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Jannink J.-L.,Cornell University | Jannink J.-L.,U.S. Department of Agriculture | Lorenz A.J.,U.S. Department of Agriculture | Iwata H.,Japan National Agricultural Research Center
Briefings in Functional Genomics and Proteomics | Year: 2010

We intuitively believe that the dramatic drop in the cost of DNA marker information we have experienced should have immediate benefits in accelerating the delivery of crop varieties with improved yield, quality and biotic and abiotic stress tolerance. But these traits are complex and affected by many genes, each with small effect. Traditional marker-assisted selection has been ineffective for such traits. The introduction of genomic selection (GS), however, has shifted that paradigm. Rather than seeking to identify individual loci significantly associated with a trait,GS uses all marker data as predictors of performance and consequently delivers more accurate predictions. Selection can be based on GS predictions, potentially leading to more rapid and lower cost gains from breeding. The objectives of this article are to review essential aspects of GS and summarize the important take-home messages from recent theoretical, simulation and empirical studies.We then look forward and consider research needs surrounding methodological questions and the implications of GS for long-term selection. © The Author 2010. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.


Iwasaki K.,Osaka University | Iwasaki K.,Japan Science and Technology Agency | Omura T.,Japan National Agricultural Research Center
Current Opinion in Structural Biology | Year: 2010

Visualizing the viral life cycle in the host challenges us to extend our understanding of the viral infection mechanism. Three-dimensional images obtained by advanced electron tomographic imaging techniques, if resolved to molecular resolution, are helpful for bridging the atomic structural information of proteins to cellular events. Characteristic large structures appear in virus-infected host cells through the life cycle of various viruses. These structures are likely to provide clues to understanding viral infection mechanisms, such as how viruses move in host cells, how they are assembled, how they egress and how they spread cell-to-cell. Here we review recent advances in the studies of the molecular architecture of virus machinery involved in the mechanism of virus infection using comprehensive electron tomographic imaging techniques. © 2010 Elsevier Ltd.


Takahashi S.,Japan National Agricultural Research Center
Journal of Plant Nutrition and Soil Science | Year: 2013

Characterization of the forms of phosphorus (P) in organic soil amendments was conducted by sequential P fractionation. More than 60% of total P was inorganic P (Pi). The major Pi forms in the cattle-manure composts were NaHCO3- and HCl-extractable P fractions. HCl-extractable Pi was the predominant P form and a considerable proportion of the total P was present in the HCl-extractable organic P fraction in the poultry manure composts and combined organic fertilizers. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Herbivore-induced plant volatiles (HIPVs) emitted from lima bean leaves infested with the two-spotted spider mites Tetranychus urticae strongly attract the predatory mites Neoseiulus californicus. Among these HIPVs, methyl salicylate and linalool can attract the predators. Three green-leaf volatiles (GLVs) of (Z)-3-hexen-1-ol, (Z)-3-hexenyl acetate and (E)-2-hexenal, found in the odor blends from T. urticae-infested leaves and physically damaged leaves, can also attract the predators. To search for a strong predator attractant, the olfactory responses of N. californicus to each synthetic compound or their combinations were investigated in a Y-tube olfactometer. When presented a choice between a mixture of the five compounds (i.e. the two HIPVs and the three GLVs) and T. urticae-infested leaves, N. californicus did not discriminate between these odor sources. The same trend was observed when either a mixture of the two HIPVs or methyl salicylate vs. T. urticae-infested leaves were compared. In contrast, the predators preferred T. urticae-infested leaves to linalool, each of the three GLVs, or a mixture of the three GLVs. These results indicated that methyl salicylate is a strong predator attractant, and its potential attractiveness almost equaled that of the blend of HIPVs from T. urticae-infested leaves. © 2009 Springer Science+Business Media B.V.


Hayashi T.,Japan National Institute of Agrobiological Science | Iwata H.,Japan National Agricultural Research Center
BMC Genetics | Year: 2010

Background: In genomic selection, a model for prediction of genome-wide breeding value (GBV) is constructed by estimating a large number of SNP effects that are included in a model. Two Bayesian methods based on MCMC algorithm, Bayesian shrinkage regression (BSR) method and stochastic search variable selection (SSVS) method, (which are called BayesA and BayesB, respectively, in some literatures), have been so far proposed for the estimation of SNP effects. However, much computational burden is imposed on the MCMC-based Bayesian methods. A method with both high computing efficiency and prediction accuracy is desired to be developed for practical use of genomic selection.Results: EM algorithm applicable for BSR is described. Subsequently, we propose a new EM-based Bayesian method, called wBSR (weighted BSR), which is a modification of BSR incorporating a weight for each SNP according to the strength of its association to a trait. Simulation experiments show that the computational time is much reduced with wBSR based on EM algorithm and the accuracy in predicting GBV is improved by wBSR in comparison with BSR based on MCMC algorithm. However, the accuracy of predicted GBV with wBSR is inferior to that with SSVS based on MCMC algorithm which is currently considered to be a method of choice for genomic selection.Conclusions: EM-based wBSR method proposed in this study is much advantageous over MCMC-based Bayesian methods in computational time and can predict GBV more accurately than MCMC-based BSR. Therefore, wBSR is considered a practical method for genomic selection with a large number of SNP markers. © 2010 Hayashi and Iwata; licensee BioMed Central Ltd.


Yoshida M.,Japan National Agricultural Research Center | Nakajima T.,Japan National Agricultural Research Center
Phytopathology | Year: 2010

The manner in which deoxynivalenol (DON) and nivalenol (NIV) accumulation progresses in wheat grain infected with Fusarium graminearum and the influence of the time of infection on the accumulation of toxins were investigated. Four cultivars were tested in a greenhouse environment, where the plants were spray inoculated at three different stages with a mixture of DON and NIV chemotypes of F. graminearum. The results indicate that high levels of DON and NIV can be produced beyond 20 days after anthesis (DAA), even by early infection. The results of field experiments performed on seven cultivars, where inoculation was conducted using colonized maize kernel inoculum, were consistent with the greenhouse results. In addition, in the greenhouse experiments, late infection, at least as late as 20 DAA, caused grain contamination with these toxins even without clear disease symptoms on the spike. These results indicate the importance of the late stage in grain development in DON and NIV contamination, suggesting that control strategies that cover the late as well as the early stage of grain development should be established to effectively reduce the risk of these toxins' contaminating wheat. © 2010 The American Phytopathological Society.


Takahashi M.,Japan National Agricultural Research Center
Reproductive Medicine and Biology | Year: 2012

In most mammalian species including cattle, heat stress has deleterious effects on nutritional, physiological and reproductive functions. Exposure of animals to a hot environment causes an increase in body temperature in mammals, including domestic animals. High ambient temperature also causes a decrease in the length and intensity of estrus by disturbing ovarian function as well as decreasing pregnancy rate after artificial insemination. Therefore, it is important to understand the effects of heat stress on reproductive function in order to improve the production of domestic animals. Heat stress decreases appetite, weight gain, and milk yield in dairy cattle. It also adversely affects the reproductive performance of both sexes. In males, it reduces spermatogenic activity, while in females it adversely impacts oogenesis, oocyte maturation, fertilization development and implantation rate. Detection and evaluation of the deteriorating effects of heat stress on reproductive organs and cells can help to design measures to prevent them and improve reproductive functions. In this review, we discuss the impacts of heat stress on reproductive functions. © Japan Society for Reproductive Medicine 2011.


Yamakawa H.,Japan National Agricultural Research Center | Hakata M.,Japan National Agricultural Research Center
Plant and Cell Physiology | Year: 2010

High temperature impairs grain filling by inhibiting the deposition of storage materials such as starch and protein. To comprehend its impact on grain filling metabolism in rice (Oryza sativa), levels of metabolites and transcripts related to central pathways of metabolism were simultaneously determined in developing caryopses exposed to high temperature (33°C/28°C) and a control temperature (25°C/20°C) during the milky stage. A capillary electrophoresis-based metabolomic analysis revealed that high temperature increased the accumulation of sucrose and pyruvate/oxaloacetate-derived amino acids and decreased levels of sugar phosphates and organic acids involved in glycolysis/gluconeogenesis and the tricarboxylic acid (TCA) cycle, respectively. A transcriptomic analysis using a whole genome-covering microarray unraveled the possible metabolic steps causing the shortage of storage materials under the elevated temperature. Starch deposition might be impaired by down-regulation of sucrose import/degradation and starch biosynthesis, and/or up-regulation of starch degradation as well as inefficient ATP production by an inhibited cytochrome respiration chain, as indicated by the response of gene expression to high temperature. Amino acid accumulation might be attributed to the heat-stable import of amino acids into the caryopsis and/or repression of protein synthesis especially the tRNA charging step under high temperature. An atlas showing the effect of high temperature on levels of metabolites and gene expression in the central metabolic pathways is presented. © 2010 The Author.


Takahashi S.,Japan National Agricultural Research Center
Communications in Soil Science and Plant Analysis | Year: 2014

Phosphorus (P) fractionation of composted crop residues and Andosols amended with composted crop residues was conducted. Inorganic P (Pi) comprised 85% of total P in the composts. The distribution of inorganic P forms was in the following order: sodium hydroxide (NaOH) Pi > hydrochloric acid (HCl) Pi > sodium bicarbonate (NaHCO3) Pi > water (H2O) Pi. After 22 years of the compost application to two Andosols, total Pi concentration significantly increased. However, total organic P (Po) concentration in the composted soil was not significantly different from that in noncomposted soil. Among of Pi fractions, compost application distinctly increased Al-Pi concentration, followed by Fe-Pi. The ratio of Fe-Po to total P concentrations significantly decreased by compost application. Copyright © Taylor & Francis Group, LLC.


Hattori T.,Japan National Agricultural Research Center | Morita S.,University of Tokyo
Plant Production Science | Year: 2010

Bioethanol is gathering attention as a countermeasure to global warming and as an alternative energy for gasoline. Meanwhile, due to the synchronous increase in bioethanol production and grain prices, the food-fuel competition has become a public issue. It is necessary to see the issue objectively and to recognize that the real background is the change in allocation of limited resources such as farmland and water. In this review, we discuss which, where and how energy crops should be grown to establish a sustainable bioethanol production system. Several combinations of crops, areas and cultivation methods are recommended as a result of a survey of the bioethanol production system with various energy crops. In tropical and subtropical regions, sugarcane can be grown in agricultural and/or unused favorable lands. In other regions, cellulosic energy crops can be grown in abandoned and marginal lands, including lands contaminated with inorganic pollutant like heavy metals and some detrimental minerals. There also is the possibility that, for Japan and other Asian countries, rice can be grown as an energy crop in unused lowland paddy field. Regarding cultivation way, energy saving is beneficial for bioethanol production systems irrespective of energy efficiency. On the other hand, effective energy input should be considered for the systems with higher energy efficiency when available land area is limited. Exploring and developing new energy crops and varieties, which show higher biomass productivity and stress tolerances under marginal conditions, are necessary for sustainable bioethanol production because energy crop production would be restricted mostly to marginal areas in future.

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