Forensic Science International: Genetics 5 (2011) 336–338

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Forensic Science International: Genetics

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Short communication

Study of 25 X-chromosome SNPs in the Portuguese

Vânia Pereira a,b,c,*, Carmen Tomas c, António Amorim a,b, Niels Morling c, Leonor Gusmão b,
Maria João Prata a,b
a
Faculty of Sciences, University of Porto, Porto, Portugal
b
IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
c
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

A R T I C L E I N F O A B S T R A C T

Article history: The importance of X-chromosome markers in individual identifications, population genetics, forensics
Received 27 June 2010 and kinship testing is getting wide recognition. In this work, we studied the distributions of 25 X-
Received in revised form 22 September 2010 chromosome single nucleotide polymorphisms (X-SNPs) in population samples from Northern, Central
Accepted 5 October 2010
and Southern Portugal (n = 305). The data were also compared with previous data from the
Mediterranean area confirming a general genetic homogeneity among populations in the region. The
Keywords: X-SNP distribution in the three Portuguese regional samples did not show any significant substructure
X-chromosome
and the X-SNP distributions did not differ significantly from those of the majority of Mediterranean
SNPs
populations.
Portuguese population
ß 2010 Elsevier Ireland Ltd. All rights reserved.

1. Introduction X-chromosome allows the simultaneous study of both genders,

Recombination in the mammalian X-chromosome occurs
exclusively in females. Thus, in each generation, two thirds of
the X-chromosomes recombine making linkage disequilibrium
greater when compared to the autosomes and the size of regions
with a common genetic history larger. Due to the effective number
of X-chromosomes in a population compared to the autosomes
(three quarters), X-chromosome diversity is lower and the effects
of genetic drift or substructure in a given population are more
pronounced [1].
A previous work from our group that focused on mtDNA and Y-
chromosome diversity in the Portuguese population has already
yielded additional insights in Sub-Saharan and Mediterranean
migrations that occurred at different time periods, especially in
Southern Portugal [2]. This African and Mediterranean influence
can be explained by the influx of African slaves into Portugal
between the 15th and 19th centuries and by ancient contacts with
Mediterranean populations such as Greeks, Phoenicians and
Carthaginians, who established important trading networks all
over the region.
Unlike mtDNA or Y-chromosome analyses that exclusively
inform about the history of female and male lineages, the
* Corresponding author at: IPATIMUP-Institute of Molecular Pathology and
Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto,
Portugal. Tel.: +351 225570700; fax: +351 225570799.
E-mail address: vpereira@ipatimup.pt (V. Pereira).
making it an ideal system for studying population genetic
differences between males and females [1]. Currently, few data
on X-chromosome single nucleotide polymorphisms (X-SNPs)
have been published [3]. Among other characteristics, these
markers have low mutation rates when compared to STRs and
like them can be amplified in short fragments making them very
useful in old and degraded samples where the amount of DNA is
limited.
In this work, we have studied 25 X-SNPs in male individuals
from Northern, Central and Southern Portugal aiming at assessing
the patterns of X-SNP diversity in Portugal. The results were
compared with previously reported data on Mediterranean
populations.
2. Material and methods
A total of 305 blood samples were collected from unrelated male
individuals in three Portuguese regions: North (n = 73), Central
(n = 129) and South (n = 103). Genomic DNA was extracted by
standard phenol–chloroform methods. Samples were analysed for
25 X-chromosome SNP markers previously investigated (Table 1)
[3]. All the markers were amplified in one PCR reaction, followed by a
multiplex single base extension reaction using the SNaPshot1 kit
(Applied Biosystems). The laboratory procedures concerning SNP
selection and typing were previously reported [3,4]. Allele
frequencies, diversity indices, pairwise FST and pairwise linkage
disequilibrium values were calculated with Arlequin v.3.11 [5]. p-
Values were corrected using Bonferroni’s correction for multiple

1872-4973/$ – see front matter ß 2010 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.fsigen.2010.10.004
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V. Pereira et al. / Forensic Science International: Genetics 5 (2011) 336–338 337

Table 1
X-chromosome SNPs analysed on this study [3].

Code rsNumber Region Physical

location (bps)

X004 rs2056688 Xp22.3 3.463.191

X009 rs2128519 Xp22.3 5.013.412
X018 rs1534285 Xp22.3 11.178.926
X029 rs763056 Xp22.2 17.353.443
X036 rs1373592 Xp22.1 24.981.639
X046 rs993010 Xp21 33.293.733
X047 rs1557054 Xp21 34.834.831
X056 rs1243792 Xp11.4 39.716.166
X059 rs925178 Xp11.4 41.692.761
X062 rs1207480 Xp11.3 46.512.334
X076 rs1936313 Xq12 65.433.873
X085 rs1977719 Xq13 76.438.402
X108 rs1372687 Xq21 92.501.309
X109 rs1857602 Xq21 93.150.340
X121 rs985425 Xq22 102.300.968
X122 rs933315 Xq22 104.631.674 Fig. 1. Principal component analysis of 25 X-chromosome markers in Portuguese
X131 rs2190288 Xq24 114.496.852 and Mediterranean populations. Codes are as follows: PT-N: Northern Portugal; PT-
X134 rs1991961 Xq25 117.802.044 C: Central Portugal; PT-S: Southern Portugal; CAN: Catanzaro; COS: Cosenza; IBZ:
X135 rs1931662 Xq25 118.816.972 Ibiza; IRQ: Iraq; MAJ: Majorca; MOR: Morocco; REG: Reggio di Calabria; SIC: Sicily;
X142 rs149910 Xq25 124.270.150 TUN: Tunisia; TUR: Turkey; VAL: Valencia. The Portuguese populations are
X143 rs1573704 Xq26 126.204.493 represented by filled circles.
X159 rs1340718 Xq27 137.864.963
X165 rs1930674 Xq27 141.948.792
X168 rs1339597 Xq27 142.926.858 After correction for multiple analyses, statistically significant
X175 rs1981452 Xq28 148.898.241 values were found between: Northern Portugal and (1) Turkey and
(2) Morocco, and between Central Portugal and (1) Cosenza, (2)
Ibiza and (3) Morocco. The Moroccan population differed
analyses [6]. Principal component analysis was calculated with genetically from all the others having significant pairwise FST
STATISTICA (Statsoft). The results were compared with previously values with 7 out of the 13 analysed populations, including
reported data of Mediterranean populations [3]. Southern Portugal.
A principal component analysis was performed with allele
3. Results and discussion frequency data in order to visualize the relationships between the
populations. The first two principal components (PC) account for
All markers were polymorphic in the populations studied. The 37.5% of the global variability (Fig. 1).
minor allele frequencies ranged between 14.6% (X159 in Southern The Portuguese populations, especially the population from
Portugal) and 50% in several markers and populations. Southern Portugal, did not differ from the Mediterranean
The average gene diversities were very similar in all populations. As previously reported, the Moroccan population
populations studied (Table 2). The values observed in Portugal differs slightly from the others. Our results are in accordance
were among the lowest in the populations compared. No with the results of Tomas et al. [3] where an overall
haplotype was shared between any of the individuals investi- homogeneity of X-SNPs was observed in the populations of
gated. the Mediterranean basin. The Portuguese population did not
Concerning the three Portuguese regions, pairwise linkage show any significant structure concerning the 25 X-SNP markers
disequilibrium analysis revealed no linkage disequilibrium be- analysed and was were similar to the populations of the
tween the markers after correction for multiple analyses [6] Mediterranean area.
(p = 0.000167).
To assess the genetic similarity between the Portuguese and the Role of funding
Mediterranean populations, pairwise FST-values were calculated.
This work was partially supported by the Portuguese Founda-
tion for Science and Technology (FCT) through PhD grant SFRH/BD/
Table 2
Average gene diversity in the populations analysed.
47569/2008, Calouste Gulbenkian Foundation and Ellen and Aage
Andersen’s Foundation. IPATIMUP is an Associate Laboratory of the
Population n Ha Portuguese Ministry of Science, Technology and Higher Education
Northern Portugal 73 0.450  0.229 and is partially supported by FCT.
Central Portugal 129 0.447  0.226
Southern Portugal 103 0.444  0.225
Catanzaro 61 0.452  0.230 Conflict of interest
Cosenza 37 0.456  0.235
Ibiza 108 0.450  0.228 None.
Iraq 63 0.461  0.234
Majorca 100 0.456  0.231
Morocco 89 0.439  0.223 References
Reggio di Calabria 100 0.452  0.229
Sicily 119 0.452  0.229 [1] S.F. Schaffner, The X chromosome in population genetics, Nat. Rev. Genet. 5
Tunisia 100 0.461  0.233 (2004) 43–51.
Turkey 57 0.449  0.229 [2] V. Pereira, V. Gomes, A. Amorim, L. Gusmão, M.J. Prata, Genetic characterization of
Valencia 60 0.454  0.231 uniparental lineages in populations from Southwest Iberia with past malaria
endemicity, Am. J. Hum. Biol. 22 (2010) 588–595.
n: sample size. [3] C. Tomas, J.J. Sanchez, A. Barbaro, C. Brandt-Casadevall, A. Hernandez, M. Ben
a
H: average gene diversity. Dhiab, M. Ramon, N. Morling, X-chromosome SNP analyses in 11 human Mediter-
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Africans (Moroccans), BMC Evol. Biol. 8 (2008) 75. for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50.
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