Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle

The Hanwoo traceability system currently includes 11 dinucleotide repeat microsatellite (MS) markers; however, dinucleotide repeat markers have a reported high incidence of PCR artifacts, such as stutter bands, making it difficult to read alleles accurately. Therefore, we analyzed the polymorphisms of 11 dinucleotide repeat MS markers, four trinucleotide repeat MS markers, and one tetranucleotide repeat MS marker in 1,106 Hanwoo cattle. We further investigated the 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 PI_sibs values were 3.89 × 10⁻⁵, 9.6 × 10⁻³, and 3.69 × 10⁻⁷. The probability of exclusion₁ (PE₁)was 0.999864 for the 11 dinucleotide repeat markers, 0.981141 for five the tri- and tetranucleotide repeat markers, and > 0.99 for all 16 markers; the respective PE₂ values were 0.994632, 0.901369, and > 0.99; and the respective PE₃ 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.