Effect of Chromosome Number on Genomic Prediction Accuracy under Different Levels of Heritability

Genome structure may influence the accuracy of genomic prediction, but the effect of chromosome number under different levels of heritability remains insufficiently understood. This study evaluated the effects of chromosome number and heritability on genomic prediction accuracy using a controlled simulation framework. Four populations with ۵, ۱۰, ۲۰, and ۳۰ chromosomes were simulated, with each chromosome containing markers and QTL. Three heritability levels (۰.۱, ۰.۳, and ۰.۵) were considered, resulting in ۱۲ simulation scenarios with ۵۰ independent replicates per scenario. Genomic breeding values were predicted using GBLUP, and prediction accuracy was assessed as the Pearson correlation between genomic estimated breeding values and true breeding values. A two-way factorial ANOVA was used to evaluate the effects of chromosome number, heritability, and their interaction. Both chromosome number and heritability significantly affected prediction accuracy (P < ۰.۰۱), whereas their interaction was not significant (P = ۰). Mean prediction accuracy increased from ۰.۳۴ at heritability ۰.۱ to ۰.۶۹ and ۰.۸۴ at heritability ۰.۳ and ۰.۵, respectively. The five-chromosome population showed significantly higher accuracy (۰.۷۶) than the ۱۰-, ۲۰-, and ۳۰-chromosome populations (۰.۷۳, ۰.۶۵, and ۰.۶۲, respectively), while these three populations did not differ significantly. These results demonstrate that both trait heritability and genome-scale characteristics can affect GBLUP prediction accuracy and should be considered when designing and interpreting genomic prediction simulations.

کلیدواژه ها:

Genomic prediction ، GBLUP ، chromosome number ، heritability ، prediction accuracy ، genome architecture ، simulation study