Propagation path of a flowering cherry (Cerasus × yedoensis) cultivar 'Somei-Yoshino' traced by somatic mutations.

In the long history of human relations with flowering cherry trees in Japan, 'Somei-Yoshino' occupies an exceptional position among a variety of flowering trees: it is a self-incompatible interspecific hybrid but has been enthusiastically planted by grafting throughout Japan, due most likely to its flamboyant appearance upon full bloom. Thus, 'Somei-Yoshino' gives us a rare opportunity to trace and investigate the occurrence and distribution of somatic mutations within a single plant species through analysis of the genomes of the clonally propagated trees grown under a variety of geographical and artificial environments. In the studies presented here, a total of 46 samples of 'Somei-Yoshino' trees were collected and their genomes were analyzed. We identified 684 single nucleotide mutations, of which 71 were present in more than two samples. Clustering analysis of the mutations indicated that the 46 samples were classified into eight groups, four of which included 36 of the 46 samples analyzed. Interestingly, all the four tree samples collected in Ueno Park of Tokyo were members of the four groups mentioned above. Based on comparative analysis of their mutations, one of the four trees growing in Ueno Park was concluded to be the closest to the original ancestor. We propose that somatic mutations may be used as tracers to establish the ancestral relationship amongst clonally propagated individuals.

Allele-Specific Mutation Genotyping with Mismatches in Primer Design.

Genotyping technologies for single nucleotide polymorphisms (SNPs) and other mutation types have evolved to become essential tools in various fields. Although high-throughput genotyping technologies occupy a key position in handling large amounts of SNP data, simple, low-cost, and conventional genotyping technologies remain in demand. Allele-specific (AS) polymerase chain reaction (PCR) and its related improved methods can effectively identify target SNPs and allele types using AS primers that introduce instability through mismatched bases at and around the SNP site. In this chapter, we present what is known from the literature on primer design with mismatches for AS-PCR and describe three cases of mutation detection (SNPs and insertions/deletions) associated with functional genes of crop species, which could be useful to guide future AS-PCR experiments.

Effects of freeze-drying of samples on metabolite levels in metabolome analyses.

Freeze-drying (FD) is a useful technique for removing water from biological tissues, such as food samples. Cellular components freeze at once, and the ice sublimates under conditions of high vacuum and low temperatures. Because biological activity is restricted during FD, the degradation of cellular metabolites is often believed to be limited. However, the cellular structure is damaged by several factors, such as the increase in cell volume during freezing, and this has serious effects on the levels of some cellular metabolites. We studied these effects of FD on metabolite levels when using it as a sample preparation step in metabolome analysis. We observed significant decreases in the levels of some metabolites, such as succinate and choline, in Arabidopsis and pear, respectively. We also found that the effects of FD on certain metabolite levels differed between Arabidopsis plants and pear fruits. These results suggest that it is necessary to confirm the metabolite recovery in each sample species when FD is used for sample preparation.

Development of an Agrobacterium-mediated transformation method for pear (Pyrus communis L.) with leaf-section and axillary shoot-meristem explants.

We have developed a new Agrobacterium-mediated transformation method for the low-frequency-regenerating pear (Pyrus communis L.) cvs. Silver bell and La France. Leaf sections derived from in vitro shoots were initially used for the transformation procedure. Under optimum transformation conditions, which included culture and selection on 30 mg/l kanamycin (Km) combined with 500 mg/l sulbenicillin, a 3.2% transformation efficiency was obtained for cv. Silver bell, but no transformants of La France were obtained because of the very low regeneration frequency. Axillary shoot meristems were then examined as potential explants for La France. Selection in 5 mg/l Km and 375 mg/l carbenicillin resulted in transformed shoots being produced at an efficiency of 4.8%, and the apparent white Km-sensitive shoots were not formed during a 2-year subculture on micropropagation medium containing 50 mg/l Km. Therefore, transformations using axillary shoot meristems may be an alternative method for pear cultivars recalcitrant to regeneration from leaf sections.

Direct observations of the redox states of frozen cherry buds by a unique in vivo ESR.

Low temperatures cause cellular damage in flower buds of the sweet cherry (Prunus avium L. cv. Satohnishiki). In this study, the redox states within the cherry buds suffering freezing damage were non-destructively observed by a unique in vivo electron spin resonance (ESR) technique with a spin probe such as carbamoyl-PROXYL. The ESR signals of carbamoyl-PROXYL-treated bud were continuously recorded under freezing and thawing condition, which was decreased to approximately -4 degrees C and maintained for 1.5h, and then returned to room temperature. Most of the buds began to freeze at -2.5 to -3.9 degrees C. The peak areas of the ESR signals significantly increased during the period of temperature rise. These results show that the reduced carbamoyl-PROXYL within the frozen bud was re-oxidized and became ESR-detectable while the bud was thawing. Our in vivo ESR technique has confirmed the oxidative transition of the redox states within the buds during thawing.