Efficiency of genomic selection for developing superior pure lines

Abstract Developing elite pure lines is the most common breeding process for self-pollinating crops. The objective of this study was to assess the efficacy of genomic selection in pure line breeding, using a simulated dataset from F₂ plants to F₈ selected progeny. The simulated genome included 1000 genes and 49825 SNPs, distributed on 10 chromosomes of 100 cM. We used genomic selection with partial phenotyping over generations and phenotyping only in F₂. We assessed the significance of selection intensity, training set size, selecting in F₂, dominance, and major genes. The efficacy of the genomic selection was based on genetic gains and probability of selecting elite pure lines. Genomic selection with partial phenotyping in each cycle maximized the probability of selecting superior F₈ progeny and provided the higher total genetic gain, comparable to the selection based on the true genotypic value. Training set size and selection intensity are important factors affecting the development of elite pure lines. Dominance does not significantly affect the genomic selection efficiency. The existence of QTLs increases the genomic selection efficiency, proportional to the proportion of the phenotypic variance explained by the QTLs. There is no justification for selecting in F₂. Pedigree-based BLUP cannot be disregarded as a genetic assessment method in pure line breeding. All selection methods provided high decrease in the genotypic variance at F₈. The prediction accuracies with genomic selection showed almost perfect correlation with the genetic gains. A challenger in pure line breeding is minimizing the random fixation of the unfavorable alleles in heterozygotes.