Optimal population size to detect quantitative trait locus in Korean native chicken: a simulation study

Objective A genomic region associated with a particular phenotype is called QTL. To detect the optimal F_2 population size associated with QTLs in native chicken, we performed a simulation study on F_2 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 F_1 population which was composed of different breed to create two different F_2 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 is that to compare 100, 500, 1000 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 shows that five QTLs were detected. To sum up, RP size and heritability are playing a key role to detect QTLs in 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 F_2 chicken population.