Transposable elements (TEs) are mobile genetic elements in the eukaryotic genome. They are divided into two classes (class I: retrotransposons and class II: DNA transposons) based on their structure and manner of transposition. TEs are major components of the eukaryotic genome and retrotransposons are especially abundant in higher-plant genomes. As retrotransposon insertions with high copy numbers are dispersed throughout the genome and are inherited genetically, insertion polymorphisms among crop cultivars have been used as molecular markers. Recently, we developed an efficient method for screening the long terminal repeats (LTRs) of retrotransposon families that exhibit high levels of insertion polymorphisms among crop cultivars using a next-generation sequencing (NGS) platform. This method focuses on the primer binding site (PBS) that is adjacent to the 5' LTR and has a conserved DNA sequence among different LTR retrotransposon families. Construction of a sequencing library through PCR amplification using the PBS conserved sequence allowed us to acquire a large number of LTR sequences and their insertion sites throughout the genome. From our data analysis, we screened the LTR sequences that showed high levels of insertion polymorphism among closely related cultivars. In addition, we identified the insertion sites of these identified LTR retrotransposon families at the genome-wide scale in a number of cultivars with an NGS platform, which enabled us to reveal the genetic relationships among the cultivars and acquire a number of molecular markers for cultivar screening. Our results indicated that the target sequencing of these retrotransposon insertion sites was highly effective for DNA genotyping and marker development without requiring any whole-genome sequence information. This review describes the genomic structure and evolutionary aspects of TEs and discusses the development of molecular markers based on retrotransposon insertion polymorphisms.

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The effect of bark washing with a high-pressure washer on deciduous trees contaminated during dormancy by radiocaesium fallout derived from the Fukushima Daiichi Nuclear Power Plant accident was examined using peach [Prunus persica (L.) Batsch] and Japanese persimmon (Diospyros kaki Thunb.). Eighteen-year-old peach trees (‘Akatsuki’) were bark-washed twice with a high-pressure washer on July 5 and 27, 2011. Seven-year-old peach trees (‘Kawanakajima Hakuto’) were bark-washed on January 24, 2012, and thirty-year-old Japanese persimmon trees (‘Hachiya’) were bark-washed on December 21, 2011. For the peach trees, most of the bark was not removed by washing with a high-pressure washer. In contrast, the rough bark of Japanese persimmon was removed completely. No significant differences in the ¹³⁷Cs concentration of ‘Akatsuki’ fruit were found between the treatments conducted in the summer of 2011. Upon the bark washing of peach ‘Akatsuki’ trees in summer, the possibility of secondary contamination of leaves via the leachate containing ¹³⁷Cs was likely. The ¹³⁷Cs concentrations in fruits and leaves of peach ‘Kawanakajima Hakuto’ collected in summer 2012 were decreased significantly by washing treatment conducted in winter 2011–2012. In the year after treatment, the ¹³⁷Cs concentrations in fruits and leaves of Japanese persimmon were significantly decreased by the treatment. The effect of the bark washing on decreasing ¹³⁷Cs contents in fruits and leaves was greater in Japanese persimmon than in peach. The results for ‘Kawanakajima Hakuto’ and ‘Hachiya’ demonstrated the possibility of additive contamination.

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Ionomic analysis was performed in three diverse fruit crops in order to characterize element concentrations in edible parts and to compare element concentrations between edible parts and vegetative organs and between species. Nineteen elements, including elements essential for human health, toxic elements, and elements with radioisotopes from nuclear reactors, were analyzed in apple (Malus domestica), Japanese pear (Pyrus pyrifolia), eggplant (Solanum melongena), and edamame (Glycine max). The concentrations of elements were shown as basic information needed for biofortification, and high mobilities depending on plant species were found for some elements whose mobilities are believed to be low. Classification of element profiles into the leaf (or the leaf blade) and other organs containing edible parts, except the calyx, by principal component analysis revealed similarity in the element concentrations across species. The present study may contribute to progress in the ionomic studies of fruit crops.

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In the context of global warming, freezing injury has tended to occur more frequently in cultivated Japanese chestnuts. To elucidate the cause of such freezing injury, we studied the effect of nitrogen (N) supplementation from livestock waste compost added to gray lowland soil on the freezing tolerance of Japanese chestnut trees in terms of their carbohydrate, water and N statuses. We also investigated the relationship between the endodormancy status and freezing tolerance of trees grown with or without livestock waste compost application. The freezing tolerance of Japanese chestnut trees planted in an excess of livestock waste compost was apparently lower than for trees grown only in gray lowland soil. The current season’s shoots from trees grown in soil only had the highest total sugar content, but the differences in total sugar content were not statistically significant, even though the N supplementation from livestock waste compost reduced the freezing tolerance. By contrast, higher water and N contents were recorded in the current season’s shoots grown in the presence of excessive livestock waste compost than in those grown in gray lowland soil only, all of which led to a reduction in the rate of winter survival among trees treated with livestock waste compost. The date of reaching 70% bud sprouting was delayed by one month or more, but bud break initiation was accelerated by the application of livestock waste compost, possibly due to a disturbance in the normal endodormancy progression. Collectively, these results suggest that normal endodormancy progression can be obstructed by higher water and N contents in trees treated with excessive livestock waste compost; thus, freezing tolerance sufficient to survive winter could not be acquired.

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An understanding of the genetic mechanism underlying capsaicinoid biosynthesis is important for breeding both pungent and non-pungent peppers. Although Capsicum is one of the earliest domesticated plant genera, only mutations in acyltransferase (Pun1) and putative aminotransferase (p-AMT) have been reported as genetic causes of loss of pungency. ‘No.3341’ (C. chinense) from Bolivia is a non-pungent cultivar. To determine the reasons underlying the non-pungency of ‘No.3341’, its expression levels and deduced amino acid sequences of Pun1 and p-AMT were analyzed. In ‘No.3341’, the expression levels and deduced amino acid sequences of both genes were normal compared with those of the pungent cultivar ‘Habanero’. Inheritance of the non-pungency was analyzed in F₁ and F₂ populations obtained by crossing ‘No.3341’ with ‘Habanero’. The segregation ratio indicated that the non-pungency of ‘No.3341’ is controlled by a single recessive gene. Moreover, since F₁ populations obtained by crossing ‘No.3341’ with a non-pungent pepper, ‘NMCA30036’ harboring a mutation in Pun1, or with ‘No.2’ and ‘No.80’ harboring mutations in p-AMT, were all pungent, Pun1 and p-AMT could not account for the non-pungency of ‘No.3341’. It appears that a novel genetic mechanism is responsible for the loss of pungency in ‘No.3341’.

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Tomato yellow leaf curl virus (TYLCV) infections result in decreased tomato growth and reduced yields, and the production is almost entirely lost if plants are infected during early growth. ‘Kyo-temari’ is the commercial name for the parthenocarpic tomato ‘MPK-1’, which has been vegetatively propagated and distributed to local farmers in Kyoto City for commercial cultivation. During the winter of 2013, the typical yellow leaf curl symptoms of TYLCV were observed in 10 parthenocarpic tomato cultivars, including ‘MPK-1’, maintained as mother stock for vegetative propagation at Kyoto University. When microtissue direct polymerase chain reaction was conducted, a begomovirus-specific amplicon was detected in the plants with yellow leaf curl symptoms. Sequencing and phylogenetic analysis clarified that a TYLCV-Mild isolate was infecting the parthenocarpic tomatoes. Because signals of TYLCV were not detected in the shoot apical meristems (SAMs) of TYLCV-infected ‘MPK-1’ by in situ hybridization, elimination of TYLCV was conducted by regenerating plants from leaf primordia (LP)-free SAMs of parthenocarpic tomato cultivars. By combining the LP-free SAM culture and in vitro grafting, TYLCV-free plants were obtained in approximately three months. The technique developed in this study will contribute to the efficient elimination of TYLCV from vegetatively propagated parthenocarpic tomatoes.

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We investigated the effects of applied gibberellin A₃ (GA₃) and uniconazole P (UCP), a GA biosynthesis inhibitor, on tillering in Welsh onion, also known as Japanese bunching onion ‘Hangzhou’, a cultivar with very high tillering capacity. The number of tillers was increased by GA₃ treatment and reduced by UCP treatment. The tillering-inhibitory effect of UCP was counteracted by GA₃ treatment. GAs were considered to be involved in not axillary bud outgrowth but its initiation for the following results: UCP treatment raised the leaf position with the first tiller, and the tillering-promoting effect of GA₃ treatment became apparent about 8 weeks after the treatment, which mostly corresponded to the period during which an axillary bud initiated near the shoot apex develops to become visible. To clarify the relationship between the diversity of tillering capacity in Welsh onion cultivars and GAs, we investigated the levels of endogenous GAs and the responsiveness to GA₃ treatment in several cultivars possessing different tillering capacities. There was a negative correlation between the tillering capacity and the level of GA₄, a major bioactive GA in Welsh onion. On the other hand, there was a positive correlation between the tillering capacity and the responsiveness to GA₃ treatment; GA₃ treatment markedly promoted tillering in ‘Hangzhou’, but not in ‘Raitei-Shimonita’ and ‘Hanemidori-Ipponbuto’, cultivars with very low tillering capacity. These results suggest that the sensitivity to GAs is a factor causing the diversity of tillering capacity in Welsh onion.

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It has been reported that parthenocarpic cucumbers with many female flowers and heavy fruit load often show fruit abortion and reduced fruit yield. To achieve the stable fruit production, it is necessary to elucidate the mechanism involved in fruit abortion in cucumbers via fruit load and endogenous plant hormones. In Exp. 1, the effects of exogenous plant growth regulators (PGRs) on yield and fruit growth were examined in a gynoecious, parthenocarpic cucumber (Cucumis sativus L.). Four types of PGR [indole-3-acetic acid (IAA), 2,3,5-triiodobenzoic acid (TIBA), benzyl adenine (BA), and gibberellic acid (GA₃)], which have been shown to enhance fruit growth in non-parthenocarpic cucumbers, were applied using lanolin paste to the peduncles at each node (6–25) of cucumber plants at anthesis. TIBA and BA applications significantly decreased the rate of fruit abortion, thereby increasing yield. IAA and GA₃ treatments increased the rate of fruit abortion at the middle and upper nodes, thereby reducing fruit yield. In Exp. 2, to clarify whether PGRs affected the concentrations of endogenous plant hormones, and whether IAA of high concentration increased fruit abortion under low-fruit-load conditions, we applied these PGRs (two concentrations of IAA, BA, and TIBA) to cucumber plants bearing only one fruit at node 11 or 12. No fruit abortion occurred following any PGR or control treatment, although both IAA and BA treatments inhibited fruit growth. BA application increased the production of cytokinins (Z, ZR, iP, and iPR) to a level similar to that after TIBA application one day after anthesis. However, compared with the response to TIBA treatment, after BA treatment, the peak in endogenous cytokinin production occurred at an earlier stage of fruit development. Additionally, both IAA and TIBA treatments increased endogenous IAA and cytokinin concentrations in fruit. These results suggest that exogenous PGRs affect the overall concentration of PGRs, as well as that of other endogenous plant hormones. However, PGRs may not be associated with fruit abortion when the fruit load is low. In conclusion, fruit load may have a greater influence on fruit abortion than that of PGRs.

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We analyzed the sequence variations in chloroplast DNA (cpDNA) for 31 Hosta cultivars, which may have been derived from Hosta sieboldiana and H. albomarginata in Japan, in order to elucidate the population origins of Hosta cultivars in their native habitats. In a previous study, we identified 39 haplotypes of cpDNA with specific regional features in the native habitats (16 and 23 in H. sieboldiana and H. albomarginata, respectively). These regional features of cpDNA variations were used to explore the maternal population origins of Hosta cultivars. We found that multiple Hosta cultivars may have originated from H. sieboldiana and H. albomarginata. We also observed some additional haplotypes that had not been detected previously. It is possible that these haplotypes originated from populations that were not investigated in previous studies, or that mutations occurred in the cultivar sequences after breeding.

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Reciprocal crosses between nine evergreen azalea species and Rhododendron uwaense were performed to clarify the pre- and post-fertilization barriers in this interspecific hybridization for the purpose of obtaining fragrant evergreen azaleas. Unilateral incompatibility appeared in this hybridization. When evergreen azalea species were used as a seed parent, many pollen tubes stopped elongating in a style and no seed could be obtained. The reverse crosses exhibited inhibition of pollen tube penetration into ovules, chlorophyll deficiency in cotyledons, and death of young seedlings in some cross combinations. These pre- and post-fertilization barriers reduced hybridization but did not arrest it completely. As a result, many putative hybrid seedlings could be obtained. RAPD analysis revealed that 10 of the putative hybrid seedlings examined (two vigorous plants selected from respective crosses of R. uwaense #1 × five evergreen azalea species) possessed specific bands derived from both parents. The plastid DNA (ptDNA) of these seedlings was inherited maternally except for seedlings of R. uwaense #1 × R. yedoense var. poukhanense, and the ptDNA of hybrid ones obtained from R. uwaense #1 × R. yedoense var. poukhanense was inherited paternally.

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