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].