Single nucleotide polymorphism genotyping of the barley waxy gene by polymerase chain reaction with confronting two-pair primers

A high‐throughput single nucleotide polymorphism (SNP) genotyping procedure was developed to select amylose‐free barley mutants whose waxy genes had a C‐ to T‐base substitution in exon 5, which converted Gln‐89 of the wild‐type gene into a termination codon. An F₂ population carrying an amylose‐free waxy gene was checked for segregation. Polymerase chain reaction with confronting two‐pair primers (PCR‐CTPP) produced allele‐specific PCR products that have different sizes and are inherited in a co‐dominant manner. Two alleles of the barley waxy gene with SNP were correctly identified in parental strains using the PCR‐CTPP procedure. Segregation of the SNP as detected by PCR‐CTPP in an F₂ population fitted the expected 1:2:1 ratio. The PCR‐CTPP procedure can provide a time saving and cost‐effective alternative to derived cleaved amplified polymorphic sequence in marker‐assisted selection.     

Phyllochron Dynamics Under Controlled Environments in Rice (Oryza Sativa L.)

Previously, we reported that phyllochron of rice greatly fluctuated in the course of development under natural conditions. The present study was carried out to examine the phyllochron dynamics using the five near-isogenic lines (NILs) for heading time and the recurrent parent. The change of phyllochron was investigated under four different controlled conditions regarding daylength and temperature. Growth duration (days to heading) showed a large variation among different growth regimes as well as genotypes. Changes of phyllochron were evaluated in the genotypes by using a quartic polynomial regression that was well fitted to the change of phyllochron in the present controlled environments as previously observed under natural conditions. Phyllochron began to drastically increase after around the 5th phytomer order and decreased with the progress of reproductive development in similar manners under different environments. The pattern of phyllochron change varied from a flat to non-flat shape. The shape of the equation was affected by genotypes as well as daylengths and temperatures. In addition, the shape was closely related to the growth duration (days to heading) of the genotype, suggesting that the phyllochron might internally increase depending on the genotype controlling the heading date. Therefore, the present results showed that the sufficient examination of phyllochron dynamics is necessary for understanding a variation in the heading date of rice.     

Recovery of antioxidant activity from carnosol quinone: antioxidants obtained from a water-promoted conversion of carnosol quinone

Carnosol is one of the main antioxidants in sage and rosemary. Although carnosol quinone is the antioxidation product of carnosol and has a very weak antioxidant activity, its treatment in water-containing solvent restored its strong antioxidant activity. HPLC analysis of the water-stimulated recovery reaction of the antioxidant activity revealed that the strong activity was due to the reproduced carnosol. The analysis also showed that an almost equal amount of quinone derivatives of rosmanol (rosmanol quinone) was produced in the reaction along with the carnosol. The rosmanol was formed by the addition of 1 equiv of water and the following isomerization from carnosol quinone in the water-containing solvent. The formed rosmanol was also found to be oxidized by the remaining carnosol quinone to produce rosmanol quinone. At the same time, carnosol quinone was reduced to afford carnosol. This redox phenomenon is an important part of the mechanism for the recovery of the antioxidant activity from carnosol quinone under the water-containing conditions.     

Genotypic variation in Fe concentration of barley grain

Abstract

Iron deficiency in humans is the most prevalent micronutrient deficiency worldwide. To screen for high Fe cultivar, genotypic variation in Fe concentration of barley grain was investigated in two collections of barley: 274 standard varieties selected at the Barley Germplasm Center of the Research Institute for Bioresources, Okayama University (SV) and 135 varieties from the Barley Core Collection of Americas (BCCAM). The Fe concentration of barley grain showed large variation, ranging from 24.6 to 63.3 mg kg^?1 in SV, from 21.0 to 83.0 mg kg^?1 in BCCAM barleys. The Fe concentration was not affected by the key characters of barley varieties, kernel row types, and hulled or hull-less. The Fe concentration was also not related to the place of origin of the barley variety. About 90% of total Fe was localized in the grain without hull. These results provide fundamental data for breeding Fe-rich cultivars and for studying the mechanisms involved in genotypic variation in Fe concentration.     

Mapping genes for deep-seeding tolerance in barley

Deep-seeding tolerance, the emergence of seedlings from deep seeded conditions, is involved in stand establishment in semi-arid regions, where the soil surface is too dry for seed germination. Genes determining deep-seeding tolerance in barley were mapped using two doubled haploid populations derived from the following crosses: Harrington × TR306 (H/T)and Step toe × Morex (S/M). Significant quantitative trait loci (QTLs) for deep-seeding tolerance were found in each population. Two QTL sex plained 40% of the phenotypic variation in the H/T population and one QTL (S/M) 8% of the total phenotypic variance. Multiple QTLs accounting for coleoptile length and first internode length were detected in both populations. In the H/T population, there were coincident QTLs for deep-seeding tolerance, coleoptile length and first internode length on the long arm of chromosome 5H. These QTLs correspond with previously reported QTLs for abscisic acid and gibberellic acid response. QTL coincidence may be due to the pleiotropic effects of alleles at a single locus. This information may be useful for breeding programs manipulating morphological and physiological traits in order to develop varieties for semi-arid regions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inheritance of gramine content in barley

The inheritance of gramine indole alkaloid was studied in F1 and F2 generations derived from crosses between wild ( Hordeum vulgare subsp. spontaneum) and cultivated ( H. vulgare subsp. vulgare) barley at adult stage in the field. The means of gramine content were very low in F1s and F2s in April and May. The ratio of progeny containing gramine to those without gramine (near zero or undetectable) fit a mono-genic or di-genic model in F2 generation. However, the content of gramine might be controlled by minor genes in the gramine-containing plants. The direction of dominance was toward lower gramine content. The averages of dominance ( h/d) in F1 and F2 ranged from partial to complete. Broad-sense heritabilities were high (0.70 to 0.77). The usefulness of hybrids for breeding aphid resistance and possibility increasing palatability of grazing pasture for sheep and cattle is discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Behavior of four broad-leaved tree species used to revegetate eroded granite hill slopes

Information on primary growth behavior after planting is required for mixed-plantation revegetation using broad-leaved species. To estimate primary growth, especially from the perspective of crown coverage and changing growth rates, we examined the growth and survival of four broad-leaved species that are frequently used in erosion-control plantations in Japan. The species studied were Myrica rubra Sieb. et Zucc., Alnus pendula Matsum., Quercus glauca Thunb., and Q. serrata Thunb. The survival, height, and basal diameter of planted trees were measured over a 4-year period, and crown area was calculated over a 3-year period. We found a negative relationship between relative growth rate (RGR) and survival rate, suggesting that fast growth may be fatal when resources are severely limited. The relative height growth rate (RHGR) of A. pendula was especially high during the early period of the study (1997–1999) and then drastically declined, whereas the opposite tendency was observed in Q. glauca. The results of stem allometry analyses conformed to the specific relationships between height growth and diameter growth of the four species; increases in stem thickness based on height increments were smaller in the pioneer species A. pendula. Between-species differences in coverage per planted tree (mean crown area multiplied by survival rate) were small as a result of the negative relationship between coverage area and survival rate.     

Leaf-fall phenology along a topography-mediated environmental gradient in a cool–temperate deciduous broad-leaved forest in Japan

Leaf-fall phenology was studied in a cool–temperate deciduous broad-leaved forest in central Japan in relation to the topographic environmental gradients that occur along a short mountain slope. Leaf-fall phenology was described quantitatively using data from leaf litter collected along the slope. In autumn, leaf fall at the study site tended to occur slightly earlier on the upper slope than on the lower slope. This pattern was found at both the stand and the species levels. Our results suggest that leaf-fall phenology may be affected by difference in microclimatic conditions, because environmental conditions are thought to be more severe on the upper slope than on the lower slope. The less intensive methods used in this study, the litter trap method, and Dixon’s model succeeded in quantifying the phenological patterns of leaf fall within stands and within species along the short mountain slope.     

Life cycles of individual roots in fine root system of Chamaecyparis obtusa Sieb. et Zucc.

Recent studies have remarked on differences in the life cycles of individual fine roots. However, the dynamics of individual roots with different life cycles, such as ephemeral and perennial, during root system development are still unknown. We examined individual roots during fine root system development in a mature stand of Chamaecyparis obtusa Sieb. et Zucc. (Cupressaceae) using the sequential ingrowth core method and an anatomical method. The visual classification, i.e., orange, red, brown, intact dead, and fragmented dead, of fine roots corresponded well with the anatomical classification. Orange and red roots contained passage cells, and brown roots contained cork cambium. The proportions of protoxylem groups differed among visual classes. Brown secondary roots were mainly triarch (43%) and tetrarch (40%) and rarely diarch (12%), whereas fragmented dead roots, which constituted more than 95% of the dead roots, were mainly diarch (67%). These results imply that triarch and tetrarch roots tend to form secondary roots, whereas diarch roots tend to become dead roots without secondary growth. Using the numbers of root tips and clusters, root system development could be classified into three stages: colonization, branching within the root system, and maintenance. During the colonization stage, mainly triarch and tetrarch roots, which tend to be secondary growth, invaded ingrowth cores. During the branching stage, primarily diarch roots, which tend to be ephemeral, emerged. Fine root system development involved the recruitment of different individual roots during the life cycle depending on the growth stage.     

Leaf-litter decomposition of 15 tree species in a lowland tropical rain forest in Sarawak: decomposition rates and initial litter chemistry

In a lowland tropical rain forest in Sarawak, leaf-litter decomposition and the initial litter chemistry of 15 tree species were studied. During 13 months of field experiment, weight loss of litter samples was between 44% and 91%, and calculated decomposition rate constants (k) ranged from 0.38 to 2.36 year⁻¹. The initial litter chemistry also varied widely (coefficients of variation: 19%–74%) and showed low N and P concentrations and high acid-insoluble residue (AIS) concentration. For nutrient-related litter chemistry, correlations with the decomposition rate were significant only for P concentration, C/P ratio, and AIS/P ratio (r _s = 0.59, −0.62, and −0.68, n = 15, P < 0.05, respectively). For organic constituents, correlations were significant for concentrations of AIS and total carbohydrates, and AIS/acid-soluble carbohydrate ratio (r _s = −0.81, 0.51, and −0.76, n = 15, P < 0.05, respectively). These results suggested that the relatively slow mean rate of decomposition (k = 1.10) was presumably due to the low litter quality (low P concentration and high AIS concentration), and that P might influence the decomposition rate; but organic constituents, especially the concentration of AIS, were more important components of initial litter chemistry than nutrient concentrations.