A. thaliana genotyping with a CAPS marker for a pks3

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Application Note
A. thaliana genotyping with a CAPS marker for a pks3
mutant allele
Martine Trevisan and Christian Fankhauser; Center for Integrative Genomics, University of Lausanne, Switzerland
The QIAxcel® system was used for genotyping A. thaliana with CAPS markers, following mutations in the PKS3 gene
(At1g18810), and to identify mutants in various crosses.
Introduction
Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant
cellular and molecular biology. Its genome sequence is known and is available through the
Arabidopsis Information Resource (TAIR), as well as other sources, including seed stocks and
collections of genetic and physical markers.
The short life cycle (approximately 6 weeks from germination to seed maturation), enables highly
efficient preparation of mutants for in-depth analysis of gene function. Once a mutant of interest has
been identified, cleaved amplified polymorphic sequences (CAPS) are used to map the mutation
(1). CAPS markers are also used to genotype known mutations.
Previously, no mutations were known for the phytochrome kinase substrate protein 3 (PKS3) gene
(At1g18810), a member of a small gene family in A. thaliana (2). The “targeting induced local
lesions in genomes” (“tilling”) approach was used to identify a mutant in the PKS3 gene, pks3-7.
Subsequently CAPS markers were used for genotyping, allowing the mutant to be followed in various
genetic crosses.
Materials and Methods
Small arabidopsis leaves were homogenized by grinding in an Eppendorf® tube in 500 μl of
200 mM Tris (pH 7.5), 250 mM NaCl, 25 mM EDTA, and 0.5% SDS. After centrifugation, DNA
was precipitated by adding equal amounts of isopropanol to the supernatant. After an additional
centrifugation at 12,000 x g for 10 minutes, the DNA pellet was washed with 70% ethanol, air
dried, and resuspended in 100–200 μl 10mM Tris, 1 mM EDTA (pH 8.0).
PCR amplification was performed with Taq DNA polymerase (proprietary preparation) understandard
reaction conditions in a 20 μl volume. PCR amplification using the CF523 (AAACA AGCCG ACATG
GAACG) and CF524 (TCGTT ATGTT CTCAA TCTCG) primers yielded a prominent 518 bp fragment.
Sample to Insight
PCR product (10 μl) was digested in a total volume of 40 μl with 10 U MboI (New England
BioLabs) by incubating for 70 minutes at 37°C. The 518 bp wild-type fragment was digested into
3 fragments: 29 bp, 182 bp, and 307 bp. The pks3-7 mutant sequence is missing an MboI restriction
site, and digestion of the mutant 518 bp fragment yielded 2 fragments: 211 bp and 307 bp.
Digested samples were analyzed using the QIAxcel capillary electrophoresis system with the
QIAxcel DNA Screening Kit and the AM320 method. The QX Alignment Marker 50 bp/500 bp
and QX DNA Size Marker 50 bp–800 bp were included in the analysis.
The QIAxcel capillary electrophoresis system processes samples in batches of 12 and allows
analysis of up to 96 samples without manual intervention. The results can be displayed as an
electropherogram as well as a gel-like image.
Results and Discussion
CAPS analyses were performed to screen the progeny of a backcross of pks3-7 against its isogenic
wild-type control. By analyzing the F2 generation for the presence of the pks3-7 mutation using a
specific CAPS marker, it was possible to follow the mutant allele through various crosses.
The results of a CAPS analysis using the QIAxcel system are shown in Figure 1. In lanes 2, 4, and
6, DNA fragments from the wild type PKS3 gene are present (29 bp, 182 bp, and 307 bp). The
fragments present in lane 3 (211 bp and 307 bp) indicate a homozygote for the pks3-7 mutation.
The fragments in lanes 5, 7, and 8 (29 bp, 182 bp, 211 bp, and 307 bp) indicate heterozygosity
for the pks3-7 mutation. The sizes of the DNA fragments estimated by BioCalculator Software are
given in Table 1.
Although the size differences between the fragments are small, the sharp banding patterns
achieved using the QIAxcel system allowed more accurate size estimation than is possible with
agarose gel electrophoresis (data not shown).
1
2
3
4
5
6
7
8
9
Figure 1. CAPS analysis for the A. thaliana PKS3 gene.
CAPS of the PKS3 gene were prepared from individual
A. thaliana plants and resolved on the QIAxcel system
using the QIAxcel DNA Screening Kit.
1: negative control;
2, 4, 6: wild type;
3: homozygous pks3-7 mutant;
5, 7, 8: heterozygote pks3-7 mutant;
9: QX DNA Size Marker 50 bp/800 bp.
2
A. thaliana genotyping with a CAPS marker for a pks3 mutant allele
08/2016
Table 1. BioCalculator analysis of the gel image in Figure 1
Lane
Estimated fragment size (bp)
1
41
2
180
306
3
210
303
4
179
304
5
179
210
304
6
29
170
300
7
34
171
204
8
178
210
303
9
50
100
150
299
200
250
300
400
500
600
700
800
Conclusions
• The sharp banding patterns achieved with the QIAxcel capillary electrophoresis system simplified
and accelerated the routine sizing of wild type and mutant DNA fragments. Due to the
accurate sizing of DNA fragments compared to conventional agarose gel electrophoresis (data
not shown), the QIAxcel system enabled unambiguous size estimation in significantly shorter
time.
• Up
to 96 samples can be analyzed in a single run without manual intervention using the
QIAxcel system. In addition, the QIAxcel system provides more information from CAPS analyses
than traditional methods, saving time and effort. Controlled running conditions and automated
data acquisition ensure data safety, reliability, and reproducibility.
• QIAxcel capillary electrophoresis uses only minute quantities of DNA for electrokinetic injection,
allowing the samples to be used for downstream procedures, such as sequencing or cloning.
References
1. K
onieczny, A., and Ausubel, F.M. (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotypespecific
PCR-based markers. Plant J. 4, 403.
2. D
e Carbonnel, M. et al. (2010) The arabidopsis PHYTOCHROME KINASE SUBSTRATE2 protein is a phototropin signaling
element that regulates leaf flattening and leaf positioning. Plant Physiol. 152, 1391.
A. thaliana genotyping with a CAPS marker for a pks3 mutant allele
08/2016
3
Ordering Information
Product
Contents
Cat. no.
QIAxcel Advanced System
Capillary electrophoresis device, including computer, and
QIAxcel ScreenGel Software; 1-year warranty on parts and labor
9001941
QIAxcel DNA High
Resolution Kit (1200)
QIAxcel DNA High Resolution Cartridge, Buffers, Mineral Oil,
QX Intensity Calibration Marker, 12-Tube Strips
929002
QIAxcel DNA Screening Kit
(2400)
QIAxcel DNA Screening Cartridge, Buffers, Mineral Oil,
QX Intensity Calibration Marker, 12-Tube Strips
929004
QIAxcel DNA Fast Analysis Kit
(3000)
QIAxcel DNA Fast Analysis Cartridge, Buffers, Mineral Oil,
QX Intensity Calibration Marker, QX DNA Size Marker
50 bp – 1.5 kb, QX Alignment Marker 15 bp/3 kb, 12-Tube Strips
929008
QIAxcel RNA QC Kit v2.0
(1200)
For 100 runs of 12 samples: QIAxcel RNA Quality Control
Cartridge, Buffers, Mineral Oil, QX Intensity Calibration Marker,
QX RNA Alignment Marker, QX RNA Size Marker 200–6000 nt,
QX RNA Denaturation Buffer, 12-Tube Strips
929104
For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user
manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN
Technical Services or your local distributor.
Visit www.qiagen.com/CAPS-analysis and find out how automated gel electrophoresis can benefit your lab!
Trademarks: QIAGEN®, Sample to Insight ®, QIAxcel® (QIAGEN Group); Eppendorf ® (Eppendorf AG). Registered names, trademarks, etc. used in this document, even when not specifically marked as such, are not to be
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