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Comparison of different DNA extraction methods
from hair root follicles to genotype Finnish Landrace

boars with the Illumina PorcineSNP60 BeadChip
Anu Sironen*, Pekka Uimari, Johanna Vilkki

MTT Agrifood Research Finland, Biotechnology and Food Research, FI-36100 Jokioinen, Finland

*email: anu.sironen@mtt.fi

Recent developments in sequencing methods have enabled whole genome sequencing of several species
and the available sequence information has allowed the development of high throughput genotyping chips.
However, these genotyping methods require high quality DNA. The possibility to genotype samples based on
DNA from non-invasive sources would permit retrospective genotyping of previously collected samples and
also facilitate the analysis of large populations e.g. for genomic selection. In this study we have developed
and evaluated different DNA preparation methods from porcine hair root follicles for high throughput geno-
typing with the PorcineSNP60 Genotyping BeadChip (Illumina). We describe a method for DNA extraction
from porcine hair root samples, which produces results from high throughput genotyping with the same
high degree of accuracy as previously reported for DNA extracted from sperm, blood or tissue samples.
This method was used for the genotyping of 273 hair follicle samples. When the DNA concentration was
> 30 ng/µl all samples had the same high call rate ( > 99%) as sperm samples confirming the robustness
of this DNA extraction method for high throughput genotyping. Our data also establishes the suitability of
the PorcineSNP60 BeadChip for genotyping the Finnish Landrace population.

Key-words: DNA extraction, Finnish Landrace, genotyping, hair follicles, pig, SNP

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Introduction

High throughput single-nucleotide polymorphism
(SNP) genotyping methods are becoming increas-
ingly important in population (Decker et al. 2009,
Vonholdt et al. 2010) and association studies
(Goddard and Hayes 2009) and also for genomic
selection (Meuwissen et al. 2001). High throughput
genotyping is now feasible due to the large number
of SNP discovered by genome sequencing of vari-
ous species and the development of new methods
to efficiently genotype a large numbers of SNPs
(Hayes et al. 2009). Genomic selection is based
on a large reference population, in which animals
are both phenotyped and genotyped. Previously
collected samples from a reference population with
reliable breeding values are required to predict
genomic breeding values (GEBV) in subsequent
generations. Similarly, existing samples can be used
for the analysis of population diversity and identi-
fication of disease associated genomic regions by
high throughput genotyping. DNA extracted from
sperm, blood or tissue samples can be used for high
quality genotyping using chip technology (Li et al.
2008, Jiang et al. 2010), but invasive procedures
are required to collect such samples causing un-
necessary pain and distress for sampled animals.
Furthermore, these samples are also expensive and
time consuming to collect.

The hair root is known to contain DNA and
therefore represents a non-invasive source of DNA.
The collection, transportation and storage of hair
samples do not require any special procedures
and as a result offers a painless and inexpensive
alternative to the sampling of other tissues. Sev-
eral methods have been described for polymerase
chain reaction (PCR) amplification of single mark-
ers from hair samples (Amendola-Pimenta et al.
2009, Hayashida et al. 2009, Sironen et al. 2010).
However, the low quality of DNA obtained has pre-
vented the use of these samples for high throughput
genotyping. In this study, we have assessed several
possible methods for DNA preparation from por-
cine (Sus scrofa) hair roots for genotyping with the
chip technology. Based on our analysis we have
developed a reliable method for the preparation of

DNA from the hair root for genotyping with the
PorcineSNP60 Genotyping BeadChip (Illumina).

Material and Methods

DNA samples
Genomic DNA was prepared from porcine (Finn-
ish Landrace) hair roots collected during years
2000–2006 (samples of 273 boars were used for this
study) and stored at room temperature. Control DNA
was extracted from sperm samples using a phenol/
chloroform extraction protocol. For the assessment
of various DNA preparation methods replicate of
samples (n > 4) including the hair follicle of 5–15
hairs were used:

1. The hair roots were lysed in lysis buffer
[proteinase K 0.5 mg/ml and 2 µl Mg-free PCR
Buffer (Dynazyme DNA polymerase, Finnzymes)
in dH2O] at 55 ºC for 60 min following Proteinase
K inactivation at 98 ºC for 10 min.

2. DNA purification from the lysed samples
(first preparation method) by ethanol (EtOH) pre-
cipitation with 100% ethanol and sodium acetate
(0.3M, pH 5.2) at -20 °C for 30 min following cen-
trifugation at 13000 rpm for 10 min. Any residual
salt was washed with 70 % ethanol and centrifuged
at 13000rpm for 10min. Precipitated DNA was air
dried and dissolved in 20 µl of distilled H2O.

3. DNA extraction from the lysed samples (first
preparation method) by phenol/chloroform.

4. DNA purification from the lysed samples
(first preparation method) by InstaGene matrix
(BioRad) following the protocol supplied by the
manufacture.

5. Hair roots were lysed in ATL lysis buffer
(Qiagen) with proteinase K (10 mg/ml) at 55 ºC
for 60 min following Proteinase K inactivation at
98 ºC for 10 min. Thereafter the DNA was purified
with ethanol precipitation.

6. Hair roots were lysed in lysis buffer (10mM
Tris HCl, pH 8.0, 100mM NaCl, 1mM EDTA,
0.5% SDS) with proteinase K (10 mg/ml) at 55 ºC
for 60 min following Proteinase K inactivation at

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98 ºC for 10 min. Thereafter, DNA was purified by
precipitation with ethanol.

7. Extraction of DNA with DNeasy Blood &
Tissue Kit (Qiagen) according to the instructions
supplied by the manufacturer.

For the lysis protocols (1, 5–6) the effect of ad-
dition of MgCl2 (2mM) and DTT (100µM) and dis-
solution of the hair root by mechanical force (with
a rod or FastPrep homogenization system) were
also tested. The concentration of extracted DNA
was measured with a Nanodrop spectrophotometer
(NanoDrop Technologies) and a Qubit Quantitation
Platform (Invitrogen). Nanodrop was also used for
analysing the purity of extracted DNA. Absorbance
at 260 nm quantified the amount of DNA and pro-
tein contamination was detected at 280 nm. The
ratio of absorbance at A260/280 and A230/260 was
used to determine the purity of DNA samples. The
Qubit platform uses fluorescence-based Quant-
iT™ assays, where fluorescence label binds specifi-
cally to DNA. Although the specificity to dsDNA
increases the accuracy of the DNA concentration,
this detection system does not give any information
about the purity of the sample. The accuracy of
these concentration measurements were also con-
firmed by quantitative PCR (qPCR).

The qPCR was performed with an ABI 7000
Sequence Detection System in 96-well microtiter
plates using Absolute qPCR SYBR Green ROX
Mix (VWR). DNA was amplified using primers for
the microsatellite marker SW2411 (Forward CCT-
GGACTCATTCTTGCTTTG, reverse TTCCTAT-
TCTGTCCTGCCTTG). Amplification by qPCR
contained 12.5 μl of Absolute qPCR SYBR Green
Mix, 20 ng of DNA, and 70 nM of each primer in a
final volume of 25 μl. Amplifications were initiated
with 15 min enzyme activation at 95 °C followed
by 40 cycles of denaturation at 95 °C for 15 s, prim-
er annealing at 60 °C for 30 s, and extension at 72
°C for 30 s. All samples were amplified in duplicate
and a water sample was used as a negative control.
A standard curve was produced by serial dilutions
of DNA extracted from boar sperm (quantified with
Nanodrop spectrophotometer). Quantities of DNA
in the sample were estimated from the standard
curve. Raw data were analyzed with the sequence
detection software (Applied Biosystems).

Genotyping

For high throughput genotyping selected samples
were analyzed on the PorcineSNP60 Genotyping
BeadChip (Illumina Ltd) in the Institute for Molecu-
lar Medicine Finland (FIMM). The PorcineSNP60
BeadChip has recently been developed as an out-
come from the porcine whole genome sequencing
project (Ramos et al. 2009). The concentration of
samples analyzed by the BeadChip was estimated by
Qubit measurements and the purity was confirmed
by Nanodrop. The concentration varied between
2–100 ng/µl.

DNA samples of three boars with three differ-
ent DNA preparation methods (1, 2 and 7) from
hair roots and a reference sample extracted from
sperm were selected for genotyping with the Porci-
neSNP60 BeadChip. Furthermore, a duplicate sam-
ple of DNA from boar sperm was included on the
chip in order to compare the differences amongst
identical sperm samples and variation between
DNA preparation methods and sperm samples.
Based on these analyses the most reliable DNA
extraction method for hair samples was selected
and an additional 280 samples were analyzed with
the PorcineSNP60 BeadChip.

Statistical analysis

The effect of DNA concentration and genotyping
batch on call rate was evaluated by multivariate
ANOVA-method (SAS Enterprise Guide 4.3, SAS
Institute Inc.).

Results and discussion

Evaluation of DNA preparation methods
A wide range of DNA preparation methods were
tested including a basic lysis protocol with different
lysis buffers. The hair root lysis has been success-
fully implemented in single marker analysis (Sironen

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et al. 2010), however the purity is extremely low in
these samples. No clear differences in DNA yield or
purity were detected between lysis buffers (methods
2, 5 and 6) or following modification of the lysis
protocol (addition of DTT/MgCl2 or dissolution,
Table 1). The most consistent results were produced
using 15 hair roots, even though 10 or even 5 hair
roots yielded adequate amounts of DNA depend-
ing on the sample (data not shown). Therefore the
lysis buffer (method 1) used in our previous studies
(Sironen et al. 2010) with 15 hair roots was selected
for further purification.

DNA extraction with the InstaGene matrix
(method 4) and by chloroform/phenol (method
3) resulted in low DNA concentrations (Table 1).
Ethanol precipitation (method 2) and a commercial
extraction kit (method 7) yielded relatively high
amounts of good quality DNA (Table 1). Thus, for
high throughput genotyping, DNA extracted from
samples using methods 2 and 7 were selected. In
addition, samples prepared by lysis (method 1)
were also genotyped, since the concentration of
DNA was assumed to be highest in these samples
although the purity was low and interfered with

the determination of DNA concentration by Qubit
and Nanodrop.

Comparison of different concentration
assays

The concentration of DNA in various preparations
was evaluated with the Nanodrop spectrophotometer
and Qubit platform. Concentrations of DNA were
found to be approximately 10 times higher based
on the Nanodrop than Qubit analysis (Table 1).
Therefore, the determination of DNA concentration
was evaluated further by qPCR and a standard curve
prepared from DNA extracted from boar sperm
(quantified with Nanodrop spectrophotometer).
The same amount (20 ng) of DNA based on each
concentration assay was added to the qPCR am-
plification and the concentration was compared to
the standard curve. Qubit measurements appeared
to be consistent with the results from qPCR and
were therefore used to evaluate the concentration
of DNA for chip genotyping.

Table 1. Protocols tested for the preparation of total DNA from porcine hair roots. Results from two different concen-
tration measurement methods are presented. Sample purity (260/280 and 260/230 ratios) was assessed by Nanodrop.

Protocol (n)
Nanodrop ng/µl

(mean, SD)
260/280

ratio
260/230 ratio

Qubit ng/µl
(mean, SD)

1. Lysis (10) 58–500 (202, 157) <1 <0.5 0.9–29 (12, 11.7)

2.Lysis+EtOH precipitation (36) 15–500 (168, 137) 1.8–2 0.9–1.5 1.5–100 (21, 17)

3.Lysis+phenol/chloroform (3) 22–47 (36, 12.5) 1.8–1.9 2 –

4. Lysis+BioRad matrix (5) 35–83 (58, 24) 1.3–1.7 0.8 0.5–3 (1.8, 1.2)

5. ATL Qiagen lysis (5) 2.5–21.7 (11, 8) <1 <0.6 0.2–0.5 (0.35, 0.12)

6. SDS+EDTA lysis (5) 2–22 (12, 8.5) <1 <0.5 0.14–0.5 (0.3, 0.15)

7. Qiagen kit extraction (28) 32–450 (144, 139) 1.8–2 0.5–1.8 2–100 (38, 26)

n = number of samples

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SNP quality measures of the Porcine-
SNP60 Genotyping BeadChip

The total number of SNPs in the PorcineSNP60
BeadChip is 62163. However, 2815 SNPs did not
work for any of the genotyped samples and 9216
SNPs were monomorphic in the data set of Finnish
Landrace pigs. Excluding those SNPs, the average
minor allele frequency was 0.25 (SD = 0.14). Fur-
thermore, the observed distribution of P-values of
the Hardy-Weinberg equilibrium test statistic did
not differ from expectations; 183 SNPs (exclud-
ing the SNPs on the X-chromosome) had p-values
lower than 1.0E-06 which is much less than could
be expected by chance. Thus, the PorcineSNP60
BeadChip appears to be a robust and reliable method
for genotyping of Finnish Landrace pigs.

Quality of the PorcineSNP60 BeadChip
genotyping results with hair root sam-

ples
The comparison of the genotyping results from three
different DNA preparation methods illustrated the
importance of the quality of analysed DNA samples.
The lowest call rate (CR, 90–93 %, Table 2) was
detected with the unpurified lysis samples (method
1). When compared with the sperm sample, the
percentage of missing alleles was 2–5 % and the
percentage of different allele calls (e.g. A in one
sample and G in the other) was 0.09–0.31 % (Table
3). These differences substantially reduce the reli-
ability of genotypes produced from lysed hair root
samples. Samples of DNA extracted by the ethanol
precipitation (method 2) and Qiagen purification
(method 7) methods showed high call rates; 94–95
% and 95% for methods 2 and 7, respectively (Table
2) and very low percentage of differences when
compared with sperm samples (Table 3). These
values are consistent with the differences seen in
duplicate DNA samples extracted from sperm (Table
3). Excluding the 2815 SNPs, that did not work
for any of the genotyped samples, the average CR

Table 2. The overall call rate (CR) for three samples (1-
3) prepared by different DNA extraction methods and
a control sample (4a and 4b) after Illumina Beadchip
genotyping. The corrected CR indicates the CR after
excluding SNPs that did not work for any of the sam-
ples analyzed. The number or letter listed in the method
column indicates the DNA preparation method: S=DNA
extracted from sperm, 1=lysis, 2=lysis+EtOH precipita-
tion and 7=Qiagen kit.

Sample Method CR CR corrected
1 S 0.950 0.995
1 1 0.901 0.944
1 7 0.950 0.995
1 2 0.940 0.985
2 S 0.950 0.995
2 1 0.931 0.975
2 7 0.950 0.995
2 2 0.950 0.994
3 S 0.950 0.995
3 1 0.913 0.956
3 7 0.950 0.995
3 2 0.937 0.981
4a S 0.950 0.994
4b S 0.950 0.994

for all Qiagen and EtOH precipitated samples was
0.9982 (SD = 0.007).

Additional extractions of DNA were performed
using the Qiagen Blood and Tissue kit (method 7),
since the overall call rates were slightly higher in
these samples compared with EtOH precipitated
samples. However, the EtOH precipitation from
hair root lyses appears to be a feasible method for
DNA preparation for high throughput genotyping.
The CR for 231/270 (86 %) additional hair root
samples was > 99 % (after exclusion of SNPs that
did not work in any samples). For 28 samples the
call rate was > 90 %, for 18 samples > 72 % and
three samples did not work. The purity (260/280
ratio) was > 1.7 for all genotyped samples and did
not explain the lower call rates, but the DNA con-
centration of the samples varied between 2–100
ng/µl. Samples with a lower DNA concentration
were also genotyped, because for some hair root
samples it was extremely difficult or even impos-
sible to obtain a sufficiently high DNA concentra-

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Table 3. Differences in allele calls after Beadchip genotyping of hair root samples prepared by
various DNA extraction methods. Missing genotypes: number of genotypes that are missing in the
comparison between hair and sperm samples. Different genotypes: number of genotypes that are
different in the comparison between hair and sperm samples. The letter or number after the iden-
tification number indicates the DNA preparation method: S=DNA extracted from sperm, 1=lysis,
2=lysis+EtOH precipitation and 7=Qiagen kit.

Missing
genotypes

% Different
genotypes

PIG.1S PIG.1_1 3068 4.94 193 0.31
PIG.1S PIG.1_7 48 0.08 32 0.05
PIG.1S PIG.1_2 618 0.99 38 0.06
PIG.1_7 PIG.1_2 604 0.97 71 0.11

PIG.2S PIG.2_1 1197 1.93 53 0.09
PIG.2S PIG.2_7 18 0.03 19 0.03
PIG.2S PIG.2_2 69 0.11 18 0.03
PIG.2_7 PIG.2_2 63 0.10 25 0.04

PIG.3S PIG.3_1 2301 3.70 157 0.25
PIG.3S PIG.3_7 18 0.03 37 0.06
PIG.3S PIG.3_2 822 1.32 57 0.09
PIG.3_7 PIG.3_2 816 1.31 44 0.07

PIG.4aS PIG.4bS 64 0.10 52 0.08

tion (> 50 ng/µl). Thus, with the aim of genotyping
a large population of animals with minimal effort
the range in DNA concentration was considered
acceptable. When the call rates were analysed in
groups based on the DNA concentration, a clear as-
sociation between concentration and CR was iden-
tified (Fig. 1). With low DNA concentrations (<
30 ng/µl) the proportion of samples with adequate
call rates was lower than when the concentration
exceeded 30 ng/µl. Based on pair-wise compari-
sons using the Tukey’s test there was a significant
difference between sperm samples and hair sam-
ples when DNA concentration fell below 30 ng/
µl, but no difference when the concentration was
higher than 30 ng/µl (Table 4). Significant differ-
ences were also found between batch number four
and batch number three (Table 4). Part of this may
be due to the age and storage conditions of the hair
samples, but some variation may also arise from
handling of the sample during DNA extraction
protocol. The acceptable limit for DNA concen-

Fig. 1. Distribution plot of call rates against DNA con-
centration of hair root samples. At low concentrations
the proportion of samples with an adequate call rate is
lower than with samples containing DNA concentration
above 30 ng/µl.

0.6

0.7

0.8

0.9

0 20 40 60 80 100

Callrate

Qubit ng/µl

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tration appeared to be 30 ng/µl producing CR > 99
% corresponding to the CR with DNA extracted
from sperm or blood. However, samples with lower
concentration of DNA also exhibited high call rates
indicating that some deviation can be tolerated for
successful genotyping. Therefore, depending on
the experimental design, it may be necessary to
increase sample numbers by decreasing the DNA
concentration streshold.

Conclusion

Our results show that DNA from porcine hair roots
using an appropriate extraction method gener-
ates reliable genotyping results with the Illumina
PorcineSNP60 Genotyping BeadChip. These data
allow a straightforward and inexpensive means of
genotyping previously collected samples and/or

large animal populations. The concentration of DNA
appears to be the limiting factor in genotyping DNA
from hair roots and can be used to confirm the high
CRs. However, if the genotyping of large popula-
tions is required analysis of samples containing
lower DNA concentrations may remain viable. The
Qubit platform appeared to be a valid method for the
measurement of DNA concentration. Furthermore,
the SNPs on PorcineSNP60 BeadChip were highly
polymorphic in the Finnish Landrace population
highlighting the feasibility of this technology for
genotyping of Finnish Landrace pigs.

Acknowledgements. Funding for this study was
provided by the Finnish Ministry of Agriculture and
Forestry (Makera). The assistance of Tiina Jaakkola
and Tarja Hovivuori in DNA extraction and Päivi
Lahermo (Institute for Molecular Medicine Finland,
FIMM) in genotyping with PorcineSNP60 Geno-
typing BeadChip (Illumina) is greatly appreciated.

Table 4. Descriptive statistics of call rates (CR) for hair samples containing different DNA concen-
trations (ng/µl Qubit) and between different extraction batches. The CR for samples extracted from
hair root follicles with a low DNA concentration (< 30 ng/µl) was significantly different from CR
for DNA samples extracted from sperm. The LS mean corresponds to multivariate ANOVA least
square mean estimate. P–value refers to the significance of differences between sperm samples and
different DNA concentrations extracted from hair roots and between batch 4 and other batches based
on Tukey’s test statistics.

DNA source Class n Mean SD LS mean p–value
Hair root <10 24 0.885 0.084 0.900 <.0001
Hair root 10 – 30 80 0.953 0.052 0.969 0.005
Hair root 30 – 50 71 0.979 0.004 0.994 1
Hair root 50 – 100 98 0.980 0.005 0.994 1
Sperm 130 0.993 0.007 0.995

DNA batch 1 21 1.000 0.0002 0.975 0.099
2 87 0.995 0.0003 0.970 0.103
3 16 0.990 0.0139 0.981 0.003
4 279 0.963 0.0453 0.954

Overall 403 0.973 0.041

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Comparison of different DNA extraction methods from hair root follicles to genotype Finnish Landrace boars with the Illumina PorcineSNP60 BeadChip
Introduction
Material and Methods
DNA samples
Genotyping
Statistical analysis

Results and discussion
Evaluation of DNA preparation methods
Comparison of different concentration assays
SNP quality measures of the Porcine-SNP60 Genotyping BeadChip
Quality of the PorcineSNP60 BeadChip genotyping results with hair root samples

Conclusion
References