Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.     

Microbial community profiles in intercellular fluid of rice

Plants harbor microorganisms that are thought to stimulate plant defense systems or promote plant growth. Individual species in these intercellular microbial communities are often not sufficiently abundant to be easily described, although some endophytic microorganisms amenable to culture have been characterized. To better understand the microbial population of plants, we collected intercellular fluid (IF) from leaf blades and sheaths of rice and subsequently isolated DNA from the IF. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S and 18S rDNA fragments amplified from IF DNA by PCR indicated that these band patterns were distinguishable from those of a leaf surface-wash fluid (SF). Analysis of a set of rDNA fragments amplified from IF DNA of rice with different genotypes, paddies or growth stages for the primary survey of overall microbial community in the IF suggested that this approach is suitable for analyzing microbial diversity in the IF from various plant samples. Actually, comparative analysis of amplified rDNA fragments of rice and other five plant species indicated that the microbial diversity in IF is likely to vary substantially among plant species. We can also use sequence analysis of 16S rDNA fragments amplified from rice IF DNA to identify species including unculturable bacteria and proteobacteria and Xanthomonas and 18S rDNA fragments to identify Tilletiaria anomala, Tilletia iowensis, Ustilago maydis and unculturable eukaryotes. Thus, IF DNA analysis seems to be a good tool to further study the microbial ecology of plants.     

Plasma vitamin K concentration in horses supplemented with several vitamin K homologs

The effect of several vitamin K homologs on plasma vitamin K concentration was determined to assess their potential as a vitamin K supplement for adult horses. Sixteen Thoroughbred horses consisting of 8 mares and 8 geldings, aged 8.4 ± 3.6 yr and weighing 520.8 ± 36.1 kg, were allocated to 4 groups (n = 4). Each group was given phylloquinone, menaquinone-4, or menadione at 58 μmol/d, or no vitamin K supplement for 7 d. Plasma samples were collected before feeding, and 2, 4, and 8 h after feeding on d 7, and plasma concentrations of phylloquinone and menaquinone-4 were determined. Plasma phylloquinone concentration was greater in the phylloquinone group than in the other groups (P < 0.001). The phylloquinone concentration quadratically increased (P < 0.001) after feeding in the phylloquinone group but no changes in the plasma phylloquinone concentration were observed after feeding in the other groups. Plasma menaquinone-4 concentration was greater (P < 0.001) in the menadione group than the other groups, including the menaquinone-4 group. Menaquinone-4 concentration did not change (P = 0.192) after feeding in each group. Menaquinone-4 has been considered the most potent vitamin K homolog for bone metabolism; therefore, the present experiment indicates that menadione is a good source of vitamin K for bone health in horses because it is the only vitamin K homolog that increased the plasma concentrations of menaquinone-4.     

Highly invasive intracranial malignant schwannoma in a rat

A highly invasive intracranial malignant schwannoma containing several masses was detected in a 28-week-old male Crl:CD(SD) rat. Macroscopically, 3 masses were noted in the cranial cavity; one was present at the bottom of the cranial cavity and involved the trigeminal nerve, and the other two were in the parietal bone. Histologically, each mass consisted of fusiform cells with interlacing fascicular, wavy and nuclear pseudopalisading arrangements and round cells with cystic lesions. The tumor cells invaded not only the brain but also the parietal bone. In the brain, the tumor cells infiltrated diffusely into the leptomeningeal and perivascular spaces and parenchyma, in which the tumor cell morphology and invasive pattern closely resembled those of malignant astrocytoma and malignant reticulosis. Immunohistochemically, the tumor cells in the masses showed positive reactions for both S-100 protein and GFAP, while those in the cerebral invasion sites were negative for GFAP and less positive for S-100 protein. Electron microscopically, a single basal lamina layer and short intricate cell processes were confirmed in the tumor cells. From these results, the present tumor was diagnosed as a malignant schwannoma arising in the cranial cavity, probably originating from the trigeminal nerve. The present tumor is considered to be a relatively unique malignant schwannoma based on its growth and invasion patterns.     

Interaction between manganese and zinc in growth of rice plants

Many instances of antagonistic relationships among various micro-elements and between micro- and macro-elements in their absorption, translocation, and functions in plant growth have been reported (1). In a series of our researches on the effect of micro-elements on the growth of rice plants, it was observed that manganese toxicity symptom of rice plants was markedly reduced by increasing the concentration of zinc in the nutrient sdution. Although it has been reported that manganese toxicity symptoms of crops were reduced by addition of Fe (2,3), A1 (4), Ca (5) and silicate (6) to the medium, there have been few reports of the effect of Zn on Mn toxicity of rice plants. In this paper, the interaction between Mn and Zn in the growth of rice plants was reported.     

Effect of sulphur fertilization on grain yield and yield components of winter wheat

Abstract

The effect of sulphur application on winter wheat yield and yield components on two different soils in northern Estonia and southern Estonia during 2004–2009 was investigated. Sulphur was applied with NS-fertilizer Axan or Axan Super at the rate of S 10 or 13.6 kg ha^?1 accompanied with nitrogen background of N 100 kg ha^?1, which effect was compared to effect of ammonium nitrate at the same rate of N. The rates of fertilizers were divided into two portions and applied at the growth stages 21–22 and 25–30. The effect of sulphur fertilization on the formation of wheat yield varied on a quite large scale depending on soil and weather conditions of trial locations. The yield components were closely related: when one component was changed, the other components sometimes compensated for grain yield.

Sulphur deficiency symptoms appeared on the break-stony soil at Saku in a somewhat stronger form than on the pseudopodzolic soil at Auksi. The results of field trials conducted at Saku during the four years can be summarized as follows: the application of sulphur increased the number of ears per unit area by an average of 14.0% and the number of grains per ear by an average of 18.6%. At the same time, sulphur decreased the 1000-grain weight. As a final result, sulphur application on break-stony soil increased the wheat yield by 1.16 t ha^?1 on average, i.e. by 23.0%. Sulphur application in trials conducted on pseudopodzolic soil at Auksi during years with different weather conditions in growing season proved highly effective in three of five trials. As an average of all trials in Auksi, the sulphur application increased the number of ears per unit area and the number of grains per ear by 23.9% and 7.7%, respectively. The grain yield increased under the influence of sulphur on the average of all trials conducted on pseudopodzolic soil by 1.25 t ha^?1, i.e. by 22.4%.     

The content and quality of protein in winter wheat grains depending on sulphur fertilization

Abstract

On soils lacking in water-soluble sulphur, the sulphur fertilization of winter wheat, in general, increases the yields. There are not sufficient investigations about the influence of sulphur on the quality of yield. The objective of this work was to investigate the content and quality of protein in wheat grain depending on sulphur fertilization. The present study relies on field trials conducted on two different soils during 2004–2009. Sulphur was applied with NS-fertilizer Axan or Axan Super at the rate of S 10 or 13.6 kg ha^?1 accompanied by a nitrogen background of N 100 kg ha^?1. The rates of N- and NS-fertilizers were divided and applied at the beginning and at the end of tillering. At harvest, the grain samples from trial variants in four replications were taken, and the contents of crude protein, wet gluten, amino acids (lysine, threonine, cysteine, methionine) and gluten index in wheat grain were determined. Besides, the contents of amino acids were recalculated on their concentrations in protein. The protein and wet gluten contents in grain varied significantly depending on weather conditions of the trial years. On break-stony soil, sulphur increased the yield by 1.16 t ha^?1 on average, i.e. by 21.7%. With increasing yields the protein and wet gluten concentrations in grain decreased. Under the influence of sulphur, the gluten index increased significantly – from 58 to 74, i.e. by 27.6%. In 2004 and 2005, sulphur increased the cysteine and methionine content in wheat grain. Although sulphur application in many cases decreased the protein and wet gluten contents in wheat grain, it improved the biological quality of protein because the concentrations of above-mentioned amino acids recalculated on their concentrations in protein increased significantly. The sulphur application in pseudopodzolic soil had a weaker effect on the grain quality than in break-stony soil.     

Residual effects of organic acid-treated phosphate rocks on some soil properties and phosphate availability

The effects of the application of organic acid-treated phosphate rocks on the growth and nutrient uptake of Italian rye grass (Lolium multiflorum Lam. cv. Tachiwase) and some properties of the soil were evaluated in a greenhouse pot experiment. Phosphate rocks (PRs) collected from six countries; China, Florida (USA), Jordan, Sri Lanka, Togo, and Tanzania, were treated with 1 M oxalic or tartaric acid at the ratio of 2.5 mL g^-1 PR. The organic acid-treated PRs, containing 12–31% water soluble P, were applied to a granitic regosol (pH 5.8) at 200 mg P pot^-1 (4 kg soil). Untreated PRs and single superphosphate (SSP) were included in the treatments. Italian ryegrass was grown for 175 dafter planting (DAP) with ample supply of other nutrients and water. Shoots were harvested at 56, 119, and 175 DAP and the soils were analyzed for pH and Olsen-P after the experiment. Application of organic acid-treated PRs consistently increased the dry matter yield and P uptake of the plants compared with the application of untreated PRs at each harvest, but they were less effective than SSP. A larger amount of P (calculated per unit water-soluble P applied) was recovered from the organic acid-treated PRs than from SSP. The amount of residual extractable P in the soils with the organic acid-treated PRs was about the same as or significantly larger than that in the soil treated with SSP. Soil pH was also significantly higher than in the control and SSP soils. The results suggest that organic acids could be used to improve the P availability of PRs to plants with favorable residual effects in terms of available P and soil pH, without exerting any adverse effects on plant growth or nutrient acquisition.     

Effect of CO2 enrichment on biomass production,photosynthesis, and sink activity in Soybean cv. Bragg and its supernodulating mutant nts 1007

Soybean (Glycine max L. Merr.) cv. Bragg and its supernodulating mutant nts 1007 were grown in pots containing vermiculite with a N-free nutrient solution in order to examine the effect of elevated CO₂ concentration (100+20 Pa CO₂ ) on biomass production, photosynthesis, and biological nitrogen fixation. The whole plant weight increase in Bragg was higher than in the mutant at a high CO₂ concentration. Apparent photosynthetic activities of the upper leaves in both Bragg and the mutant increased up to 14 d after treatment initiation by the CO₂ enrichment and thereafter decreased to some extent. Both leaf area and leaf thickness of Bragg increased more than in nts 1007. With the elevated CO₂ concentration, biological nitrogen fixation (BNF) also responded in the same manner as biomass production in both Bragg and nts 1007. The increase of BNF in Bragg was largely due to an increase in nodule weight. Starch contents in the leaves of both Bragg and the mutant increased significantly by CO₂ enrichment, with a higher increase in Bragg than in its mutant. Sugar content in leaf differed only slightly in both Bragg and the mutant. N content in leaf decreased in both Bragg and its mutant, with the decrease being more pronounced in Bragg. However, in other plant parts (roots, stem, and petiole + pods), N content increased in the mutant while in Bragg, it decreased in the pod. N accumulation rate was higher in Bragg than in the mutant and increased more in Bragg than in the mutant by CO₂ enrichment. The ureide content in leaf decreased in Bragg but increased in the mutant by elevated CO₂ concentration. In the nodules, ureide content increased in both Bragg and the mutant by CO₂ enrichment. Based on these results, it is suggested that in terms of biomass production and photosynthetic rate, Bragg responded more to elevated CO₂ concentration than its mutant nts 1007. The alleviation of the stunted vegetative growth of the mutant by CO₂ enrichment was limited despite the significant increase in the photosynthetic activity, presumably due to the limitation of sink activity in the growing parts and not to insufficient supply of N through BNF.     

Growth and canopy structure of rice plants grown under field conditions as affected by Si application

Abstract

The ontogenetic changes of N, P, and K contents in leaves of rice, maize, soybean, adzuki bean, potato, and sugar beet were studied as the following results were obtained.

1. N content of rice and maize drastically changed at the primordia formation stage, while that of other crops did not show clear changes depending on the stage of growth.

2. P content of rice and maize was higher in upper leaves than lower leaves, but did not change appreciably in other crops.

3. K content of potato and sugar beet remained constant for a long period of time compared to other crops.

4. P-N relationship in rice and maize distinctly differed between upper and lower leaves; ratio of P content to N content of upper leaves was higher than that of lower leaves.

5. K-N relationship in potato and sugar beet was very different from that in other crops; K content remained constant regardless of the decrease in N content except for the lower leaves.

Thus, as the P-N balance of rice and maize (Gramineae crops) and K-N balance of potato and sugar beet (root crops) showed distinctive characteristics compared to other crops, the physiological significance of the mineral balance must be further investigated.