Genomic selection for growth characteristics in Korean red pine (Pinus densiflora Seibold & Zucc.)

Abstract

Traditionally, selective breeding has been used to improve tree growth. However, traditional selection methods are time-consuming and limit annual genetic gain. Genomic selection (GS) offers an alternative to progeny testing by estimating the genotype-based breeding values of individuals based on genomic information using molecular markers. In the present study, we introduced GS to an open-pollinated breeding population of Korean red pine (Pinus densiflora), which is in high demand in South Korea, to shorten the breeding cycle. We compared the prediction accuracies of GS for growth characteristics (diameter at breast height [DBH], height, straightness, and volume) in Korean red pines under various conditions (marker set, model, and training set) and evaluated the selection efficiency of GS compared to traditional selection methods. Training the GS model to include individuals from various environments using genomic best linear unbiased prediction (GBLUP) and markers with a minor allele frequency larger than 0.05 was effective. The optimized model had an accuracy of 0.164–0.498 and a predictive ability of 0.018–0.441. The predictive ability of GBLUP against that of additive best linear unbiased prediction (ABLUP) was 0.86–5.10, and against the square root of heritability was 0.19–0.76, indicating that GS for Korean red pine was as efficient as in previous studies on forest trees. Moreover, the response to GS was higher than that to traditional selection regarding the annual genetic gain. Therefore, we conclude that the trained GS model is more effective than the traditional breeding methods for Korean red pines. We anticipate that the next generation of trees selected by GS will lay the foundation for the accelerated breeding of Korean red pine.