Search

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

Complex cell shapes are generated first by breaking symmetry, and subsequent polar growth. Localized bending of anticlinal walls initiates lobe formation in the epidermal pavement cells of cotyledons and leaves, but how the microtubule cytoskeleton mediates local cell growth, and how plant pavement cells benefit from adopting jigsaw puzzle-like shapes, are poorly understood. In Arabidopsis (Arabidopsis thaliana), the basic Pro-rich protein (BPP) microtubule-associated protein family comprises seven members. We analyzed lobe morphogenesis in cotyledon pavement cells of a BPP1;BPP2;BPP5 triple knockout mutant. New image analysis methods (MtCurv and BQuant) showed that anticlinal microtubule bundles were significantly reduced and cortical microtubules that fan out radially across the periclinal wall did not enrich at the convex side of developing lobes. Despite these microtubule defects, new lobes were initiated at the same frequency as in wild-type cells, but they did not expand into well-defined protrusions. Eventually, mutant cells formed nearly polygonal shapes and adopted concentric microtubule patterns. The mutant periclinal cell wall bulged outward. The radius of the calculated inscribed circle of the pavement cells, a proposed proxy for maximal stress in the cell wall, was consistently larger in the mutant cells during cotyledon development, and correlated with an increase in cell height. These bpp mutant phenotypes provide genetic and cell biological evidence that initiation and growth of lobes are distinct morphogenetic processes, and that interdigitated cell geometry effectively suppresses large outward bulging of pavement cells.

To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N50 = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets., Clonal plants produce genetically identical offspring through vegetative growth. A ‘ramet’ refers to a single physiological individual produced by clonal propagation; a ‘genet’ refers to a group of ramets that originate from a single seed. Here we investigated how ramets that belong to different genets distribute in a natural population of Carrdamine leucantha using a genome-wide SNP markers. We applied the method to 372 samples collected at 1-m interval grids within a 20 × 20 m plot, and identified 61 genets with high inequality in terms of genet size and patchy distribution.

We present the technique of instrumental delay calibration for the dual-beam system of VLBI Exploration of Radio Astrometry (VERA), namely, the horn-on-dish method, in which artificial noise sources are mounted on the antenna feedome base and a wide-band radio noise is injected into the dual-beam receivers after reflection by a subreflector. We introduce the basic concept of calibration with the horn-on-dish method, and also present results of the experiments to evaluate its calibration accuracy. Detailed comparisons between model path calculations and measured paths from the noise sources show that the horn-on-dish method can calibrate the dual-beam delay difference in the antenna structure and receiver within an � 0.1 mm level. We estimated that the systematic error in

We observed the SiO (v = 1 and v = 2, J = 1–0) maser emissions toward the Mira variable IK Tauri (IK Tau, NML Tau, IRC +10050) over nine epochs from 2003 November to 2005 April using the VLBI Exploration of Radio Astrometry (VERA) telescope array. We found that the SiO maser distributions around IK Tau are highly variable, depending on the stellar pulsation phase. The velocity structures were complex and also time-variable, and are inconsistent with a simply rotating shell that was suggested by previous observations. Based on fittings of the SiO maser distributions to elliptical ring models, we found that the ring size seems to vary in correlation with the pulsation phase, as previously found for TX Cam. Comparisons of the v = 1 and v = 2 maser distributions reveal that 42–50% of the maser pairs have a positional offset less than 0.5 mas, suggesting that the maser pumping in these spots is likely to be dominated by line overlapping or collisional pumping, rather than pure radiative pumping. In order to model the velocity structure of the spoke-like features observed in IK Tau, we propose a ballistic-orbit model, in which a gas clump ejected from the stellar surface moves radially outward with a gravitational deceleration, and argue that the stellar mass can be deduced from that model.

We report on results of five-epoch VLBI observations of H2O maser emission in the M-type star IRC � 10414, carried out with the VLBI Exploration of Radio Astrometry (VERA). The maser distribution extends over an area of 70 mas � 260 mas and exhibits a bipolar structure. The relative proper motions of 17 maser features were measured during the monitoring observations spanning nine months. The distance to IRC � 10414 was re-estimated on the basis of the statistical treatment of parallax and the model-fitting method, yielding D = 3.1 ˙ 0.4 kpc and D = 2.0 ˙ 0.2 kpc, respectively. The estimated distance, D = 2–3 kpc, is much larger than that previously adopted. The stellar luminosity of IRC � 10414 is also re-estimated to be L� � 9 � 10 4 (D=2 kpc) 2 Lˇ, much brighter by a factor of 10–20 than previously adopted (L� � 10000 Lˇ). The maser motions exhibit not only a spherically expanding flow with a velocity of � 10 (D=2 kpc) km s � 1 , but also a faster bipolar outflow with a major axis in the north–south direction and at a small inclination angle with respect to the celestial sphere. These characteristics of the star and the

We report on results of multi-epoch VLBI observations of H2O masers associated with a low-mass young stellar object, IRAS 16293 2422 in Oph East, and a fringe-phase and position reference source, ICRF J162546.8 252738, using the VLBI Exploration of Radio Astrometry (VERA) for high-precision astrometry. We obtained an annual parallax of a maser feature to be = 5.6 0:5 mas, corresponding to a distance of D= 178 +18 37 pc. We also found 10 relative proper motions of maser features with respect to the maser feature mentioned above. The motion of the accompanying young stellar object (YSO) has already been found in thermal continuum emission previously observed with the Very Large Array. The intrinsic motions of masers have been estimated from the relative proper motions after the YSO’s motion is subtracted from, and a systemic secular motion of the position reference feature is added to the proper motions originally measured. The intrinsic maser kinematical structure may trace a bipolar outflow.

In this paper we discuss the potential use of VERA (VLBI exploration of radio astrometry) to study black holes based on phase-referencing VLBI astrometry. First we present a brief overview of the project, from system design to scientific targets, and then we discuss the possibilities to investigate black holes and other high energy phenomena that are possibly linked to black holes.