Rice Metabolomics

Metabolomics is a recently developed technology for comprehensive analysis of metabolites in organisms. Plant metabolites that are produced for the growth, development, and chemical defense of plants against climatic alterations or natural predators are also useful to us as nutrients or medicines; hence, it is important to comprehend the amounts and varieties of plant metabolites. Besides providing an understanding of the metabolic state in plants under various circumstances, metabolomic techniques are applicable to the clarification of the functions of unknown genes by using natural variants or mutants of the target plants. Furthermore, a metabolomic approach might be useful in the breeding of crops, since valuable plant traits such as taste and yield are closely related to metabolic conditions. Here, we describe the methodology of metabolomics including sample extraction and preparation, metabolite detection, and data processing and analysis, and introduce the application of metabolomic studies to rice.     

Field level damage of deepwater rice by the 2011 Southeast Asian Flood in a flood plain of Tonle Sap Lake,Northwest Cambodia

The 2011 flood damaged about 11 % of planting area in Cambodia, but the damaged proportion reached 30 % in Sangke district, Battambang province, located in the flood plains of Tonle Sap Lake. The aim of this study was to characterize completely damaged deepwater rice production due to the flood along the transect from the town-side shallower fields to the lake-side deeper fields. The flooding water from Tonle Sap Lake rose with 7 cm/day in September and October in the deeper fields where floating rice was grown and 8–10 cm/day in October in the shallower fields where lowland rice was grown. The maximum water was recorded on 16 October with 3.2 and 2.0 m at the deepest and shallowest edge fields. The area was characterized as flatness with only 1.2 m elevation differences in 4.3 km distance along the transect. The flooding water took 13.7 h for approaching 100 m distance. Complete recession of flood water was end of November at the shallow edge and at late December in the deep edge in 2011. The flooding duration deeper than 50 cm was 2.5 month and nearly 3 months in the middle zone and deeper floating rice area, respectively. The complete submergence started first in some fields in the middle zone on 12 September, followed by the shallower lowland rice area, and finally in the deep floating rice area by 1 October. Countermeasures to improve rice production in deepwater rice area in the floodplain of Tonle Sap Lake were proposed.     

Growth of juvenile chub mackerel Scomber japonicus in the western North Pacific Ocean: with application and validation of otolith daily increment formation

The growth of juvenile chub mackerel Scomber japonicus collected in the western North Pacific Ocean in 2007 and 2009 was examined based on the evidence of otolith daily increment formation in captive specimens. There was a significant difference in the relationship between known age and number of increments in the frontal and sagittal planes. Repeated markings on the otolith using Alizarin complexone and the coefficient of variation in number of increments suggest that the increments in the frontal plane of the otolith are more suitable for age estimation than those in the long and short axes of the sagittal plane. The increments in the frontal plane formed daily, and the first ring was usually deposited 3 days after hatch. Age of wild juveniles ranged from 24 to 211 days after hatch based on the frontal plane method. The estimated hatching periods of specimens ranged from February to June, but the April-hatched specimens were collected throughout the sampling periods of 2007 and 2009. The Gompertz growth model showed a difference in growth pattern in specimens between 2007 and 2009. The juveniles in 2009 appeared to grow more quickly than those in 2007 until summer, but thereafter the 2009 specimens seemed to grow more slowly.     

Soil seedbanks in slash‐and‐burn rice fields of northern Laos

Crops in shifting cultivation fields often suffer from severe weed infestation when long fallow periods are replaced by short fallow periods. The soil seedbank as a source of weed infestation was studied in four fields that differed in their last fallow duration. The effect of burning was analysed by comparing adjacent pre‐burn and post‐burn samples (two sites). Surface vegetation was monitored from burning to harvest in the plots from which soil samples were taken to determine the fraction of the seedbank germinating (three sites). Seedbank size (1700–4000 seedlings m^?2) varied depending on a single species, Mimosa diplotricha. Burning reduced emergence of most species, but stimulated emergence in others. Densities in the seedbank were not correlated with above‐ground abundances in the field, except for some species. Most species emerging after 50 days from the soil samples (40% of seedlings) were absent from the field after 190 days. Whilst the data from this study are derived from only four fields, the weed problems after short‐term fallowing appeared to be due to a larger fraction of the seedbank emerging, possibly due to shallow burial, and to a floristic shift towards adaption to burning, rather than the size of the seedbank per se.     

Occurrence of bacterial black shoot disease of European pear in Yamagata Prefecture

Black lesions on shoots of European pear trees observed in an orchard in Yamagata Prefecture in May 2007 were suspected to be caused by a bacterial pathogen. The surface of the colonies isolated on a high sucrose medium did not have the crater morphology that is characteristic of E. amylovora bvs. 1–3, and a specific DNA fragment was amplified from the isolates in the PCR using the EprpoD primer set. The partial sequences of the 16S rRNA gene placed the isolates in the genus Erwinia. The isolates differed serologically from E. amylovora biovars and E. pyrifoliae in an Ouchterlony double-diffusion test although their bacterial properties suggested that they are closely related to E. amylovora biovars and E. pyrifoliae. In a DNA–DNA hybridization test, the relatedness between the isolates and E. amylovora biovars or E. pyrifoliae did not exceed 70% level, indicating that they are independent species. Thus, the isolates belongs to the genus Erwnia but are not E. amylovra or E. pyrifoliae. After succulent pear shoots were injected with bacterial suspensions (10⁹, 10⁸, 10⁷ and 10⁶ cfu/ml) of the isolates, lesions formed with 10⁹ and 10⁸ cfu/ml, but the disease incidence with 10⁸ cfu/ml was much lower than with E. amylovora and E. pyrifoliae. Virulence of the present isolates is thus thought to be very weak. On the basis of these results, we consider that this is a new shoot disease of European pear. In the 2007 season, all affected trees were pulled out after harvest. No symptoms have been observed in field surveys since the fruitlet season in 2007.     

Basic studies on hybrid wheat breeding using the 1BL-1RS translocation chromosome / Aegilops kotschyi cytoplasm system 1. Development of male sterile and maintainer lines with discovery of a new fertility-restorer

The Aegilops kotschyi cytoplasm and a 1BL-1RS translocation chromosome that consists of the long arm of wheat chromosome 1B and the short arm of rye chromosome 1R were transferred to six spring common wheat cultivars by repeated backcrossing. Resistance to leaf rust race 21B conditioned by the Lr26 gene and a secalin subunit encoded by the Sec-1 gene, both on the 1RS arm, were used as the selection markers of the translocation chromosome. Five of the six cultivars used were converted to complete male steriles, whereas the remaining one, cv. Kitamiharu 48, retained normal fertility, after transfer of both the 1BL-1RS chromosome and Ae. Kotschyi cytoplasm. Conventional gene analysis suggested that Kitamiharu 48 carries an incompletely dominant fertility-restoring gene. The F₁ hybrids between the male steriles and ordinary common wheat cultivars recovered fertility only at a low level, indicating that a single dose of the Rfv1 gene on the 1BS arm of wheat is insufficient for full fertility restoration under spring-sowing condition. Our results are in clear contrast to complete fertility restoration under fall-sowing condition reported by Nonaka et al. (1993). Combination of the 1BL-1RS chromosome / Ae. Kotschyi cytoplasm system with a new fertility-restoring gene discovered in Kitamiharu 48 may provide a breakthrough for spring-type hybrid wheat. This revised version was published online in August 2006 with corrections to the Cover Date.     

Quantitative trait loci analysis for growth and carcass traits in a Meishan x Duroc F2 resource population

We constructed a pig F2 resource population by crossing a Meishan sow and a Duroc boar to locate economically important trait loci. The F2 generation was composed of 865 animals (450 males and 415 females) from four F1 males and 24 F1 females and was genotyped for 180 informative microsatellite markers spanning 2,263.6 cM of the whole pig genome. Results of the genome scan showed evidence for significant quantitative trait loci (<1% genomewise error rate) affecting weight at 30 d and average daily gain on Sus scrofa chromosome (SSC) 6, carcass yield on SSC 7, backfat thickness on SSC 7 and SSC X, vertebra number on SSC 1 and SSC 7, loin muscle area on SSC 1 and SSC 7, moisture on SSC 13, intramuscular fat content on SSC 7, and testicular weight on SSC 3 and SSC X. Moreover, 5% genomewise significant QTL were found for birth weight on SSC 7, average daily gain on SSC 4, carcass length on SSC 6, SSC 7, and SSC X and lightness (L value) on SSC 3. We identified 38 QTL for 28 traits at the 5% genomewise level. Of the 38 QTL, 24 QTL for 17 traits were significant at the 1% genomewise level. Analysis of marker genotypes supported the breed of origin results and provided further evidence that a suggestive QTL for circumference of cannon bone also was segregating within the Meishan parent. We identified genomic regions related with growth and meat quality traits. Fine mapping will be required for their application in introgression programs and gene cloning.     

An outbreak of systemic granulomatous disease in cows with high milk yields

Seven of 92 lactating Holstein cows on a dairy farm developed urticaria with alopecia and decreased milk production, and three of the seven died over the course of 7 to 18 days. Pathologic examination of the three cows, including the two dead and one euthanized cow, revealed that the skin, liver, spleen, kidneys, heart, salivary glands, pancreas, adrenal glands, mammary glands, lymph nodes, and trigeminal ganglia had lymphocytic to lymphogranulomatous inflammation. Inflammation predominated by lymphocytic infiltration was prominent in the heart, pancreas, mammary glands, adrenal gland, and trigeminal ganglia. Severe granulomatous inflammation with multinucleated giant cells was present in the spleen and kidneys. These lesions and their distributions were most similar to those seen in suspected cases of citrus pulp toxicosis and hairy vetch toxicosis. The outbreak of this disease resolved with the elimination of Citrus pulp from the feed. Immunohistochemical detection of lymphocytes and macrophage markers confirmed dramatic hyperplasia of CD3-positive T lymphocytes in these lesions. This strongly suggested that a type 4 hypersensitivity reaction played a role in the development of the lesions.