Marker-assisted seedling selection (MASS) has much potential to improve the efficiency of traditional apple breeding. Theoretical and empirical evaluation of selection cost and theoretical evaluation of genetic gain in previous studies support this promise. However, there is a lack of empirical validation of MASS efficiency reported in tree fruit crops for genetic gain and cost nor even genetic gain alone. To determine the optimal way of conducting MASS especially when genotypic information is less predictive than phenotypic information, which is the case for many quantitative traits, this study evaluated the genetic gain and cost of applying a multi-locus DNA test targeting fruit acidity, crispness, and firmness in a multi-family apple seedling population. Variance component analysis indicated that the DNA test explained 12%, 16%, and 17% of the additive variance of apple acidity, crispness, and firmness, respectively. Two-stage seedling selection was estimated to outperform traditional seedling selection for both genetic and cost efficiency: when 70% of the total seedlings were selected in the first stage based on marker score and 20% in the second stage based on phenotype, compared to phenotypic selection, two-stage selection identified 4% more individuals with breeding values within target ranges for acidity and firmness while achieving selection cost savings at DNA testing prices of less than $4.5/sample. This empirical validation of MASS suggested that when predictiveness of a DNA test is lower than heritabilities of the traits, properly weighting genotypic and phenotypic information through two-stage selection can lead to a higher genetic gain while reducing selection cost compared to phenotypic seedling selection.

标记辅助幼苗选择（MASS）在提高传统苹果育种效率方面具有巨大潜力。在先前的研究中，选择成本的理论和经验评估以及遗传增益的理论评估都支持这一前景。然而，缺乏对树果作物中关于遗传增益和成本甚至仅遗传增益的MASS效率的经验验证。为了确定进行MASS的最佳方法，尤其是当基因型信息的预测性不如表型信息（对于许多定量性状而言）时，本研究评估了针对水果酸度，松脆度，应用多位点DNA测试的遗传收益和成本多科苹果幼苗种群中的硬度和硬度。方差成分分析表明，DNA测试可解释12％，16％，和分别为苹果酸度，松脆度和硬度的17％的累加变化。在遗传和成本效率方面，估计两阶段苗的选择优于传统幼苗选择：与表型相比，第一阶段基于标记得分选择的幼苗总数为70％，第二阶段基于表型选择的幼苗总数为20％筛选，分两个阶段进行筛选，可确定多出4％的个体，其育种值在酸度和坚固度目标范围内，同时以DNA测试价格低于$ 4.5 /样品实现选择成本节省。对MASS的经验验证表明，当DNA测试的预测性低于性状的遗传力时，