Ornamental peaches cv. ‘Yaguchi’ (Prunus persica (L.) Batsch) can be propagated via seeds. The establishment of efficient seed treatments for early germination and seedling growth is required to shorten nursery and breeding periods. It is important, therefore, to identify potential candidate genes responsible for the effects of rinsing and chilling on seed germination. We hypothesized that longer rinsing combined with chilling of seeds can alter the genes expression in related to dormancy and then raise the germination rate in the peach. To date, most molecular studies in peaches have involved structural genomics, and few transcriptome studies of seed germination have been conducted. In this study, we investigated the function of key seed dormancy-related genes using next-generation sequencing to profile the transcriptomes involved in seed dormancy in peaches. De novo assembly and analysis of the transcriptome identified differentially expressed and unique genes present in this fruit. De novo RNA-sequencing of peach was performed using the Illumina Miseq 2000 system. Paired-end sequence from mRNAs generated high quality sequence reads (9,049,964, 10,026,362 and 10,101,918 reads) from ‘Yaguchi’ peach seeds before rinsed (BR) and after rinsed for 2 or 7 days with a chilling period of 4 weeks (termed 2D4W and 7D4W), respectively. The germination rate of 7D4W was significantly higher than that of 2D4W. In total, we obtained 51,366 unique sequences. Differential expression analysis identified 7752, 8469 and 506 differentially expressed genes from BR vs 2D4W, BR vs 7D4W and 2D4W vs 7D4W libraries respectively, filtered based on p-value and an adjusted false discovery rate of less than 0.05. This study identified genes associated with the rinsing and chilling process that included those associated with phytohormones, the stress response and transcription factors. 7D4W treatment downregulated genes involved in ABA synthesis, catabolism and signaling pathways, which eventually suppressed abscisic acid activity and consequently promoted germination and seedling growth. Stress response genes were also downregulated by the 7D4W treatment, suggesting that this treatment released seeds from endodormancy. Transcription factors were upregulated by the BR and 2D4W treatment, suggesting that they play important roles in maintaining seed dormancy. This work indicated that longer rinsing combined with chilling affects gene expression and germination rate, and identified potential candidate genes responsible for dormancy progression in seeds of ‘Yaguchi’ peach. The results could be used to develop breeding programs and will aid future functional genomic research in peaches and other fruit trees.

Lotus root ( Nelumbo nucifera ) is an edible rhizome that the consumption/production has continuously increased as more consumers demand convenient and ready-to-eat foods. However, the processing, storage, and transportation of fresh-cut fruits and vegetables promotes physiological deterioration, such as browning, which leads to a reduction in the value of the product. This study aimed to reduce the browning of lotus root pericarps during long-term storage and long-distance transport , and to clarify the functions of unigenes and browning-associated metabolic pathways using RNA-sequencing techniques. Intact lotus root cv. ‘Kanasumi No.34’ browning decreased after the roots were packed along with an anti-browning solution . Over 200 million short single-end reads were mapped onto the N. nucifera consensus coding sequence set. The significantly differentially expressed genes (DEGs) were identified. Based on the Uniprot, GO, and KEGG databases, secondary metabolism, lipid metabolism, and redox state genes were significantly upregulated in the un-packed (UP) and packed with water (PW) treatments compared to after harvest (AH) sample. Additionally, 16 expected differentially expressed genes (e.g., PPO, PAL, POD, CHS , PDCR , and SOD ), which are affected by browning development, were differentially regulated in lotus root pericarp. The gene expression data presented in this study will help elucidate the molecular mechanism underlying browning development in intact lotus root during long-term storage. The results may also inform future research on improving the post-harvest life of lotus roots.