title: Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch).
abstract: 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.
authors: United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.|Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
authors: Worarad
authors: W
authors: Kanjana
authors: Bioscience Education and Research Center, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
authors: Tomohiro
authors: T
authors: Suzuki
authors: Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
authors: Kazuo
authors: K
authors: Ishii
authors: Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
authors: Toshinori
authors: T
authors: Kozaki
authors: Bioscience Education and Research Center, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.|Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
authors: Masayuki
authors: M
authors: Iigo
authors: Bioscience Education and Research Center, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan. yamane@cc.utsunomiya-u.ac.jp.|Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan. yamane@cc.utsunomiya-u.ac.jp.
authors: Kenji
authors: 0000-0003-0255-0842
authors: K
authors: Yamane
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018525:Germination / Q000235:genetics; D058977:Molecular Sequence Annotation; D057445:Plant Dormancy / Q000235:genetics*; D000068239:Prunus persica / Q000235:genetics*; D015203:Reproducibility of Results; D012639:Seeds / Q000235:genetics*; D059467:Transcriptome
keywords: Chilling; Ornamental peach; Rinsing; Seed germination; Transcriptome