Identification of Quantitative Trait Loci of Fruit Quality and Color in Pineapples

The pineapple (Ananas comosus (L.) Merr.) is an economically important tropical fruit crop. In this study, we performed quantitative trait locus (QTL) analysis using 168 individuals of the F₁ population of ‘Yugafu’ × ‘Yonekura’ for 15 traits: leaf color (L*, a*, b*), harvest day, crown number, slip number, stem shoot number, sucker number, fruit weight, fruit height, fruit diameter, fruit shell color, soluble solid content, acidity, and ascorbic acid content. The constructed single-nucleotide polymorphism (SNP)-based genetic linkage map consisted of a total genetic distance of 2,595 cM with 3,123 loci, including 22,330 SNPs across 25 chromosomes. QTL analysis detected 13 QTLs for 9 traits: leaf color a*, harvest day, fruit weight, fruit height, fruit diameter, fruit shell color, soluble solid content, acidity, and ascorbic acid content. The causative gene for each QTL was predicted with two genes identified as candidate genes. The AcCCD4 gene on Aco3.3C08 was the predicted causative gene for the shell color QTL, which negatively controls shell color by carotenoid degradation. The Myb domain protein-encoding gene on Aco3.3C02 was the predicted causative gene for shell color and leaf color a* QTL, which positively regulates anthocyanin accumulation. The QTL and gene information provided here contributes to future marker-assisted selection for fruit quality.