Genetic dissection of black grain rice by the development of a near isogenic line

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. ‘Koshihikari’, which is a leading variety in Japan. We used Oryza sativa L. ‘Hong Xie Nuo’ as the donor parent and backcrossed with ‘Koshihikari’ four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F₂ plants derived from a cross between the black rice NIL and ‘Koshihikari’ was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of ‘Okunomurasaki’, an existing black rice variety. The isogenicity of the black rice NIL to ‘Koshihikari’ was very high.     

Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.     

Objective evaluation of whiteness of cooked rice and rice cakes using a portable spectrophotometer

The whiteness of cooked rice and rice cakes was evaluated using a portable spectrophotometer with a whiteness index (WI). Also, by using boiled rice for measurement of Mido values by Mido Meter, it was possible to infer the whiteness of cooked rice without rice cooking. In the analysis of varietal differences of cooked rice, ‘Tsuyahime’, ‘Koshihikari’ and ‘Koshinokaori’ showed high whiteness, while ‘Satonoyuki’ had inferior whiteness. The whiteness of rice cakes made from ‘Koyukimochi’ and ‘Dewanomochi’ was higher than the whiteness of those made from ‘Himenomochi’ and ‘Koganemochi’. While there was a significant correlation (r = 0.84) between WI values and whiteness scores of cooked rice by the sensory test, no correlation was detected between the whiteness scores and Mido values, indicating that the values obtained by a spectrophotometer differ from those obtained by a Mido Meter. Thus, a spectrophotometer may be a novel device for measurement of rice eating quality.     

Inhibitory effect of heat‐killed Lactobacillus strain on immunoglobulin E‐mediated degranulation and late‐phase immune reactions of mouse bone marrow‐derived mast cells

This study investigated the in vitro effect of Lactobacillus strains, a major group of probiotic lactic acid bacteria, on immunoglobulin E (IgE)‐ and antigen‐induced mast cell degranulation and subsequent gene expression. Bone marrow‐derived mast cells (BMMCs) from DBA/2 mice were cultured with heat‐killed Lactobacillus strains for 24 h. Some strains significantly inhibited IgE‐ and antigen‐induced β‐hexosaminidase release from BMMCs. Furthermore, Lactobacillus reuteri NBRC 15892, which exhibited the strongest inhibitory activity, significantly reduced the elevated interleukin (IL)‐4, IL‐13, tumor necrosis factor‐α, and cyclooxygenase‐2 expression levels that was induced by 1–2 h of stimulation with IgE and antigens. The suppressive effect of NBRC 15892 strain on BMMC degranulation was significantly reduced in the presence of a toll‐like receptor (TLR)2‐neutralizing antibody. In addition, downregulation of cell surface FcεRIα expression was observed after 6 h of NBRC 15892 treatment. These results suggest that some Lactobacillus strains inhibited IgE‐mediated mast cell degranulation and subsequent late‐phase reactions involving mast cells via a TLR2‐dependent mechanism with FcεRIα downregulation.     

Flowering ability of commercial Calibrachoa cultivars as compared to that of natural species

To evaluate and describe the current status of Calibrachoa cultivars as bedding plants, the seasonal flowering of 91 commercial cultivars were compared to those of natural species using principal components analysis. The predominant flowering of the cultivars, that is, floriferous in late spring to early summer with a tendency to reduce flower production toward winter, seems to have remained unchanged from that of natural species. However, properties desired in bedding plants, such as early flowering and continuous flowering under short-day and/or low temperature conditions, appear to have been improved in a considerable number of cultivars, although there is still room for improvement. Seasonal and total floral counts were higher in many cultivars compared to natural species. Several natural species were selected for their unique flowering ability and should be evaluated as gene resources for improving the flowering of Calibrachoa cultivars.     

Assessment of decay risk of airborne wood-decay fungi

The decay risk of airborne wood-decay fungi was investigated by using an air sampler. Japanese cedar disks 7.8 cm in diameter and about 3 mm in thickness with moisture content of about 100% were placed in a “BIOSAMP” air sampler and exposed to 1000 l air. Air sampling was carried out from June to September at the same sampling site in Tsukuba, Japan. The exposed disks were then incubated for 16 weeks in a damp container kept at 26° ± 2°C. During the incubation period, wood mass loss ranged from −15 to 807 mg with a mean mass loss of 244 mg. Factors affecting mass loss were explored. Wood moisture content and ratio of heartwood area proved to be significant factors. In addition, six weather factors were found to influence mass loss. Disks that were sampled on a cloudy day showed significantly higher mean mass loss compared to those sampled on a sunny day. Subculturing of filamentous fungi from 16-week incubated disks suggested one-third of the isolated fungi produced ligninolytic enzymes.     

Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar

Rice landraces tolerant of up to 2 weeks of complete submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of SUBMERGENCE 1 (SUB1), a robust quantitative trait locus from the submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete submergence. At the molecular level, SUB1 is a variable polygenic locus encoding two or three ethylene responsive factor (ERF) DNA binding proteins. All Oryza sativa accessions encode SUB1B and SUB1C at this locus. An additional ERF, SUB1A, is present at SUB1 in FR13A and other tolerant accessions. The induction of SUB1A expression by ethylene during submergence disrupts the elongation escape strategy typical of lowland and deepwater rice, by limiting ethylene-induced gibberellic acid-promoted elongation. Microarray and metabolite studies confirm that SUB1A orchestrates its effects on metabolism and growth in a submergence-dependent manner. Due to the conditional activity of SUB1A, new “Sub1” mega-varieties effectively provide submergence tolerance without apparent ill effect on development, productivity, or grain quality.     

Marine bacterial sialyltransferases

Sialyltransferases transfer N-acetylneuraminic acid (Neu5Ac) from the common donor substrate of these enzymes, cytidine 5'-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac), to acceptor substrates. The enzymatic reaction products including sialyl-glycoproteins, sialyl-glycolipids and sialyl-oligosaccharides are important molecules in various biological and physiological processes, such as cell-cell recognition, cancer metastasis, and virus infection. Thus, sialyltransferases are thought to be important enzymes in the field of glycobiology. To date, many sialyltransferases and the genes encoding them have been obtained from various sources including mammalian, bacterial and viral sources. During the course of our research, we have detected over 20 bacteria that produce sialyltransferases. Many of the bacteria we isolated from marine environments are classified in the genus Photobacterium or the closely related genus Vibrio. The paper reviews the sialyltransferases obtained mainly from marine bacteria.     

Resource level as a proximate factor influencing fluctuations in male flower production in Cryptomeria japonica D. Don

Airborne pollen of Cryptomeria japonica causes severe pollinosis, and the number of people suffering from pollinosis has increased rapidly during recent decades. Male flower production in C. japonica shows annual variability; thus, predicting male flower production for the following spring could be a countermeasure against pollinosis. We analyzed factors that explain fluctuations in male flower production of C. japonica according to parameters reflecting internal resource dynamics based on field observations. In addition, we carried out experiments to regulate available resource levels using artificial shading to test the effect of internal resource levels on the number of male flowers produced. We found that temperature and precipitation in the previous summer and a relative increase in male flower production in the previous year were negatively related, whereas sunshine duration in the previous summer and diameter at breast height were positively related to the current year increase in male flower production. The number of male flowers was significantly reduced by the shading treatment and was positively correlated with the amount of total non-structural carbohydrates in the root. These results suggest that understanding the parameters controlling internal resource levels could lead to more accurate predictions of male flower production.     

Effects of the lateral growth rate on wood quality of Gmelina arborea from 3.5-, 7- and 12-year-old plantations

? Awareness of the shortage of fossil resources leads to an increasing demand for woody biomass. We investigated the feasibility of using fast-growing Gmelina arborea wood for material production. Gmelina arborea wood samples were collected from trees of varying cambium ages in Indonesia, from 3.5-, 7- and 12-year-old plantations.

? The lateral growth rate and the cambium age did not significantly affect the longitudinal released strain of the growth stress, xylem density, or microfibril angle at the outermost surface of the secondary xylem at any sampling site. However, fiber length in the 3.5-year-old plantation tended to be shorter in smaller diameter trees, whereas in larger diameter trees it was almost the same as that in trees from the 7- and 12-year-old plantations. This suggests that smaller diameter trees in the 3.5-year-old plantation had not yet produced mature wood.

? Xylem qualities had already reached values appropriate for harvesting, except in the smaller diameter trees from the 3.5-year-old plantation. This indicates that the larger diameter trees had already matured, regardless of their cambium age. These results suggest that the next step is to develop silvicultural treatments to increase the lateral growth rate during the early growing stage, in order to produce as much mature wood as possible, as quickly as possible.