Selection Efficiency of Marker-assisted Selection for a Single Quantitative Trait Locus of Soluble Solids Content with Low Genetic Contribution in a Pineapple (Ananas comosus (L.) Merr.) Cross-seedling Population

Marker-assisted selection (MAS) using DNA markers linked to a single or a few quantitative trait loci (QTL) with low genetic contribution has not been effectively and practically applied due to the significant loss of target offspring. High sugar content (soluble solids content, SSC) is an important breeding goal for fresh pineapple in Japan. We investigated the efficiency of MAS performed before primary phenotypic selection for a first-fruited F₁ pineapple population of ‘Yugafu’ × ‘Yonekura’ for a single QTL with 11.6% genetic contribution controlling SSC. Four genotypes at this QTL were detected by a SNP marker and segregated 1:1:1:1. Statistical analysis was performed using logSSC values. The logSSC means in the four genotypes were significantly separated, the distributions within each genotype were close to normal distribution, and the variances within genotypes were not significantly different. The target offspring (> 17 Brix%) in this population was estimated to be 5.3%. Among four genotypes in the QTL, MAS of selecting the genotype with the highest mean SSC and MAS of selecting the top two genotypes for mean SSC were called 25% MAS and 50% MAS, respectively. Selection efficiency (Se) was defined as the ratio of the target offspring selected by MAS to the target offspring present in the initial population before MAS. Se was 0.51 and 0.81 for 25% and 50% MAS, respectively, resulting in a loss of 49% and 19% of the target offspring. To compensate for this loss and obtain the same number of target offspring achieved by conventional phenotypic selection without MAS, the initial population needed to be increased by ×(1/Se), which was defined as the effective MAS scale (EMSS). The EMSS was 1.95 and 1.24 for 25% MAS and 50% MAS, respectively, and the population sizes after MAS were 0.49 and 0.62 times the population without MAS, respectively, indicating a small difference between the 25% and 50% MAS. Considering this result and the cost of MAS, 50% MAS was recommended over 25% MAS for the population. These results showed that efficient MAS without reducing the number of target offspring was achievable by expanding the initial population size by EMSS.