Polymorphism of selected microsatellite DNA sequences in

Polymorphism of selected microsatellite DNA sequences in

Animal Science Papers and Reports vol. 24 (2006) Supplement 2, 71-77
Institute of Genetics and Animal Breeding, Jastrzębiec, Poland
Presented at the III Conference
“Genetic and environmental possibilities
of adjusting the slaughter value and meat quality
of animals to consumers’ requirements”
7-8 September 2006, Lublin-Krasnobród, Poland
Polymorphism of selected microsatellite
DNA sequences in Simmental cattle chosen
for identification of QTLs for meat traits
Bogumiła Choroszy1, Andrzej Janik2, Zenon Choroszy1, Tomasz Ząbek3
1
Department of Animal Genetics and Breeding, National Research Institute of Animal Production,
Krakowska 1, 32-083 Balice, Poland
2
Department of Animal Nutrition and Feed Science, National Research Institute of Animal
Production, Krakowska 1, 32-083 Balice, Poland
3
Department of Animal Immuno- and Cytogenetics, National Research Institute of Animal
Production, Krakowska 1, 32-083 Balice, Poland
The polymorphism of microsatellite DNA markers (TGLA227, BM2113, TGLA53, ETH10, SPS115,
TGLA126, TGLA122, INRA23, ETH3, ETH225, BM1824) was determined in Simmental bulls
chosen for identification of QTLs of meat traits. Genomic DNA isolated from blood was amplified
in a Gene Amp PCR System 9600 thermocycler in a multiplex PCR, using starter sequences from
the commercial Stock Marks for Cattle Parentage Verification Kit, Bovine II version 2”. Automated
DNA sizing technology was applied. The results showed that the 11 DNA microsatellite markers
considered were highly polymorphic and the selected population of Simmental bulls was highly
heterozygous. The microsatellite DNA sequences analysed could be useful for the identification of
QTLs for meat traits in Simmental cattle.
KEY Words: cattle / beef / meat traits / microsatellite DNA sequences / QTL / Simmental
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Bogumiła Choroszy et al.
Many cattle production traits of economic importance, such as milk yield, milk
composition, milk technological value, growth rate, carcass quality and meat quality,
are quantitative traits. The values of these traits result from overlapping of genes
known as quantitative traits loci (QTL) and environmental factors [Kurył 2000].
These genes can be identified and mapped by analysing their linkages with genetic
markers [Soller 1991]. The first studies on the linkages between QTL and genetic
markers were conducted using markers such as blood groups, polymorphic proteins or
histocompatibility antigens. The discovery of molecular markers such as microsatellite
DNA sequences and the development of methods for their analysis (identification)
opened up new possibilities for such studies. Microsatellite markers are highly
polymorphic and occur within the whole genome, which makes them a very useful
tool for the identification and mapping of QTL. The relationship or linkage between
a marker and the level of a quantitative trait can indicate the probable localization of
the gene affecting this trait on the same chromosome and in the area of the marker’s
locus [Kurył et al. 1997].
In most countries, and in Poland, Simmental cattle, one of the most popular
breeds in the world, represent the dual-purpose type, with good dairy traits and welldeveloped beef traits [Choroszy and Choroszy 2004a].
Because of selective breeding to improve meat performance, a considerable
increase in growth intensity has been achieved in the European population of cattle.
The standard of slaughtered cattle has been raised as a result of breeding for increased
carcass muscling without excessive fatness. Simmental cattle play a significant role in
beef production. Their bulls’ semen accounts for approximately 30% of inseminations
in commercial crossbreeding. High slaughter performance is characteristic not only
of purebred Simmentals, but also of their crosses with dairy breeds [Choroszy and
Choroszy 2004b]. The good beef performance of the breed in question and the great
interest from breeders result from consistent breeding work, in which the appropriate
selection of tested bulls for reproduction plays a significant role. A potentially
important element of breeding work is the preliminary selection of breeding bulls as
early as possible, by working out the genome of Simmental cattle and, if possible, by
identifying QTL(s) for meat traits [Janik et al. 2001, Sőlkner et al. 2005].
The identification of QTL for meat traits in Simmental cattle is organized into
three stages:
- the analysis of DNA polymorphism in Simmental bulls tested for meat traits
and chosen for the identification of QTL(s) for meat traits;
- the evaluation of meat traits in bulls from the population studied;
- the analysis of linkages between microsatellite loci and meat traits.
The aim of the present study, which is the first stage in research on the identification
of QTL for meat traits in Simmental cattle, was to determine the polymorphism of 11
DNA microsatellite sequences in a selected population and to evaluate their usefulness
for studies on the identification of QTL for meat traits.
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Adjusting the slaughter value and meat quality of animals to consumers’ requirements
Material and methods
A total of 92 Simmental bulls were used, station-evaluated for live and post mortem
meat traits. The meat traits to be analysed for linkages included net daily live weight
gain, carcass weight, meat content of carcass, and the area of the longissimus dorsi
muscle. The polymorphism of 11 microsatellite DNA markers (TGLA227, BM2113,
TGLA53, ETH10, SPS115, TGLA126, TGLA122, INRA23, ETH3, ETH225 and
BM1824) of known localization in the genome was determined in blood samples.
Genomic DNA isolated from blood samples was amplified in a Gene Amp PCR System
9600 thermocycler in a multiplex PCR, using starter sequences from the commercial
Stock Marks for Cattle Parentage Verification Kit, Bovine II version 2. Automated
DNA sizing technology was applied in an ABI PRISM 377 automatic DNA sequencer.
The size of the DNA fragments analysed and the genotype of the animals studied were
determined using specialist software (GeneScan v.2.1 and Genotyper 2.0).
The results were evaluated including (i) calculation of the frequency of the
alleles identified at particular loci after Lubieniecka et al. [1999], (ii) the degree of
heterozygosity (H) after Ott [1992] and (iii) the polymorphism information content
(PIC) after Botstein et al. [1980].
Results and discussion
Among the basic indicators most often used for analysing the polymorphism of
microsatellite DNA sequences in different breeds or populations of animals are the
number and frequency of alleles identified at individual loci, the effective number of
alleles per locus, the degree of hetero/homozygosity and the PIC.
In the Simmental population considered, a total of 80 alleles were identified at 11
loci of DNA microsatellites, their number ranging from four (loci ETH3 and BM1824)
to 16 (locus TGLA53). The mean number of alleles per locus was 7.27 (Tab. 1). In
10 of the 11 loci analysed, considerable differences were found in the frequency of
the identified alleles. High frequency was characteristic of all four alleles with 178
bp (0.1703), 180 bp (0.3297), 182 bp (0.1593) and 188 bp (0.3407) detected at the
BM1824 locus. Janik et al. [2001] also observed a high allele frequency (180 bp,
182 bp, 184 bp, 190 bp) at this locus in Simmentals. However, on the basis of earlier
research it is impossible to give conclusive reasons for the distribution of alleles at
this locus. Most of the microsatellite loci analysed presented high polymorphism, as
indicated by the number of alleles detected at particular loci and by the PIC value,
which was above 0.5. The most polymorphic of the 11 loci were: TGLA53 (16 alleles
with sizes ranging from 146 to 190 bp, PIC=0.851), TGLA227 (10 alleles ranging
from 77 to 97 bp, PIC=0.824), BM2113 (8 alleles ranging from 125 to 139 bp,
PIC=0.744), SPS115 (8 alleles ranging from 248 to 262 bp, PIC=0.615) and INRA23
(8 alleles ranging from 198 to 218 bp, PIC=0.665). The high polymorphism at these
loci in the Simmental breed has already been described by Janik et al. [2001]. Very
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Bogumiła Choroszy et al.
Table 1. Polymorphism at the 11 microsatellite loci in Simmental cattle raised in Poland
74
Locus
Number
of alleles
Alleles
Allele
frequency
TGLA227
10
77
79
81
83
87
89
91
93
95
97
BM2113
8
TGLA53
ETCH10
PIC*
H**
0.0110
0.0934
0.3022
0.0879
0.0879
0.0989
0.0879
0.0495
0.0275
0.1538
0.824
0.890
125
127
129
131
133
135
137
139
0.0220
0.1264
0.0055
0.3736
0.0824
0.0769
0.0879
0.2253
0.744
0.758
16
146
154
160
162
164
166
168
170
172
174
176
182
184
186
188
190
0.0055
0.1703
0.0275
0.0275
0.0824
0.0549
0.2033
0.1538
0.1648
0.0055
0.0220
0.0165
0.0330
0.0220
0.0055
0.0055
0.851
0.747
6
213
215
217
219
221
223
0.0055
0.0165
0.7418
0.1813
0.0165
0.0385
0.376
0.418
Adjusting the slaughter value and meat quality of animals to consumers’ requirements
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Bogumiła Choroszy et al.
high polymorphism at the TGLA53 locus was also reported by Heyen et al. [1997] in
American Simmentals.
The high degree of heterozygosity observed in 10 of the 11 DNA microsatellite
loci analysed (from 0.593 at the ETH3 locus to 0.890 at the locus TGLA227) shows
considerable variation within the Simmental population studied. A high heterozygosity
at the loci of the same set of microsatellites (from 0.580 at the TGLA126 locus to
0.880 at the locus TGLA227) in Simmental cattle was previously reported by Janik et
al. [2001]. For most of the loci considered, high PIC and H values (above 0.5) were
reported by Usha et al. [1995] who studied the polymorphism of other microsatellite
markers in British Simmental cattle, by Glowatzki-Mullis et al. [1995] in Swiss
Simmentals, and by Heyen et al. [1997] in American Simmentals.
The results of the present study confirm the high polymorphism of the 11
microsatellite DNA markers considered and the high heterozygosity of the analysed
Simmental population with reference to this group of markers. Moreover, they also
show that the analysed microsatellite DNA sequences are useful in studies on the
identification of QTL(s) for meat traits in Simmental cattle, after evaluation of their
meat performance and analysis of the linkages of these traits with DNA markers.
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Bogumiła Choroszy, Andrzej Janik,
Zenon Choroszy, Tomasz Ząbek
Polimorfzm wybranych sekwencji mikrosatelitarnych
bydła simentalskiego wytypowanego do badań
nad identyfikacją QTLs cech mięsnych
Streszczenie
W badaniach nad identyfikacją QTL cech mięsności buhajków simentalskich ocenianych pod
względem cech mięsnych określono polimorfizm wybranych sekwencji mikrosatelitarnych DNA.
Wykazano rozległy polimorfizm 11 użytych do badań markerów mikrosatelitarnych DNA oraz wysoką
heterozygotyczność analizowanej populacji bydła simentalskiego. Badane sekwencje mikrosatelitarne
DNA mogą być przydatne w identyfikacji QTLs cech mięsnych tego bydła.
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