Gene targeting (GT) via homologous recombination (HR) is a powerful tool for the precise modification of the target gene. In spite of many efforts, GT frequency in higher plants is still low. An efficient transformation system, enhancement of the HR and efficient selection of the gene targeted cells are thought to be essential for the development of an efficient GT system in plants. Recent reports showed that the open chromatin state of host cells and/or specific induction of the DNA double strand breaks (DSBs) in the gene of interest are important to improve HR and GT. RAD54 is involved in chromatin remodeling during HR. Chromatin assembly factor 1 (CAF-1) is involved in nucleosome assembly after DNA replication. Enhancement of RAD54 function and suppression of the CAF-1 function are expected to induce the open chromatin state in plant cells which could induce HR. Zinc finger nuclease (ZFN), an artificial endonuclease composed of zinc finger domains and a nuclease domain, induce DSBs at the target sequence and enhance GT. In the next step, determining how to apply these potential effectors is a key to establish an efficient GT system.

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The RAD2 family of nucleases is a group of essential nucleases involved in 3R mechanisms (DNA replication, DNA repair and DNA recombination). The RAD2 family consists of three classes (XPG/class I, FEN-1/class II and EXO1/class III). Recent advances in plant genome projects have revealed that in addition to plant counterparts belonging to each class of the RAD2 family higher plants have a fourth set of RAD2 family members that constitute a new class in the RAD2 family (SEND-1/class IV). DNA damage generated by endogenous or exogenous factors cause mutations that threaten the survival of plants if they are misrepaired or not repaired, which results in low crop yields. Understanding the functions of plant RAD2 family members in DNA repair is important for agricultural technology enabling an enhancement of resistance to genotoxic stresses caused by DNA damages. In this review, recent advances in our understanding of plant RAD2 family members are discussed.

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Low temperatures cause a decrease in seed yield and deterioration of seed quality in soybeans and have threatened stable soybean production in cool areas. To overcome this problem, physiological and genetic analyses have been conducted as steps towards the development of efficient breeding systems. Several evaluation methods that are useful for physiological studies as well as for genetic screening have been developed. Low temperature treatment for four weeks or longer starting at the first flowering stage in plants was found to reduce all of the yield components and result in genotypic variation in chilling tolerance for seed yield during reproductive growth. Analysis of low seed fertility induced by low temperature treatment prior to flowering revealed that the tetrad stage during pollen development is the most sensitive to chilling. Browning of seed coats, a major factor causing deterioration of seed quality, was induced most severely by low temperature treatment about one week after flowering. In addition, several genetic loci associated with chilling tolerance have been identified. Cultivars and lines with the T allele at the T locus, which controls the color of pubescence, have repeatedly been demonstrated to exhibit better chilling tolerance than those with the other allele, t. Maturity loci controlling flowering time and maturity such as E1, e3 and e4 were also found to be associated with chilling tolerance for both seed yield and quality. However, evidence showing that these loci are directly involved in chilling tolerance remains to be provided.

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GFSelector (Gene Function Selector, http://alnilam.mi.mss.co.jp/rgadb/) has been developed to perform computational classification of gene models and assignment of unique biological function. It has been incorporated in RiceGAAS (http://ricegaas.dna.affrc.go.jp/usr/) which was designed to provide an analysis pipeline for user submitted genome sequences and comprehensive database for all rice gene models. The combined system facilitates accurate modelling of predicted rice genes, classification of gene structure, and assigning of function and GO (gene ontology) terms to the gene models. The reliability and accuracy are enhanced by integrating several reference databases into the system and generating multiple candidates for determining the function of the gene models. The pipeline is also fully automated thereby facilitating regularly updates of the rice gene models using the latest reference databases. Annotation of soybean, wheat and banana BAC (bacterial artificial chromosome) sequences was performed to test the applicability of the pipeline to other crops. As compared with the GenBank CDS (coding sequence) features, more than 83% of nucleotide-level sensitivity was obtained for the gene modelling by the pipeline. It was also confirmed that 95% of functional annotation by the pipeline was nearly equal or better than the corresponding GenBank CDS feature.

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We evaluated cold tolerance at the booting stage on the basis of seed fertility after cool-water treatment for three years (2005-2007) in 114 recombinant inbred lines (RILs) between temperate japonicas, Kirara397 (cold-sensitive) and Hatsushizuku (cold-tolerant). Composite interval mapping (CIM) was performed to identify quantitative trait locus (QTL) for cold tolerance. A QTL for cold tolerance at the booting stage was reproducibly detected in three trials on chromosome 1. Contribution of the QTL to the phenotypic variation ranged from 16.2 to 47.3%, and their additive effects were all towards Hatsushizuku. We also analyzed QTL for heading time and culm length, which are thought to affect cold tolerance. A QTL for heading time and that for culm length was detected every three years on the neighboring regions of chromosome 10, while no QTL for the two traits was detected on chromosome 1. These results suggest that the QTL on chromosome 1 has a major effect on the variation of cold tolerance between Kirara397 and Hatsushizuku without affecting heading time and culm length.

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Using pollinator insects or treating flowers with phytohormones is necessary for stable fruit setting in forcing culture of eggplant using plastic houses. However, these means are costly and/or labor-intensive. Use of parthenocarpic cultivars is considered to be the most cost-effective solution for stable fruit setting under sub-optimal environmental conditions such as lower temperature in forcing culture. ‘Anominori’, a parthenocarpic eggplant cultivar, was developed by the National Institute of Vegetable and Tea Science in 2006. This cultivar is the F₁ hybrid between two parthenocarpic inbred lines, ‘AE-P08’ and ‘AE-P01’. ‘AE-P08’ was selected from the cross between an F₃ plant derived from ‘Nakate Shinkuro’ × ‘Talina’ and an F₄ plant derived from ‘Talina’ × ‘Nasu Chuukanbohon Nou 1’. ‘AE-P01’ was selected from the cross between ‘Talina’ and ‘Nasu Chuukanbohon Nou 1’. ‘Anomi-nori’ can produce sufficient yields for commercial use without treating with phytohormones or using pollinator insects in forcing culture. The plant characteristics of ‘Anominori’ are the following: high plant height, long internode, thick stem and large leaves. The fruit of ‘Anominori’ at harvest stage is long egg-shaped and glossy dark purple. The flesh of fruit is very dense.

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Vibration and shock data was collected using accelerometers placed in corrugated fiberboard containers of cherries transported from Yamagata, Japan to Taipei, Taiwan. Vibration during airplane transport differed from that of transport by trucks, with much high-frequency vibration and the highest peak frequency measured at 80 Hz. Vibration features of Japanese trucks differed from those of Taiwanese trucks. Cherries loaded on trucks in Yamagata and undergoing customs procedures and inspection at Narita International Airport (Narita) showed fewer shocks and lower acceleration, < 10 G. Packaged cherries loaded on planes at Narita and unloaded at Taiwan Taoyuan International Airport (Taoyuan) showed the highest shocks. Maximum shock acceleration of 60 G throughout transport was detected in loading at Narita. Shock acceleration during quarantine and customs procedures at Taoyuan was also high like at Narita. Cherries transported by truck in Taipei underwent a maximum shock acceleration of 20 G, exceeding that in Japan truck transport.

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The impact of forest fire in 1997 and 1998 on the mycorrhzae was studied at the dipterocarp forest in East Kalimantan, Indonesia. In unaffected forest more than half of total ectomycorrhizae distributed in the organic layer but in the fire-affected forest one and a half years after the fire, total amount of mycorrhizae was smaller and they were found in deeper soil. The number of morphotypes of mycorrhizae was also smaller in fire-affected forest. An artificial plantation established after clear cut and prescribed burn had the largest amount of ectomycorrhizae, but the diversity was smaller than the unaffected forest. After four years, mycorrhizae had not yet recovered in fire-affected forest although the organic layer had recovered. Pioneer species of mycorrhizal fungi (early-stage fungi) developed sporocarps around the surviving hosts in severely affected forest and this suggests the start of secondary succession of mycorrhizae. In moderately affected forest, the species composition of mycorrhizal fungi which fruited during the study was similar to those of unaffected forest. This fact suggests that such sites may be the refugia of symbionts and be important in reforestation.

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Model experiments using mangrove mesocosm tanks were performed two times at the campus of Kasetsart University, Thailand. Replicates of 13 mangrove (Sonneratia caseolaris) saplings were planted in 7 mesocosm tanks and water and soil samples were collected during the 2 experimental periods. The nitrogen removal rate showed 57 and 73 mgN/m²/day in the tanks where wastewater from shrimp aquaculture ponds was supplied and exchanged, and 164-425 mgN/m²/day in the tanks where the additional nutrients were provided. The phosphorus removal rate was 5.7 and 17 mgP/m²/day in tanks supplied and exchanged with wastewater, and 48 and 97 mgP/m²/day in the tanks provided with additional nutrients. Both nitrogen and phosphorus showed high removal rates in the mangrove mesocosm tanks. However, there was no marked increase in the bacterial community either in the water or surface soil, despite the organic matter-rich wastewater from shrimp aquaculture ponds or high concentrations of inorganic nutrients that were supplied.

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Over-luxuriant winter wheat can always be seen when pre-winter accumulated temperature is high or too much fertilizer is applied before sowing. Over-luxuriant erectophile type wheat shows a similar canopy spectral feature to that of the planophile type. This special canopy spectral feature influences N fertilizer application decision making when using remote sensing technologies to detect N status. The objective of this study was to relatively discriminate erectophile type wheat from the planophile type and then further detect over-luxuriant canopy using seasonal changes in canopy spectral reference. Two groups of winter wheat cultivars with different canopy structures were investigated. The wheat leaf distribution feature was combined with the ratio of canopy spectral reflectance of 790 nm at elongation stage (R790_e) to that at rising stage (R790_r), i.e. R790_e/R790_r. Based on the values of both normalized R790_e (NR790_e) and normalized R790_e/R790_r (N(R790_e/R790_r)), a two-dimensional spectral coordinate system charactering seasonal change in canopy spectral reflectance was constructed. According to the distribution features, cultivars with N(R790_e/R790_r) ≥ 1 were discriminated as the planophile type in which cultivars with NR790_e ≥ 1 were normal and over-luxuriant (or dense) planophile type, and those with NR790_e < 1 were considered the sparse planophile type. On the contrary, cultivars with N(R790_e/R790_r) < 1 were grouped in the erectophile type in which cultivars with NR790_e < 1 were considered normal and sparse erectophile type, and those with NR790_e ≥ 1 were attributed to the over-luxuriant erectophile type. Thus, N(R790_e/R790_r) could be used to relatively discriminate wheat canopy structure, and NR790_e to judge wheat canopy density. The larger the NR790_e value, the higher the canopy density. The average discrimination accuracy of our method was 84.4%. Nevertheless, this method could provide the relative positions only within the investigated cultivars since both NR790_e and N(R790_e/R790_r) were relative ratios to their average.

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