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

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Genomic Analysis

Background:

• Quantitative trait loci (QTLs) are genomic regions linked to specific phenotypes.
• Identifying optimal population sizes for QTL detection is essential for efficient genetic studies in livestock.

Purpose of the Study:

• To determine the optimal reference population (RP) size for detecting quantitative trait loci (QTLs) in native chicken F2 populations.
• To evaluate the impact of heritability on QTL detection efficiency in simulated F2 chicken populations.

Main Methods:

• Simulated F2 chicken populations derived from crosses between two breeds.
• Marker genotypes simulated at 50K density across three heritability levels (0.1, 0.3, 0.5).
• Compared RP sizes of 100, 500, and 1,000 individuals for QTL detection.

Main Results:

• No QTLs were detected with an RP size of 100 across all heritability levels.
• An RP size of 500 detected two QTLs at a heritability of 0.5.
• An RP size of 1,000 detected one QTL at 0.1 heritability and five QTLs at 0.5 heritability.

Conclusions:

• Reference population size and heritability are critical factors for successful QTL detection.
• Larger reference populations and higher heritability values increase the probability of detecting QTLs in F2 chicken populations.
• Utilizing large RPs and considering heritability can enhance QTL detection strategies in poultry breeding programs.