Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

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.

[1]  M. Yamada,et al.  Sex identification of forensic specimens by polymerase chain reaction (PCR): two alternative methods. , 1991, Forensic science international.

[2]  Q. Fu,et al.  Cloning the swamp buffalo SRY gene for embryo sexing with multiplex-nested PCR. , 2007, Theriogenology.

[3]  T. Kunej,et al.  Molecular sexing assays in 114 mammalian species: In silico sequence reanalysis and a unified graphical visualization of diagnostic tests , 2019, Ecology and evolution.

[4]  M. Statham,et al.  Molecular Sex Identification of Five Mustelid Species , 2007 .

[5]  A. Janke,et al.  A sensitive and specific multiplex PCR approach for sex identification of ursine and tremarctine bears suitable for non‐invasive samples , 2013, Molecular ecology resources.

[6]  Judith A. Blake,et al.  Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse , 2016, Nucleic Acids Res..

[7]  S. Totey,et al.  Cloning and sequencing of buffalo male-specific repetitive DNA: sexing of in-vitro developed buffalo embryos using multiplex and nested polymerase chain reaction. , 1999, Theriogenology.

[8]  D. Tainturier,et al.  Early sex determination in the canine foetus by ultrasound and PCR. , 2016, Animal reproduction science.

[9]  M. Steinlechner,et al.  Rare failures in the amelogenin sex test , 2002, International Journal of Legal Medicine.

[10]  C. M. Chen,et al.  Identification of sex-specific polymorphic sequences in the goat amelogenin gene for embryo sexing. , 2011, Journal of animal science.

[11]  T. Kunej,et al.  Transcription factor HIF1A: downstream targets, associated pathways, polymorphic hypoxia response element (HRE) sites, and initiative for standardization of reporting in scientific literature , 2016, Tumor Biology.

[12]  M. Gautier.  Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model‐based classifier , 2014, Molecular ecology resources.

[13]  P. L. M. Lee,et al.  DNA amplification in the field: move over PCR, here comes LAMP , 2017, Molecular ecology resources.

[14]  A. Fernandes,et al.  DNA extraction from filter‐paper spots of vaginal samples collected after sexual violence , 2014, International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics.

[15]  J. Mosse,et al.  Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet , 2013, Molecular ecology resources.

[16]  J. Krause,et al.  A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice , 2016, PloS one.

[17]  W. Parson,et al.  TriXY-Homogeneous genetic sexing of highly degraded forensic samples including hair shafts. , 2016, Forensic science international. Genetics.

[18]  J. Lanyon,et al.  A PCR assay for gender assignment in dugong (Dugong dugon) and West Indian manatee (Trichechus manatus) , 2008, Molecular ecology resources.

[19]  K. Ralls,et al.  A reliable, non-invasive method for sex determination in the endangered San Joaquin kit fox (Vulpes macrotis mutica) and other canids , 2004, Conservation Genetics.

[20]  T. Kunej,et al.  Initiative for standardization of reporting genetics of male infertility , 2017, Systems biology in reproductive medicine.

[21]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2015 , 2014, Nucleic Acids Res..

[22]  B. Kolena,et al.  Sex determination of early medieval individuals through nested PCR using a new primer set in the SRY gene. , 2011, Forensic science international.

[23]  T. Yano.  Sexing of in vitro-fertilized preimplantation mouse embryos by the PCR method , 1993, Japanese Journal of Human Genetics.

[24]  P. Gill,et al.  A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin. , 1993, BioTechniques.

[25]  P. Taberlet,et al.  A system for sex determination from degraded DNA: a useful tool for palaeogenetics and conservation genetics of ursids , 2009, Conservation Genetics.

[26]  Gérald Quatrehomme,et al.  An alternative procedure for extraction of DNA from ancient and weathered bone fragments , 2013, Medicine, science, and the law.

[27]  R. Kumar,et al.  A Duplex PCR Assay for Sex Determination of Cattle Meat by Simultaneous Amplification of SRY, AMELX and AMELY Genes , 2012 .

[28]  Tanja Kunej,et al.  Initiative for standardization of the format of the next-generation sequencing (NGS) results , 2015, Discoveries.

[29]  L. Waits,et al.  A method for estimating population sex ratio for sage‐grouse using noninvasive genetic samples , 2013, Molecular ecology resources.

[30]  T. Kunej,et al.  Minimal Standards for Reporting microRNA:Target Interactions. , 2017, Omics : a journal of integrative biology.

[31]  A. Gutiérrez-Adán,et al.  Ovine-specific Y-chromosome RAPD-SCAR marker for embryo sexing. , 1997, Animal genetics.

[32]  T. Kunej,et al.  Molecular mechanisms of cryptorchidism development: update of the database, disease comorbidity, and initiative for standardization of reporting in scientific literature , 2016, Andrology.

[33]  D. Coltman,et al.  Sexing the Sciuridae: a simple and accurate set of molecular methods to determine sex in tree squirrels, ground squirrels and marmots , 2012, Molecular ecology resources.

[34]  Richard Li,et al.  Genetic Markers for Sex Identification in Forensic DNA Analysis , 2014 .

[35]  J. Pauli,et al.  Accuracy in molecular sexing of martens (Martes americana and Martes caurina) varies among sample types , 2010, Molecular ecology resources.

[36]  U. Frey,et al.  Amelogenin sex determination by pyrosequencing of short PCR products , 2008, International Journal of Legal Medicine.

[37]  P. Cappai,et al.  Sexing of in vitro produced ovine embryos by duplex PCR , 2004, Molecular reproduction and development.

[38]  M. Bertolini,et al.  A fast and simple method for the polymerase chain reaction-based sexing of livestock embryos. , 2016, Genetics and molecular research : GMR.

[39]  L. Caenazzo,et al.  Deletion of amelogenin Y-locus in forensics: literature revision and description of a novel method for sex confirmation. , 2013, Journal of forensic and legal medicine.

[40]  H. Hauffe,et al.  Sexing European rabbits (Oryctolagus cuniculus), European brown hares (Lepus europaeus) and mountain hares (Lepus timidus) with ZFX and ZFY loci , 2008, Molecular ecology resources.

[41]  S. Miyaishi,et al.  A new method for sex determination based on detection of SRY, STS and amelogenin gene regions with simultaneous amplification of their homologous sequences by a multiplex PCR. , 2011, Acta medica Okayama.

[42]  J. Roder,et al.  Simplex PCR assay for sex determination in mice. , 2005, BioTechniques.

[43]  P. Ruff,et al.  Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene. , 2009, Forensic science international. Genetics.

[44]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[45]  W. Parson,et al.  “GenderPlex” a PCR multiplex for reliable gender determination of degraded human DNA samples and complex gender constellations , 2009, International Journal of Legal Medicine.

[46]  T. Notomi,et al.  Rapid sexing of water buffalo (Bubalus bubalis) embryos using loop-mediated isothermal amplification. , 2006, Theriogenology.

[47]  K. Ralls,et al.  A reliable, non-invasive method for sex determination in the endangered San Joaquin kit fox (Vulpes macrotis mutica) and other canids , 2004, Conservation Genetics.

[48]  M. Schwerin,et al.  Sex determination in cattle based on simultaneous amplification of a new male‐specific DNA sequence and an autosomal locus using the same primers , 2001, Molecular reproduction and development.

[49]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[50]  J. Medrano,et al.  Amplification of the Zfy and Zfx Genes for Sex Identification in Humans, Cattle, Sheep and Goats , 1990, Bio/Technology.

[51]  S. Cseh,et al.  Sex determination using circulating cell-free fetal DNA in small volume of maternal plasma in elephants , 2019, Scientific Reports.