Genomics of pear and other Rosaceae fruit trees

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.     

Fine mapping of the gene for susceptibility to black spot disease in Japanese pear (Pyrus pyrifolia Nakai)

Black spot disease, which is caused by the Japanese pear pathotype of the filamentous fungus Alternaria alternata (Fries) Keissler, is one of the most harmful diseases in Japanese pear cultivation. We mapped a gene for susceptibility to black spot disease in the Japanese pear (Pyrus pyrifolia Nakai) cultivar ‘Kinchaku’ (Aki gene) at the top of linkage group 11, similar to the positions of the susceptibility genes Ani in ‘Osa Nijisseiki’ and Ana in ‘Nansui’. Using synteny-based marker enrichment, we developed novel apple SSR markers in the target region. We constructed a fine map of linkage group 11 of ‘Kinchaku’ and localized the Aki locus within a 1.5-cM genome region between SSR markers Mdo.chr11.28 and Mdo.chr11.34. Marker Mdo.chr11.30 co-segregated with Aki in all 621 F₁ plantlets of a ‘Housui’ × ‘Kinchaku’ cross. The physical size of the Aki region, which includes three markers (Mdo.chr11.28, Mdo.chr11.30, and Mdo.chr11.34), was estimated to be 250 Kb in the ‘Golden Delicious’ apple genome and 107 Kb in the ‘Dangshansuli’ Chinese pear genome. Our results will help to identify the candidate gene for susceptibility to black spot disease in Japanese pear.     

Vertical behavior of bigeye tuna (Thunnus obesus) in the northwestern Pacific Ocean based on archival tag data

The behavior of bigeye tuna (Thunnus obesus) in the northwestern Pacific Ocean was investigated using archival tag data for 28 fish [49–72 cm fork length (FL) at release, 3–503 days] released in Japanese waters around the Nansei Islands (24–29°N, 122–132°E) and east of central Honshu (Offshore central Honshu, 32–36°N, 142–148°E). Vertical behavior was classified into three types based on past studies: ‘characteristic’ (non‐associative), ‘associative’ (associated with floating objects) and ‘other’ (behavior not fitting into these two categories). The proportion of fish showing associative behavior decreased and that of characteristic behavior increased as fish grew, and this shift was pronounced at 60–70 cm FL. The fish usually stayed above the 20°C isotherm during the daytime and nighttime when showing associative behavior and below the 20°C isotherm during daytime for characteristic behavior. A higher proportion of characteristic behavior was seen between December and April around the Nansei Islands, and between September and December for offshore central Honshu. Seasonal changes in vertical position were also observed in conjunction with changes in water temperature. In this study, ‘other’ behavior was further classified into five types, of which ‘afternoon dive’ behavior, characterized by deep dives between around noon and evening, was the most frequent. The present study indicated that in the northwestern Pacific Ocean, the vertical behavior of bigeye tuna changes with size, as well as between seasons and regions.     

The <Emphasis Type="Italic">Arabidopsis NST3/SND1</Emphasis> promoter is active in secondary woody tissue in poplar

Wood biomass is one of the promising future materials for biofuels with no competing food uses. However, the higher cost to produce bioethanol from wood feedstocks is regarded as a priority issue. Genetic engineering techniques have been proposed to enhance the quality and quantity of wood materials to overcome the cost problem. Although many genetically engineered trees with applicable traits such as low lignin, a high syringyl to guaiacyl ratio and high cellulose content are generated, ectopic expression of an effector gene under a constitutive promoter can sometimes induce untoward side effects on plant growth and development. Our recent study demonstrated that AtNST3/SND1 promoter of Arabidopsis thaliana is a candidate tool for driving a potent activator to enhance wood biomass production in poplar without any growth retardation. However, the tissue- and cell-dependent activity of the promoter remains to be elucidated. In the present study, we generated transgenic poplar expressing AtNST3/SND1promoter::GUS to examine in detail the activity of the AtNST3/SND1 promoter. Histochemical analysis revealed that the promoter was predominantly active in secondary woody tissue. Our result indicates that the AtNST3/SND1 promoter is an option for expressing an effector gene to modify secondary cell wall components and wood biomass.     

Epidemiological survey of Border disease virus among sheep from northern districts of Japan

The first epidemiological survey of Border disease virus (BDV) was undertaken in small ruminants in Japan. Ovine sera, collected from the northern prefectures of Hokkaido, Aomori and Iwate, were examined for the presence of antibodies against BDV using the neutralization peroxidase-linked antibody test. Twenty-nine (17.6%) of one hundred and sixty-five samples were seropositive for BDV. Results were specific, excluding cross-reactions with bovine viral diarrhea virus (BVDV). Only one sample (0.6%) was positive for BVDV, and was negative for BDV. Despite serological evidence of virus circulation, there have been no clinical cases of border disease in sheep in Japan. Although no diagnostic measures were performed, the infection did not appear to be associated with a reduction in ewe fertility nor with lamb mortality.     

Arsenic accumulation and speciation in Japanese paddy rice cultivars

We examined arsenic (As) accumulation and speciation in the major cultivars currently grown in Japan, because differences in grain As levels among cultivars may influence dietary As exposure in Japanese people. Ten major cultivars (Oryza sativa L.) were grown under flooded conditions in a paddy field with a background level of As (low-As soil) or in pots filled with soil containing a high level of As (high-As soil). In the low-As soil, the total grain As ranged from 0.11 to 0.17?mg?kg^?1, with a mean concentration of 0.14?mg?kg^?1, and inorganic As was the major species in all cultivars. There were few genotypic differences in the levels of either total As or inorganic As in the grain. In the high-As soil, total grain As increased to a mean level of 2.4?mg?kg^?1 in the 10 cultivars, with markedly increased levels of dimethylarsinic acid. The genotypic variations among cultivars in the levels of both total As and dimethylarsinic acid were statistically significant. However, the genotypic variability of inorganic As levels was quite small, and these levels remained low (at about 0.2?mg?kg^?1) even when total As levels increased markedly. These results suggest that differences in grain As levels among Japanese cultivars may not influence dietary As exposure, because there is little genotypic difference in the accumulation of inorganic As, which is considered more toxic than organic As to humans. We discuss the possible mechanism of As accumulation in Japanese paddy rice, in the context of the accumulation of As species in the developing grain and in other plant tissues.     

Asparagine test in relation with the nitrogen nutritional status of crop plants II

In the previous paper it was reported that the early panicle formation is the most important period of top dressing for rice plant, and to determine the requirement of top dressing asparagine test may be used.     

Spontaneous adenocarcinoma with giant cell formation in the accessory sex glands in a male Sprague-Dawley rat

In this study, we report the features of an adenocarcinoma with giant cell formation spontaneously occurring in the accessory sex glands of a male 10-month-old Sprague-Dawley rat. A milky white mass was found in the region corresponding to the left seminal vesicle and the left coagulating gland. Histologically, tumor cells exhibited diverse growth patterns, including glandular/trabecular, cystic, and sheet-like growth areas. The tumor cells were pleomorphic, with round- or oval-shaped nuclei and abundant eosinophilic cytoplasm. Mitotic figures were occasionally observed. Giant cells were also prominent in the sheet-like growth area, with intracytoplasmic vacuoles containing eosinophilic material. The stroma was rich in collagen fibers and fibroblasts. Numerous inflammatory cells were observed in the glandular and cystic lumina and stroma. Immunohistochemically, the tumor cells were positive for cytokeratin AE1/AE3 and proliferating cell nuclear antigen. In the sheet-like growth area, some of the tumor cells and giant cells were positive for vimentin in the cytoplasm adjacent to the nucleus. Electron microscopy revealed that the tumor cells contained a small number of mitochondria and rough endoplasmic reticulum, and had no basement membrane or desmosome. The giant cells occasionally contained variably sized intracytoplasmic lumina and globular filamentous bodies, probably corresponding to vimentin. Considering these morphological features, the tumor was diagnosed as an adenocarcinoma with the formation of giant tumor cells originating from the male accessory sex glands.