The Hanwoo traceability system currently utilizes 11 dinucleotide repeat
microsatellite (MS) markers. However, dinucleotide repeat markers are known to
have a high incidence of polymerase chain reaction (PCR) artifacts, such as
stutter bands, which can complicate the accurate reading of alleles. In this
study, we examined the polymorphisms of the 11 dinucleotide repeat MS markers
currently employed in traceability systems. Additionally, we explored four
trinucleotide repeat MS markers and one tetranucleotide repeat MS marker in a
sample of 1,106 Hanwoo cattle. We also assessed the potential utility of the
tri- and tetranucleotide repeat MS markers. The polymorphic information content
(PIC) of the five tri- and tetranucleotide repeat markers ranged from 0.663 to
0.767 (mean: 0.722), sufficiently polymorphic and slightly higher than the mean
(0.716) of the current 11 dinucleotide repeat markers. Using all 16 markers, the
mean PIC was 0.718. The estimated probability of identity (PI) was 3.13 ×
10
−12
using the 11 dinucleotide repeat markers, 7.03
× 10
−6
using the five tri- and tetranucleotide repeat
markers, and 2.39 × 10
−17
using all 16 markers; the
respective PI
half-sibs
values were 2.69 ×
10
−9
, 1.29 × 10
−4
, and 3.42
× 10
−13
; and the respective PIsibs values were 3.89
× 10
−5
, 9.6 × 10
−3
, and 3.69
× 10
−7
. The probability of exclusion
1
(PE
1
) was 0.999864 for the 11 dinucleotide repeat markers,
0.981141 for five of the tri- and tetranucleotide repeat markers, and >
0.99 for all 16 markers; the respective PE
2
values were 0.994632,
0.901369, and > 0.99; and the respective PE
3
values were
0.998702, > 0.99, and > 0.99. The five investigated tri- and
tetranucleotide repeat MS markers can be used in combination with the 11
existing MS markers to improve the accuracy of individual identification and
paternity testing in Hanwoo.
