Progress in Genomics-based Breeding of Tropical Fruit Tree Species

Tropical fruits, including bananas (Musa accuminata Colla), pineapples (Ananas comosus (L.) Merr.), and mango (Mangifera indica L.), are important edible fruits worldwide. The breeding of tropical fruit tree species poses many challenges compared with the breeding of annual crops because of their long juvenile period and the high cost of raising individuals to maturity in the field. With progress in next-generation sequencing (NGS) technologies, genome sequencing and identification of trait-associated loci have greatly progressed in recent years. The whole-genome sequences of most of the major tropical fruit tree species have been reported. Recent high-accuracy long-read sequencing technologies have enabled telomere-to-telomere and haplotype-resolved genome sequencing. These technologies have also been adopted for the genome sequencing of tropical fruit tree species. Quantitative trait locus (QTL) mapping and genome-wide association studies based on NGS technologies have been conducted on tropical fruit tree species to detect trait-associated loci. These analyses helped identify multiple QTLs that may contribute to efficient breeding selection. Two issues have been raised when applying QTL information to breeding selection in pineapple programs in Japan. The first is the adaptability of various populations, for which developing haplotype-resolved QTL information has been proposed as a solution. The second is to consider multiple QTLs among multiple traits in DNA-based selection. To utilize multiple QTLs among multiple traits for DNA-based breeding selection, a scheme for accumulating preferred alleles has been proposed and applied to pineapple breeding programs in Japan.