Iwate Agricultural Research Center

Kitakami, Japan

Iwate Agricultural Research Center

Kitakami, Japan

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Takahashi H.,Iwate Biotechnology Research Center | Abe H.,Iwate Agricultural Research Center | Fujita K.,Iwate Biotechnology Research Center | Sekine K.-T.,Iwate Biotechnology Research Center
Metabolomics | Year: 2017

Introduction: Gentian spotted bleaching disease (GSBD), a novel disease of unknown etiology, affects Gentiana triflora plants that are cultivated as ornamental flowers in Japan. This disease leads to the production of necrotic leaf spots, a delay in flowering, and has thus become a serious problem for gentian production. Objectives: The objective of this study was to identify the cause of GSBD in G. triflora by analyzing differences between healthy and GSBD-affected leaves. Method: Selected metabolite concentrations in healthy and GSBD-affected leaves were quantified using capillary electrophoresis and liquid chromatography-mass spectrometry, and statistically significant differences in metabolite concentrations were assessed. GSBD-affected metabolic pathways were identified followed by examination of pathway-related gene expression and enzyme activities. Furthermore, the effects of root hypoxia on metabolite concentrations and gene expression were investigated. Results: We found that concentrations of Calvin cycle intermediates and ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity were significantly lower in GSBD-affected leaves, whereas sucrose cleavage and Ala accumulation were enhanced. Since these metabolic changes are frequently observed in plants exposed to hypoxia, the expression of hypoxia-responsive genes was investigated. Expression levels of hypoxia-responsive genes were higher in GSBD-affected plants than in the controls. Furthermore, root hypoxia induced similar symptoms and metabolic changes as those observed in GSBD-affected plants. Conclusion: Our results indicate that GSBD was likely induced by root hypoxia and that metabolome analysis is an effective tool for identifying the cause of plant disease with unknown etiologies. © 2017, Springer Science+Business Media New York.


Takagi H.,Iwate Biotechnology Research Center | Takagi H.,Iwate University | Abe A.,Iwate University | Abe A.,Iwate Agricultural Research Center | And 12 more authors.
Plant Journal | Year: 2013

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps. © 2013 The Authors The Plant Journal © 2013 Blackwell Publishing Ltd.


Hori K.,Japan National Institute of Agrobiological Science | Sugimoto K.,Japan National Institute of Agrobiological Science | Nonoue Y.,Institute of the Society for Techno innovation of Agriculture | Ono N.,Institute of the Society for Techno innovation of Agriculture | And 5 more authors.
Theoretical and Applied Genetics | Year: 2010

Backcrossed inbred lines (BILs) and a set of reciprocal chromosome segment substitution lines (CSSLs) derived from crosses between japonica rice cultivars Nipponbare and Koshihikari were used to detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance. In the BILs, we detected one QTL on chromosome 3 and one QTL on chromosome 12. The QTL on the short arm of chromosome 3 accounted for 45.0% of the phenotypic variance and the Nipponbare allele of the QTL increased germination percentage by 21.3%. In the CSSLs, we detected seven QTLs, which were located on chromosomes 2, 3 (two), 5, 8 and 11 (two). All Nipponbare alleles of the QTLs were associated with an increased rate of germination. The major QTL for pre-harvest sprouting resistance on the short arm of chromosome 3 was localized to a 474-kbp region in the Nipponbare genome by the SSR markers RM14240 and RM14275 by using 11 substitution lines to replace the different short chromosome segments on chromosome 3. This QTL co-localized with the low-temperature germinability gene qLTG3-1. The level of germinability under low temperature strongly correlated with the level of pre-harvest sprouting resistance in the substitution lines. Sequence analyses revealed a novel functional allele of qLTG3-1 in Nipponbare and a loss-of-function allele in Koshihikari. The allelic difference in qLTG3-1 between Nipponbare and Koshihikari is likely to be associated with differences in both pre-harvest sprouting resistance and low-temperature germinability. © 2010 The Author(s).


Abe A.,Iwate Agricultural Research Center | Abe A.,Iwate University | Kosugi S.,Iwate Biotechnology Research Center | Yoshida K.,Iwate Biotechnology Research Center | And 12 more authors.
Nature Biotechnology | Year: 2012

The majority of agronomic traits are controlled by multiple genes that cause minor phenotypic effects, making the identification of these genes difficult. Here we introduce MutMap, a method based on whole-genome resequencing of pooled DNA from a segregating population of plants that show a useful phenotype. In MutMap, a mutant is crossed directly to the original wild-type line and then selfed, allowing unequivocal segregation in second filial generation (F 2) progeny of subtle phenotypic differences. This approach is particularly amenable to crop species because it minimizes the number of genetic crosses (n = 1 or 0) and mutant F 2 progeny that are required. We applied MutMap to seven mutants of a Japanese elite rice cultivar and identified the unique genomic positions most probable to harbor mutations causing pale green leaves and semidwarfism, an agronomically relevant trait. These results show that MutMap can accelerate the genetic improvement of rice and other crop plants. © 2012 Nature America, Inc. All rights reserved.


Nekoduka S.,Iwate Agricultural Research Center | Nekoduka S.,Iwate University | Tanaka K.,Hirosaki University | Sano T.,Hirosaki University
Journal of General Plant Pathology | Year: 2013

Overwintering of the brown leaf spot fungus, Mycochaetophora gentianae, in infected gentian leaves was studied in Iwate, northern Japan. Sporophores were produced on overwintered, infected leaves when they were sampled from January to July, but not in August after incubation in high humidity at 15 °C. Symptoms developed on gentian plants grown in soil artificially infested with overwintered, infected leaves that were either left throughout the experiments or removed before planting. Few lesions developed when plants were grown in soil infested with conidia. These results indicate that M. gentianae can overwinter in infected leaves, which act as the primary inoculum source. © 2013 The Phytopathological Society of Japan and Springer Japan.


Okuyama Y.,Iwate Biotechnology Research Center | Kanzaki H.,Iwate Biotechnology Research Center | Abe A.,Iwate Agricultural Research Center | Yoshida K.,Iwate Biotechnology Research Center | And 10 more authors.
Plant Journal | Year: 2011

The Oryza sativa (rice) resistance gene Pia confers resistance to the blast fungus Magnaporthe oryzae carrying the AVR-Pia avirulence gene. To clone Pia, we employed a multifaceted genomics approach. First, we selected 12 R-gene analog (RGA) genes encoding nucleotide binding site-leucine rich repeats (NBS-LRRs) proteins from a region on chromosome 11 that shows linkage to Pia. By using seven rice accessions, we examined the association between Pia phenotypes and DNA polymorphisms in the 10 genes, which revealed three genes (Os11gRGA3-Os11gRGA5) exhibiting a perfect association with the Pia phenotypes. We also screened ethyl methane sulfonate (EMS)-treated mutant lines of the rice cultivar 'Sasanishiki' harboring Pia, and isolated two mutants that lost the Pia phenotype. DNA sequencing of Os11gRGA3-Os11gRGA5 from the two mutant lines identified independent mutations of major effects in Os11gRGA4. The wild-type 'Sasanishiki' allele of Os11gRGA4 (SasRGA4) complemented Pia function in both mutants, suggesting that SasRGA4 is necessary for Pia function. However, when the rice cultivar 'Himenomochi' lacking Pia was transfected with SasRGA4, the Pia phenotype was not recovered. An additional complementation study revealed that the two NBS-LRR-type R genes, SasRGA4 and SasRGA5, that are located next to each other and oriented in the opposite direction are necessary for Pia function. A population genetics analysis of SasRGA4 and SasRGA5 suggests that the two genes are under long-term balancing selection. © 2011 Blackwell Publishing Ltd.


Nekoduka S.,Iwate Agricultural Research Center | Nekoduka S.,Iwate University | Tanaka K.,Hirosaki University | Sano T.,Hirosaki University
Journal of General Plant Pathology | Year: 2010

When the influence of host species, inoculum density, temperature, leaf wetness duration, and leaf position on the incidence of gentian brown leaf spot caused by Mycochaetophora gentianae, was examined, the fungus severely infected all seven Gentiana triflora cultivars, but failed to infect two cultivars of G. scabra and an interspecific hybrid cultivar. Inoculum density correlated closely with disease incidence, and a minimum of 102 conidia/mL was enough to cause infection. In an analysis of variance, temperature and leaf wetness duration had a significant effect upon disease incidence, which increased with higher temperature (15-25°C) and longer duration of leaf wetness (36-72 h). No disease developed at temperatures lower than 10°C or when leaf wetness lasted <24 h. At 48-h leaf wetness, disease incidence was 0,28,77, and 85% at 10, 15, 20, and 25°C, respectively. Middle and lower leaves on the plant were more susceptible than upper leaves. In microscopic observations of inoculated leaves, >50% of conidia germinated at temperatures >15°C after 24-h leaf wetness. More appressoria formed at higher temperatures (15-25°C) with extended duration of leaf wetness (24-72 h). At 48-h leaf wetness, appressorium formation was 0,8,26, and 73% at 10,15,20, and 25°C, respectively. These results suggest that temperature and leaf wetness duration were important factors for infection of gentian leaves. © 2010 The Phytopathological Society of Japan and Springer.


Imaizumi T.,Japan National Agricultural Research Center | Kataoka Y.,Akita | Ogata S.,Iwate Agricultural Research Center | Uchino A.,Japan National Agricultural Research Center
Weed Research | Year: 2013

To reveal the effects of herbicide selection on genetic diversity in the outcrossing weed species Schoenoplectus juncoides, six sulfonylurea-resistant (SU-R) and eight sulfonylurea-susceptible (SU-S) populations were analysed using 40 polymorphic inter-simple sequence repeat loci. The plants were collected from three widely separated regions: the Tohoku, Kanto and Kyushu districts of Japan. Genetic diversity values (Nei's gene diversity, h) within each SU-S population ranged from h = 0.125 to h = 0.235. The average genetic diversity within the SU-S populations was HS = 0.161, and the total genetic diversity was HT = 0.271. Although the HS of the SU-R populations (0.051) was lower than that of the SU-S populations, the HT of the SU-R populations (0.202) was comparable with that of the SU-S populations. Most of the genetic variation was found within the region for both the SU-S and SU-R populations (88% of the genetic variation respectively). Two of the SU-R populations showed relatively high genetic diversity (h = 0.117 and 0.161), which were comparable with those of the SU-S populations. In contrast, the genetic diversity within four SU-R populations was much lower (from h = 0 to 0.018) than in the SU-S populations. The results suggest that selection by sulfonylurea herbicides has decreased genetic diversity within some SU-R populations of S. juncoides. The different level of genetic diversity in the SU-R populations is most likely due to different levels of inbreeding in the populations. Weed Research © 2013 European Weed Research Society534 August 2013 10.1111/wre.12027 Original Article Research Papers © 2013 The Authors Weed Research © 2013 European Weed Research Society.


Yamaguchi T.,Iwate Agricultural Research Center
Acta Horticulturae | Year: 2012

In Japan, asparagus ferns undergo yellowing in autumn, and the germination of the buds is suppressed even when they are exposed to optimum temperatures. This phenomenon is called "dormancy", and low temperatures are necessary for breaking dormancy. To harvest asparagus during winter, forcing culture is performed in part by using dug rootstocks. This method is called "Fusekomi forcing culture". While the major factor affecting the induction of dormancy is the cumulative exposure to chilling temperatures, the photoperiod is also considered to be a possible factor affecting the induction of dormancy. In this study, we investigated the effect of short-day photoperiod on asparagus growth in autumn by using 1-year-old 'Welcome' plants. The plants were sown in early February and grown in non-woven fabric pots with a diameter of 25 cm. From late August, these pots were subjected to 8-h short-day photoperiod (SD) or natural photoperiod (ND; average time, 12 h 06 min). After the treatment, the pots were placed in a greenhouse, and the soil temperature was adjusted to 16°C. There was no difference between the yellowing of asparagus ferns in the SD- and ND-treated plants. The number of stems in the SD-treated plants was slightly greater than that in the NDtreated plants; the plant height in the former group was lower than that in the latter group. The brix value of the root increased with time; the value for the ND-treated plants was greater than that for the SD-treated plants. The root weight showed a similar trend. However, if the temperature of the surroundings is suitable for breaking bud, SD and ND treatments do not have any difference. On the basis of these results, we believe that the dormancy of 1-year-old asparagus in autumn was not influenced by short-day conditions; rather, it was affected only by the reduction in photosynthesis.


Takaki K.,Iwate University | Takahata J.,Iwate University | Watanabe S.,Iwate University | Satta N.,Iwate University | And 3 more authors.
Journal of Physics: Conference Series | Year: 2013

The drainage water from plant pots was irradiated by plasma and then recycled to irrigate plants for improving the growth rate by supplying nutrients to plants and inactivating the bacteria in the bed-soil. Brassica rapa var. perviridis (Chinese cabbage; Brassica campestris) plants were cultivated in pots filled with artificial soil, which included the use of chicken droppings as a fertiliser. The water was recycled once per day from a drainage water pool and added to the bed-soil in the pots. A magnetic compression type pulsed power generator was used to produce underwater discharge with repetition rate of 250 pps. The plasma irradiation times were set as 10 and 20 minutes per day over 28 days of cultivation. The experimental results showed that the growth rate increased significantly with plasma irradiation into the drainage water. The growth rate increased with the plasma irradiation time. The nitrogen concentration of the leaves increased as a result of plasma irradiation based on chlorophyll content analysis. The bacteria in the drainage water were inactivated by the plasma irradiation. © Published under licence by IOP Publishing Ltd.

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