Fast and non-invasive PCR sexing of primates: apes, Old World monkeys, New World monkeys and Strepsirrhines
© Villesen and Fredsted; licensee BioMed Central Ltd. 2006
Received: 24 February 2006
Accepted: 08 June 2006
Published: 08 June 2006
One of the key tools for determining the social structure of wild and endangered primates is the ability to sex DNA from small amounts of non-invasive samples that are likely to include highly degraded DNA. Traditional markers for molecular sex determination of primates are developed on the basis of the human sequence and are often non-functional in distantly related primate species. Hence, it is highly desirable to develop markers that simultaneously detect Y- and X-chromosome specific sequences and also work across many species.
A novel method for sex identification in primates is described using a triple primer PCR reaction and agarose gel electrophoresis of the sex-chromosomal isoforms of the ubiquitously transcribed tetratricopeptide repeat protein gene (UTX/UTY). By comparing genomic data from several mammals we identified the UTX/UTY locus as the best candidate for a universal primate sexing marker. Using data from several species we identified a XY-conserved region, a Y conserved region and an X conserved region. This enabled the design of a triple primer PCR setup that amplifies X and Y products of different length in a single PCR reaction.
This simple PCR amplification of X and Y fragments is useful for sexing DNA samples from all species of primates. Furthermore, since the amplified fragments are very short the method can be applied to fragmented DNA extracted from non-invasive samples.
The ability to identify the sex of a DNA sample is an important tool in molecular ecology and conservation genetics. The optimal marker would work on small amounts of non-invasive samples that are likely to include highly degraded DNA and be applicable in many species.
Molecular sex identification normally works by PCR amplification of sex specific regions that differ in length. The PCR products can then be visualized using standard electrophoresis, revealing females as homozygotes (XX) and males as heterozygotes (XY). Generally, in order to detect the male sex, a Y chromosomal fragment must be amplified. This can be done by (a) amplification of a homolog region on X and Y with a length difference, (b) a triple primer PCR with a common primer X/Y and a Y specific primer (short fragment) and X specific primer (longer fragment) or (c) a multiplex PCR with a Y region and an positive control (autosomal or X region).
Several loci have been used for sex identification in humans and closely related species, e.g. the amelogenin system [1–3] the zinc-finger protein [4, 5], the SRY locus  or a combination . Detection of sex-specific restriction patterns  requires some pre-analysis development (i.e. sequencing to identify restriction sites) and enzyme restriction of PCR products, which is time consuming. The SRY locus requires co-amplification of external control regions [6, 7], which may be unreliable for non-invasive DNA samples with DNA of low quality.
The widely used amelogenin system  has recently been found to provide ambiguous results in humans such as null-alleles, primer mutations or amplification failure, resulting in erroneous gender determination [9–11]. It works in closely related apes , but not orang-utans , baboons or more distantly related species . Also, the Sullivan amelogenin system amplifies a very small X-Y size difference (6 bp), which does not consistently resolve well on agarose gels. Therefore this system needs more time-consuming and expensive acrylamide gel- or capillary electrophoresis. Recently, a new general multiplexing method was published, using the amelogenin locus, the SRY locus and group specific primers and suitable for non-invasive samples . Non-identification of males may result from non-amplification of the Y fragment and it has been argued  that all "females" (XX or XY with no Y amplification) should be verified with a second independent sex test. This calls for the development of multiple independent tests that can be carried out in parallel.
We have previously developed a new primer pair for a different region of the amelogenin gene suitable for sexing lemurs and humans and therefore possibly most primate species . However, like the zing-finger protein system , the resulting fragments are too long (> 250 bp) for non-invasive samples, which often contain highly degraded DNA. Alternatively, we then designed primers for a small region of the DEAD-BOX gene, which are able to sex apes and monkeys, but these primers do not work in prosimians – probably due to primer region mutations .
At present, genomic sequence information is only available for a few primates (human, chimpanzee, macaque) and rodents (mouse, rat) or even more distantly related species. So far, we find that it is impossible to identify suitable homolog XY regions with the desired degree of conservation for a standard two-primer PCR design that will work in all primates.
The objective of this study was to identify a suitable region for a triple primer PCR design with a shared XY primer in combination with an X- and Y-specific primer. The primers should amplify a short region and be widely conserved through primate evolution, such that the method would work on non-invasive samples from all primate species.
A region of UTY is highly conserved between human and mouse
The comparison of the repeat masked human, chimpanzee and mouse Y chromosome yielded surprisingly few results. The best hit was 248 bp with 95.56% identity between mouse and human. This region is a part of the Y-chromosomal isoform of the ubiquitously transcribed tetratricopeptide repeat protein gene (UTY). Hence, UTY and the X-chromosomal homolog (UTX) were selected for further analysis.
The UTX/UTY region is suitable for triple primer design
PCR primers, degeneracy and annealing temperatures (Ta).
Primer sequence (5'-3')1
Successful sexing of all primate species tested
Since the primers were designed in well conserved regions, no species-specific optimization was necessary and a shared PCR protocol and identical annealing temperature was used (table 1).
In this study we have established a simple, accurate and widely applicable method for determining the sex of primate DNA samples by using triple primer PCR of a small region of the UTX/UTY gene. The ubiquitously transcribed tetratricopeptide repeat protein gene (UTX/UTY) is located on the X and Y chromosomes and our analysis identified a region in the human UTY having the highest identity to the mouse Y chromosome. Due to the high conservation of this region the triple primer PCR setup works in all primate species tested. Furthermore, the method contains an internal positive control (the shared primer), but should always be tested in samples of known sex before actual analysis is carried out. Also, it may be necessary to perform species specific optimization of annealing temperature and/or primer concentrations prior to analysis.
Since the nature of the Y chromosome allows deletion of many regions, it can be expected that with an increased number of individuals tested deletion of UTY might be found in low frequency (as reported for amelogenin-Y ). Furthermore, primer region mutations may result in non-identification of males due to PCR failure, which are known in the amelogenin system [9–11]. Generally, non-identification of males may result from non-amplification of the Y fragment and it has been argued  that all "females" (XX or XY with no Y amplification) should be analysed with at least two independent sex tests. It is now possible to combine the analysis of amelogenin, SRY and UTX/UTY in parallel for most primate species, thereby obtaining reliable sex determination (e.g.  and this study) using independent PCR runs. Given the low amount of DNA usually obtained from non-invasive sampling, the optimal approach for molecular sexing would be to run a single multiplex PCR analysis, but such a protocol has not been developed yet.
Our findings show that the PCR assay based on the UTX/UTY gene is reliable for sex identification in primates. The advantage of this assay is the extreme primer conservation and wide applicability and ease of use. In combination with other single locus markers, it is now possible to reliably sex individuals of most (if not all) primate species.
Primer region identification and design
Primate Y chromosomes were downloaded from Ensembl  and compared to the mouse Y chromosome using BLAST with strict parameters (W = 18 (primer length), e = 1E-100). The region with the highest identity was found to be in the UTY gene in humans (248 bp with 95.56% identity to mouse, Human Y: 13909061-13909308), and this gene and the X homolog (UTX) was selected for further analysis.
8 UTY and 11 UTX sequences were downloaded from GenBank and aligned (UTY: Eulemur fulvus, Macaca fascicularis, Ateles geoffroyi, Hylobates lar, Pongo pygmaeus, Gorilla gorilla, Pan troglodytes, Homo sapiens UTX: Lemur catta, Cheirogaleus medius, Colobus sp., Hylobates lar, Presbytis entellus, Leontopithecus rosalia, Ateles geoffroyi, Macaca fascicularis, Gorilla gorilla, Pongo pygmaeus, Homo sapiens. The alignment files are available as additional files 1, 2).
Adequate regions were selected manually (figure 1A) and degenerate primers were designed using the Primo online software . The resulting primers were designed with relatively high annealing temperatures to allow possible mismatches to the template in distantly related species (table 1).
DNA extraction and PCR
DNA was extracted from shed or plucked hairs, ear tissue or blood. From hair samples DNA was extracted using a slight modification of the Chelex protocol : Approximately 5 mm of the root portion of 5–8 hairs from each individual was cut directly into 1.5 mL Eppendorf tubes containing 200 μl of 20% Chelex resin solution (BIO-Rad, Hercules, CA, USA). Tubes were vortexed briefly, boiled for 12 min, centrifuged 3 min at 13000 rpm and stored at minus 20°C. From tissue samples DNA was extracted using DNeasy Tissue Kit (cat. no. 69506, Qiagen), and from blood samples DNA was extracted using proteinase K digestion, followed by a protein salting-out step as described in . PCR was performed in a total volume of 10 μl and contained 1 μl buffer (1.5 mM MgCl2), 1.6 μl dNTP (1.25 mM of A, C, G, T, respectively), 4, 1 and 0.25 μl of UTY, UTXY and UTX primers (10 pmol/μl), 0.1 μl Taq polymerase (Amersham Pharmacia Biotech), topped up with distilled water to 8 μl and 2 μl template DNA was added. The different volumes of the three primers were found after optimization for equal intensity of the X and Y fragments. Cycling conditions were 94°C for 3 min, and 35 cycles of 94°C for 30 s, 57°C for 40 s and 72°C for 1 min and a final extension step of 72°C for 7 min. PCR fragments were separated on 2 % agarose gels (120 V, 1 hour 45 minutes) and visualized using SybrGreen staining.
P. Villesen was supported by the Danish Cancer Society. T. Fredsted was supported by a PhD grant from the Faculty of Science of the University of Aarhus as well as a grant from the WWF Biodiversity Fund, Denmark. We would like to thank several people and facilities for providing either primate hair, blood or DNA samples of many of the primate species tested in this study: Givskud Zoo, Denmark, Munich Zoo, Germany, C. Roos at the Gene Bank of Primates, German Primate Center, Germany, Ebeltoft Zoo/Living United, Denmark, P.M. Kappeler, M. Eberle and D. Zinner, J. Fietz, S. Sommer and K. Daussmann.
- Sullivan KM, Mannucci A, Kimpton CP, Gill P: A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin. Biotechniques. 1993, 15 (4): 636-641.PubMedGoogle Scholar
- Bradley BJ, Chambers KE, Vigilant L: Accurate DNA-based sex identification of apes using non-invasive samples. Conservation Genetics. 2001, 2 (2): 179-10.1023/A:1011847528045.View ArticleGoogle Scholar
- Fredsted T, Villessen P: Fast and reliable sexing of prosimian and human DNA. Am J Primatol. 2004, 64 (3): 345-350. 10.1002/ajp.20083.View ArticlePubMedGoogle Scholar
- Wilson JF, Erlandsson R: Sexing of human and other primate DNA. Biol Chem. 1998, 379 (10): 1287-1288.PubMedGoogle Scholar
- Morin PA, Nestler A, Rubio-Cisneros NT, Robertson KM, Mesnick SL: Interfamilial characterization of a region of the ZFX and ZFY genes facilitates sex determination in cetaceans and other mammals. Mol Ecol. 2005, 14 (10): 3275-3286. 10.1111/j.1365-294X.2005.02651.x.View ArticlePubMedGoogle Scholar
- Steiper ME, Ruvolo M: Genetic sex identification in orangutans. Anthropol Anz. 2003, 61 (1): 1-5.PubMedGoogle Scholar
- Fiore A: A rapid genetic method for sex assignment in non-human primates. Conservation Genetics. 2005, 6 (6): 1053-10.1007/s10592-005-9086-5.View ArticleGoogle Scholar
- Fernando P, Melnick DJ: Molecular sexing eutherian mammals. Molecular Ecology Notes. 2001, 1 (4): 350-353.View ArticleGoogle Scholar
- Chang YM, Burgoyne LA, Both K: Higher failures of amelogenin sex test in an Indian population group. J Forensic Sci. 2003, 48 (6): 1309-1313.View ArticlePubMedGoogle Scholar
- Michael A, Brauner P: Erroneous gender identification by the amelogenin sex test. J Forensic Sci. 2004, 49 (2): 258-259. 10.1520/JFS2003223.View ArticlePubMedGoogle Scholar
- Shadrach B, Commane M, Hren C, Warshawsky I: A rare mutation in the primer binding region of the amelogenin gene can interfere with gender identification. J Mol Diagn. 2004, 6 (4): 401-405.PubMed CentralView ArticlePubMedGoogle Scholar
- Ensminger AL, Hoffman SM: Sex identification assay useful in great apes is not diagnostic in a range of other primate species. Am J Primatol. 2002, 56 (2): 129-134. 10.1002/ajp.1069.View ArticlePubMedGoogle Scholar
- Robertson BC, Gemmell NJ: PCR-based sexing in conservation biology: Wrong answers from an accurate methodology?. Conservation Genetics. 2006, 7 (2): 267-71. 10.1007/s10592-005-9105-6.View ArticleGoogle Scholar
- Villesen P, Fredsted T: A new sex identification tool: one primer pair can reliably sex ape and monkey DNA samples . Conservation Genetics. 2006, 7 (3): 455-9. 10.1007/s10592-005-9044-2.View ArticleGoogle Scholar
- Kashyap VK, Sahoo S, Sitalaximi T, Trivedi R: Deletions in the Y-derived amelogenin gene fragment in the Indian population. BMC Med Genet. 2006, 7: 37-10.1186/1471-2350-7-37.PubMed CentralView ArticlePubMedGoogle Scholar
- Ensembl. [http://www.ensembl.org]
- Primo primer design. [http://www.changbioscience.com]
- Walsh PS, Metzger DA, Higuchi R: Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991, 10 (4): 506-513.PubMedGoogle Scholar
- Sambrook J, Fritsch EF, Maniatis T: Molecular cloning : a laboratory manual. 1989, Cold Spring Harbor, N.Y. , Cold Spring Harbor Laboratory, 2ndGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.