Differences in physiological characteristics and gene expression levels in fruits between Japanese persimmon (Diospyros kaki thunb.) ‘Hiratanenashi’ and its small fruit mutant ‘Totsutanenashi’

Japanese persimmon ‘Totsutanenashi’ (TTN) is a spontaneous small fruit mutant derived from ‘Hiratanenashi’ (HTN). To characterize the small fruit phenotype of TTN, we carried out a histological analysis, plant growth regulator treatments, and a transcriptome analysis using Illumina sequencing. The parenchymal cell number in TTN fruit was significantly less than in HTN fruit, and the parenchymal cell size in TTN fruit was also significantly smaller than that in HTN fruit at the later growing stage. However, the fruit size of TTN recovered by cytokinin treatments [50 or 200 ppm N-(2-chloro-4-pyridyl)-N′-phenylurea]. Thus, diminished cytokinin activity in TTN fruits may lead to less cell division in the early growing stage and less cell enlargement in the later growing stage. A large-scale transcriptome analysis was conducted using Illumina sequencing to determine the differences in gene expressions between TTN and HTN fruits. Illumina sequences were processed, resulting in 21,662,190 read pairs from HTN and 23,195,203 read pairs from TTN. After assembly of all sequences from HTN and TTN, 118,985 contigs (referred to as unigenes hereafter) ranging from 201 to 11,954 bases, with an average length of 915 bases, were obtained. Digital expression analyses revealed that the expression levels of 164 unigenes were significantly higher in HTN than in TTN, while the expression levels of 265 unigenes were significantly higher in TTN. A parametric analysis of gene set enrichment using the expression levels of unigenes showed that the biological process Gene Ontology categories of “cell cycle” and “regulation of cell cycle” were significantly down-regulated in TTN. The cell cycle-related differentially expressed genes included D3-type cyclin and Mitogen-Activated Protein Kinase Kinase Kinase. Based on the obtained results, the possible involvement of cell cycle-related genes in regulating the small fruit phenotype in TTN is discussed.