Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
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Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle

  • Shil Jin (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Jeong Il Won (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Hyoun Ju Kim (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Byoungho Park (Animal Breeding & Genetics Division, National Institute of Animal Science) ;
  • Sung Woo Kim (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Ui Hyung Kim (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Sung-Sik Kang (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Hyun-Jeong Lee (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Sung Jin Moon (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Myung Sun Park (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Yong Teak Sim (miDNA Genome Research institute) ;
  • Sun Sik Jang (Hanwoo Research Institute, National Institute of Animal Science) ;
  • Nam Young Kim (Hanwoo Research Institute, National Institute of Animal Science)
  • Received : 2023.09.17
  • Accepted : 2024.01.23
  • Published : 2024.07.31
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Abstract

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 PIhalf-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 exclusion1 (PE1) 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 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 triand 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.

Keywords

Acknowledgement

Thank you to all members of the Hanwoo Research Institute for their efforts.

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