Optimization of Real-Time PCR for detection of BoERVK in Holstein cattle / Branda-Sica et al.___________________________________________
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INTRODUCTION
Cholesterol deciency — CD — (OMIA 001965-9913) [19] is caused
by a loss-of-function mutation in the Apolipoprotein B (APOB) gene,
which is necessary for liver lipid metabolism, steroid biosynthesis, and
cholesterol absorption in the small intestine [17]. The APOB mutation
influences cattle (Bos taurus) fertility, growth, and health [9]. CD
disease is usually confused with other types of neonatal diarrhea [14].
The economic impact of CD is very important. A study in Germany
calculated that 3,400 recessive homozygous calves were born per year,
resulting in an annual economic loss of approximately € 1.3 million [13].
Furthermore, in the United States of America (USA), annual losses due
to that disease were calculated at USA$ 1.7 million [3]. In addition to
severe diarrhea, affected calves have hypocholesterolemia and usually
die within the rst weeks (wk) to 6 months (mon) of life [14]. Some
heterozygous calves showed reduced blood cholesterol concentrations,
whereas in recessive homozygous blood cholesterol levels and
triglyceride concentrations were virtually zero [9, 14, 21]. Gross et al.
[8] found that low cholesterol concentrations associated with the APOB
mutation in carriers are not due to primary CD at the cellular level, as
the term “CD” suggests, but a consequence of decreased cholesterol
transport capacity in blood. These authors suggest that, despite the
presence of the APOB mutation, cholesterol does not limit metabolic
adaptation or yield in heterozygous Holstein Friesian cows (HFc) [8]. The
origin of this disease was traced to the American sire Maughlin Storm,
born in 1991 and widely used in the HF population worldwide [14, 23].
This disease is caused by a 1,299 base pairs (bp) insertion of a long
transposable element (LTR_ERV2-1) between nucleotides 24 and 25 of
exon 5 of the APOB gene [17]. This insertion causes a shift in the reading
frame of the APOB gene that leads to the truncation of 97% of the
bovine APOB protein [17]. These ndings were independently conrmed
by other authors [4, 22]. This result was conrmed by Charlier [4],
albeit he estimated the size of the insertion of the bovine endogenous
retroviral element in exon 5 of the APOB gene in 7.5 Kb (BoERV); this
leads to transcriptional termination and loss of protein function. Due
to this, the protein was synthetized to only 3% of its normal size.
Although molecular methods such as Polymerase Chain Reaction
(PCR) and its variants are currently applied to diagnose the CD-causing
mutation [5, 12, 17, 22], there are no published studies in Uruguay on
the application of these techniques for the accurate and effective
detection of these transposable elements. The design of molecular
diagnostic strategies for this mutation would be important for this
Country, in order to achieve immediate results regarding the control of
this disease, since Briano-Rodriguez et al. [2] reported a prevalence
of CD carriers of 2.61% in a population sample of HF calves using the
GeneSeek Genomic Proler — GGP — Bovine 50K genotyping panel.
Hence, the purpose of this study was to optimize and implement
a reliable and economical molecular screening procedure for the
detection of the 7.5 Kb mutant insert (BoERVK) of the APOB gene
through real-time PCR analysis with melting curve analysis (real-
time PCR-melting), as well as to obtain preliminary results on its
presence in a representative sample of HFc from the Dairy Cattle
deoxyribonucleic acid (DNA) Genomic Bank of Uruguay.
MATERIALS AND METHODS
DNA samples and reference population
It worked with a representative sample of 103 second-lactation
HFc of six commercial dairy farms from different Regions of Uruguay.
Genomic deoxyribonucleic acid (gDNA) from these samples was
stored in the Dairy Cattle DNA Genomic Bank of the Biotechnology
Unit (INIA Las Brujas) as reference material for research projects
(INML-UdelaR-INIA agreement). The extraction of these gDNA samples
was initially performed from fresh blood samples at the Nuclear
Techniques Laboratory (Facultad de Veterinaria, UdelaR) in 2008
using a digestion procedure with proteinase K and salting-out [18].
For optimization of the real-time PCR-melting, two gDNA samples
were used as reference controls for comparison with the patterns of
the melting curves to be analyzed. These control samples corresponded
to: (1) gDNA of a bull (ALTALeap 011HO12336) diagnosed as a carrier of
the CD mutation, and (2) gDNA of a bull (ALTABolero 011HO11572) free of
the disease; both from AltaGenetics company (Montevideo, Uruguay).
These gDNA samples were extracted from semen with the QIAamp DNA
mini kit, according to the manufacturer’s protocol #2.
gDNA was quantied in the NanoDrop equipment (NanoDrop 8000
Spectrophotometer, Thermo Fisher Scientic, USA), obtaining a range
between 1.8 and 2.0 for the OD260/OD280 ratio. The quality of the
gDNA samples was assessed by 1% agarose gel electrophoresis in
TBE 0.5X buffer [7].
Optimization of the genotyping of the BoERVK_APOB insertion
with real-time PCR-melting
Real-time PCR reactions were performed in a RotorGene™ 6000
(Corbett Life Science, Australia) on a nal volume of 25 microliters per
sample containing 50 nanograms of genomic DNA, 1X NZY qPCR Green
Master Mix (NZYTech Genes & Enzymes, Portugal), and 0.5 microMol of
each primer. A combination of three allele-specic primers designed by
Charlier et al. [5] was used. This combination of primers discriminates
the wild type from the mutated sequence and corresponds to a forward
primer (F1: 5’ AAG GAG GCT GCA AAG CCA CCT AG 3’) and two reverse
primers (mutant R1: 5’ CCT TTG TCA CGA GTG GAA TGC CT 3’; and R2:
5’ CCT CTT GAT GTT GAG GAT GTG TT 3’).
Dip tubes without gDNA were used as a negative control to identify
the possible contamination of reagents and the possible formation
of primer dimers in each PCR reaction mix.
The cycling program consisted of a 5 minutes (min) pre-hold at
95°C; and 40 cycles of 45 seconds (s) at 95°C, 40s at 55°C, and 40s at
72°C; with a 5 min stop-hold at 72°C. The annealing temperature was
adjusted to 55°C, with activation of uorescence data in the green
channel (excitation 470; detection 510 nanometers — nm—). The melting
peak was adjusted using 1°C increments with a 5s retention for each
increase from 75 to 95°C. Melting curve analyses were performed with
the Rotor-Gene Q Series Software 2.3.1 (Build 49) of the RotorGene™
6000 thermal cycler.
Electrophoresis was performed on a 3% agarose gel in 0.5X TBE buffer
[7] in order to assess primer function and specicity; upon completion
of the PCR reaction, the PCR products had the expected fragment size.
The expected fragment sizes for each amplicon are 170 bp for the wild-
type allele, and 146 bp and 120 bp for mutant alleles A and B, respectively.
Conrmation of results by sequencing and multiple sequence
alignment
To conrm the sequence identity of the amplicons identied by
real-time PCR-melting, 23 PCR samples were selected and sent
for sequencing (Humanizing Genomics Macrogen, Seoul, Korea).
Sequencing was performed using the primers of Charlier et al. [5].