Genome-wide association study of pineapple breeding population

Pineapples (Ananas comosus (L.) Merr.) are one of the most important tropical fruits. Although pineapple breeding program has been conducted in Japan, sufficient genomic information has not been adopted for breeding. The objective of this study was to identify quantitative trait loci (QTL) for pineapple breeding-related traits that can be applied to different populations. Here, we performed a genome-wide association study using seven breeding populations, including 703 individuals with genome-wide 9574 SNPs. Eleven QTLs were detected for nine traits (flesh color, flesh color values (a*, b*), bolting days, days from bolting to harvest, fruit shell color, soluble solid content, acidity, ascorbic acid content, and fruit cracking). Phenotypic value of each genotype in each population was confirmed for each QTL. Six QTLs (acidity QTL ACID-1, ascorbic acid QTL AsA-1 and AsA-2, flesh color QTL FCOL-1 and FCOLb-1, and fruit-cracking QTL CRACK-1) showed significant intergenotypic variance among all populations with genotype segregation. The obtained QTLs and their genotype information will contribute to the selection of cross-breeding parents and marker-assisted selection in pineapple breeding programs.