Quantitative trait locus analysis of the F₁ breeding population of 180-1-08 × ‘Del Monte Gold’ pineapples

Pineapples (Ananas comosus L.) are widely cultivated in tropical and subtropical regions including in Okinawa, Japan. In Okinawa, DNA marker assisted selection (MAS) has been employed for selecting qualitative traits in pineapples. However, quantitative trait locus (QTL) based MAS has not yet been utilized as QTLs in pineapples were previously unidentified. To proceed with effective MAS for breeding selection, QTLs and their associated effects must be identified. In this study, we performed restriction-site associated sequencing (RAD-Seq) and QTL analysis for 108 individuals from the F1 population of the pineapple breeding line 180-1-08 × ‘Del Monte Gold’ For QTL analysis, 20 traits were evaluated – fruit flesh color (visual observation, L*, a*, b*), carotenoid contents (violaxanthin, cis-violaxanthin, lutein, β-cryptoxanthin, α-carotene, zeaxanthin, β-carotene, and total carotenoid), harvest day, slip number, stem shoot number, sucker number, fruit weight, soluble solids content, acidity, and ascorbic acid content. All traits were evaluated in 2016, without replications. Double digest RAD-Seq analysis and genetic linkage map construction using Lep-map3 software generated a saturated linkage map of 4,082 loci with 63,238 single nucleotide polymorphisms in 26 linkage groups, which covered 25 pseudomolecules in the pineapple genome. QTL analysis detected color related QTLs; fruit color a* (detected on chromosome 4), β-cryptoxanthin content (chromosome 9, 13 and 14), β-carotene content (chromosome 4 and 6), violaxantnin (chromosome 6), and lutein (chromosome 2). The QTL information identified in this study could contribute to effective marker-assisted selection for enhanced fruit quality.