Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Optimal population size to detect quantitative trait loci in Korean native chicken: a simulation study

  • Nwogwugwu, Chiemela Peter (Department of Animal Science, University of Calabar) ;
  • Kim, Yeongkuk (Division of Animal and Dairy Science, Chungnam National University) ;
  • Cho, Sunghyun (Division of Animal and Dairy Science, Chungnam National University) ;
  • Roh, Hee-Jong (Animal Genetic Resources Center, National Institute of Animal Science, RDA) ;
  • Cha, Jihye (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Lee, Seung Hwan (Division of Animal and Dairy Science, Chungnam National University) ;
  • Lee, Jun Heon (Division of Animal and Dairy Science, Chungnam National University)
  • Received : 2021.04.23
  • Accepted : 2021.08.16
  • Published : 2022.04.01
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Abstract

Objective: A genomic region associated with a particular phenotype is called quantitative trait loci (QTL). To detect the optimal F2 population size associated with QTLs in native chicken, we performed a simulation study on F2 population derived from crosses between two different breeds. Methods: A total of 15 males and 150 females were randomly selected from the last generation of each F1 population which was composed of different breed to create two different F2 populations. The progenies produced from these selected individuals were simulated for six more generations. Their marker genotypes were simulated with a density of 50K at three different heritability levels for the traits such as 0.1, 0.3, and 0.5. Our study compared 100, 500, 1,000 reference population (RP) groups to each other with three different heritability levels. And a total of 35 QTLs were used, and their locations were randomly created. Results: With a RP size of 100, no QTL was detected to satisfy Bonferroni value at three different heritability levels. In a RP size of 500, two QTLs were detected when the heritability was 0.5. With a RP size of 1,000, 0.1 heritability was detected only one QTL, and 0.5 heritability detected five QTLs. To sum up, RP size and heritability play a key role in detecting QTLs in a QTL study. The larger RP size and greater heritability value, the higher the probability of detection of QTLs. Conclusion: Our study suggests that the use of a large RP and heritability can improve QTL detection in an F2 chicken population.

Keywords

Acknowledgement

This work was carried out with the support of the "Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ0157852022)," Rural Development Administration, Republic of Korea.

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