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Ammiraju J.S.S.,University of Arizona | Song X.,University of Arizona | Luo M.,Huazhong Agricultural University | Sisneros N.,University of Arizona | And 12 more authors.
Breeding Science | Year: 2010

Rice was the first crop to have a high-quality reference genome sequence and is now at the forefront of intense functional and evolutionary research for two reasons-its central role in world food security, and its status as a model system for grasses. A thorough characterization of the rice genome cannot be accomplished without a deep understanding of its evolutionary history. The genus Oryza contains two cultivated and 22 wild rice species that represent 10 distinct genome types embedded within a robust phylogeny spanning a ~15 million year time span. The genus contains an untapped reservoir of agriculturally important traits and a historical record of genomic changes (especially those related to domestication, polyploidy, speciation and adaption).The two main objectives of the 'Oryza Map Alignment Project' (OMAP) were to functionally characterize the rice genome from a comparative standpoint and to provide essential tools to leverage the novel genetic diversity from wild relatives for rice improvement. The objective of this review is to summarize our efforts towards developing the most comprehensive genus-wide set of publicly available BAC resources for the genus Oryza, the first of its kind among plants (and perhaps higher eukaryotes), and their applications.

Komiya R.,National Institute of Genetics NIG | Nonomura K.-I.,National Institute of Genetics NIG
Methods in Molecular Biology | Year: 2014

The small noncoding RNAs in plants are categorized into two major classes, 21-nucleotides (nt) micro RNA (miRNA) and 21- or 24-nt small-interfering RNA (siRNA). ARGONAUTE (AGO) proteins associate with small RNAs and play central roles in transcriptional and posttranscriptional gene regulation. In plants, AGO1-miRNA complexes mainly regulate developmental processes, and AGO4-siRNA complexes suppress the activity of transposons and exogenous viral infections via RNA-directed DNA methylation. In many animal species, the PIWI-subfamily AGOs interact with PIWI-interacting RNAs (piRNAs), which are most commonly 24-34 nt, and function to tame transposons and to regulate mRNA translation and stability in the germline. The rice protein MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1) is a plant AGO member that has roles specific to development and maintenance of germ cells before meiosis. MEL1-binding small RNAs are mainly 21 nt, have a 5′-terminal cytosine, and are distinct from animal piRNAs. In this chapter, we describe methods for RNA-immunoprecipitation (RNA-IP) using a specific antibody that recognizes MEL1 and subsequent purification of MEL1-associating small RNAs from the IP fraction. We also introduce the bioinformatic procedures including mapping, annotation, and identifying small RNA clusters on the rice genome. © 2014 Springer Science+Business Media, LLC.

Arakawa T.,Aichi University of Technology | Tanave A.,National Institute of Genetics NIG | Ikeuchi S.,Okayama University of Science | Takahashi A.,National Institute of Genetics NIG | And 14 more authors.
Journal of Neuroscience Methods | Year: 2014

Background: Owing to their complex nature, social interaction tests normally require the observation of video data by a human researcher, and thus are difficult to use in large-scale studies. We previously established a statistical method, a hidden Markov model (HMM), which enables the differentiation of two social states ("interaction" and "indifference"), and three social states ("sniffing", "following", and "indifference"), automatically in silico. New method: Here, we developed freeware called DuoMouse for the rapid evaluation of social interaction behavior. This software incorporates five steps: (1) settings, (2) video recording, (3) tracking from the video data, (4) HMM analysis, and (5) visualization of the results. Results: Using DuoMouse, we mapped a genetic locus related to social interaction. We previously reported that a consomic strain, B6-Chr6CMSM, with its chromosome 6 substituted for one from MSM/Ms, showed more social interaction than C57BL/6 (B6). We made four subconsomic strains, C3, C5, C6, and C7, each of which has a shorter segment of chromosome 6 derived from B6-Chr6C, and conducted social interaction tests on these strains. DuoMouse indicated that C6, but not C3, C5, and C7, showed higher interaction, sniffing, and following than B6, specifically in males. Comparison with existing method: The data obtained by human observation showed high concordance to those from DuoMouse. The results indicated that the MSM-derived chromosomal region present in C6-but not in C3, C5, and C7-associated with increased social behavior. Conclusions: This method to analyze social interaction will aid primary screening for difference in social behavior in mice. © 2014 Elsevier B.V.

Komiya R.,National Institute of Genetics NIG | Komiya R.,Okinawa Institute of Science and Technology | Ohyanagi H.,Plant Genetics Laboratory | Ohyanagi H.,Mitsubishi Group | And 7 more authors.
Plant Journal | Year: 2014

Small RNAs that interact with Argonaute (AGO) proteins play central roles in RNA-mediated silencing. MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1), a rice AGO, has specific functions in the development of pre-meiotic germ cells and the progression of meiosis. Here, we show that MEL1, which is located mostly in the cytoplasm of germ cells, associates preferentially with 21-nucleotide phased small interfering RNAs (phasiRNAs) that bear a 5′-terminal cytosine. Most phasiRNAs are derived from 1171 intergenic clusters distributed on all rice chromosomes. From these clusters, over 700 large intergenic, non-coding RNAs (lincRNAs) that contain the consensus sequence complementary to miR2118 are transcribed specifically in inflorescences, and cleaved within the miR2118 site. Cleaved lincRNAs are processed via DICER-LIKE4 (DCL4) protein, resulting in production of phasiRNAs. This study provides the evidence that the miR2118-dependent and the DCL4-dependent pathways are both required for biogenesis of 21-nt phasiRNAs associated with germline-specific MEL1 AGO in rice, and over 700 lincRNAs are key factors for induction of this biogenesis during reproductive-specific stages. © 2014 John Wiley & Sons Ltd.

Takahashi A.,University of Tsukuba | Takahashi A.,National Institute of Genetics NIG | Takahashi A.,Graduate University for Advanced Studies | Lee R.X.,National Institute of Genetics NIG | And 9 more authors.
Journal of Neuroscience | Year: 2015

Although the dorsal raphe nucleus (DRN) has long been linked to neural control of aggression, little is known about the regulatory influences of the DRN when an animal engages in either adaptive species-typical aggressive behavior or escalated aggression. Therefore it is important to explore which neurotransmitter inputs into theDRNdetermine the escalation of aggression in male mice. Previously,we observed that microinjection of the GABAB receptor agonist baclofen into the DRN escalates aggressive behavior in male mice. Here, we used a serotonin (5-HT) neuron-specific GABAB receptor knock-out mouse to demonstrate that baclofen acts on nonserotonergic neurons to escalate aggression. Intra-DRN baclofen administration increased glutamate release, but did not alter GABA release, within the DRN. Microinjection of L-glutamate into the DRN escalated dose-dependently attack bites toward an intruder. In vivo microdialysis showed that glutamate release increased in the DRN during an aggressive encounter, and the level of glutamate was further increased when the animal was engaged in escalated aggressive behavior after social instigation. Finally, 5-HT release was increased within theDRN and also in the medial prefrontal cortex when animals were provoked by social instigation, and during escalated aggression after social instigation, but this increase in 5-HT release was not observed when animals were engaged in species-typical aggression. In summary, glutamate input into theDRNis enhanced during escalated aggression, which causes a phasic increase of 5-HT release from theDRN5-HT neurons. © 2015 the authors.

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