The impact of QTL allele frequency distribution on the accuracy of genomic prediction.

摘要: Abstract. The accuracy of genomic prediction quantitative traits based on single nucleotide polymorphism (SNP) markers depends among other factors the allele frequency distribution trait loci (QTL). Therefore, aim this study was to investigate different QTL frequency distributions and their effect estimated breeding values (GEBVs) using best linear unbiased prediction (GBLUP) in simulated data. A population 1000 individuals composed 500 males and 500 females as well as a genome 1000 cM consisting 10 chromosomes with mutation rate 2.5  ×  10 −5 per locus simulated. frequencies were derived from five including constant, uniform, U-shaped, L-shaped minor frequency (MAF) less than 0.01 (lowMAF). effects were generated standard normal distribution. number assumed be 500, simulation was done 10 replications. first-validation generation constant, uniform distribution was 0.59 and 0.57, respectively. Results showed that highest of GEBVs obtained constant followed by L-shaped, U-shaped and lowMAF distribution. regression true breeding values predicted generation was 0.94, 0.92, 0.88, 0.85 and 0.75 for L-shaped, U-shaped distributions, Depite values of coefficients, all scenarios GEBVs are biased downward. Overall, results when had lower MAF relative SNP markers, low linkage disequilibrium (LD) observed, which negative effect GEBVs. Hence, can be alleviated through using genomic relationship weighted or an LD-adjusted relationship matrix.