Plant Genomics and Plant Science

Strawberry (Fragaria × ananassa) was artificially generated in the 16th century Europe by crossing between two octoploid species, F. chiloensis and F. virginiana. It is cultivated and consumed entire the world. Strawberry is an allo-polyploidy species  (2n = 8X = 56) with an estimated genome size of 1C = 708–720 Mb. The complex structure of the polyploid genome has inhibited advances in genomics and genetic analysis We have sequenced a Japanese variety ‘‘Reikou’ with Illumina platform, and constructed subgenome-specific reference sequences by using DenovoMAGIC. A total of 62 (31 × 2 haplotypes) pseudomolecules were developed based on the linkage map in a total length of 1,125 Mb. The large structure differences among the sub-genomes were identified by comparison with the F. vesca genome. By using the constructed pseudomolecules, we have performed RNA-Seq analysis in fruit color. Genomic selection for fruit hardiness has also performed with the four strawberry breeding stations, i.e., National Agricultural Research Organization, Tochigi prefecture, Fukuoka prefecture and Chiba prefecture. The conventional GS requires genome wide genotyping for the both training and breeding populations. To decrease the cost and time for genotyping in the breeding population, we used Ensemble-based Genetic and Genomic Search (EGGS) that enable to make a model with less number of DNA markers. Genomic, genetic analysis and molecular breeding in polyploidy species is still difficult, however, the advance of NGS technologies as well as novel approaches for data analysis has made the challenge possible.