of available genetic information.
Collapse
Affiliation(s)
- Rebeka Strah
- Biotechnical Faculty, Department of Animal ScienceUniversity of LjubljanaDomzaleSlovenia
| | - Tanja Kunej
- Biotechnical Faculty, Department of Animal ScienceUniversity of LjubljanaDomzaleSlovenia
| |
Collapse
|
12
|
Horecka B. Usefulness of a Modified System of Molecular Sex Identification inMustelidaeIncluding Museum Specimens. ANN ZOOL FENN 2018. [DOI: 10.5735/086.055.0602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Beata Horecka
- Institute of Biological Bases of Animal Production, Department of General and Molecular Genetics, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, PL-20-950 Lublin, Poland
| |
Collapse
|
13
|
Hrovatin K, Kunej T. Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization. Ecol Evol 2018; 8:1009-1018. [PMID: 29375774 PMCID: PMC5773321 DOI: 10.1002/ece3.3707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/27/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023] Open
Abstract
Erstwhile, sex was determined by observation, which is not always feasible. Nowadays, genetic methods are prevailing due to their accuracy, simplicity, low costs, and time-efficiency. However, there is no comprehensive review enabling overview and development of the field. The studies are heterogeneous, lacking a standardized reporting strategy. Therefore, our aim was to collect genetic sexing assays for mammals and assemble them in a catalogue with unified terminology. Publications were extracted from online databases using key words such as sexing and molecular. The collected data were supplemented with species and gene IDs and the type of sex-specific sequence variant (SSSV). We developed a catalogue and graphic presentation of diagnostic tests for molecular sex determination of mammals, based on 58 papers published from 2/1991 to 10/2016. The catalogue consists of five categories: species, genes, SSSVs, methods, and references. Based on the analysis of published literature, we propose minimal requirements for reporting, consisting of: species scientific name and ID, genetic sequence with name and ID, SSSV, methodology, genomic coordinates (e.g., restriction sites, SSSVs), amplification system, and description of detected amplicon and controls. The present study summarizes vast knowledge that has up to now been scattered across databases, representing the first step toward standardization regarding molecular sexing, enabling a better overview of existing tests and facilitating planned designs of novel tests. The project is ongoing; collecting additional publications, optimizing field development, and standardizing data presentation are needed.
Collapse
Affiliation(s)
- Karin Hrovatin
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaDomzaleSlovenia
| | - Tanja Kunej
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaDomzaleSlovenia
| |
Collapse
|