Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.

We report our new code (named SACRA) for numerical relativity simulations in which an adaptive mesh refinement algorithm is implemented. In this code, the Einstein equations are solved in the BSSN formalism with a fourth-order finite differencing, and the hydrodynamic equations are solved by a third-order high-resolution central scheme. The fourth-order Runge-Kutta scheme is adopted for integration in time. To test the code, simulations for coalescence of black hole-black hole (BH-BH), neutron star-neutron star (NS-NS), and black hole-neutron star (BH-NS) binaries are performed, and also, properties of BHs formed after the merger and gravitational waveforms are compared among those three cases. For the simulations of BH-BH binaries, we adopt the same initial conditions as those by Buonanno et al. [Phys. Rev. D 75, 124018 (2007)] and compare numerical results. We find reasonable agreement except for a slight disagreement possibly associated with the difference in choice of gauge conditions and numerical schemes. For an NS-NS binary, we performed simulations employing both SACRA and Shibata's previous code, and find reasonable agreement between two numerical results for the final outcome and qualitative property of gravitational waveforms. We also find that the convergence is relatively slow for numerical results of NS-NS binaries, and again realize that longterm numerical simulations with several resolutions and grid settings are required for validating the results. For a BH-NS binary, we compare numerical results with our previous ones, and find that gravitational waveforms and properties of the BH formed after the merger agree well with those of our previous ones, although the disk mass formed after the merger is less than 0.1% of the total rest mass, which disagrees with the previous result. We also report numerical results of a longterm simulation (with ∼ 4 orbits) for a BH-NS binary for the first time. All these numerical results show behavior of convergence, and extrapolated numerical results for time spent in the inspiral phase agree with post-Newtonian predictions in a reasonable accuracy. These facts validate the results by SACRA.

Using our new numerical-relativity code SACRA, long-term simulations for inspiral and merger of black hole (BH)-neutron star (NS) binaries are performed, focusing particularly on gravitational waveforms. As the initial conditions, BH-NS binaries in a quasiequilibrium state are prepared in a modified version of the moving-puncture approach. The BH is modeled by a nonspinning moving puncture and for the NS, a polytropic equation of state with Γ = 2 and the irrotational velocity field are employed. The mass ratio of the BH to the NS, Q = MBH/MNS, is chosen in the range between 1.5 and 5. The compactness of the NS, defined by C = GMNS/c 2 RNS, is chosen to be between 0.145 and 0.178. For a large value of Q for which the NS is not tidally disrupted and is simply swallowed by the BH, gravitational waves are characterized by inspiral, merger, and ringdown waveforms. In this case, the waveforms are qualitatively the same as that from BH-BH binaries. For a sufficiently small value of Q < ∼ 2, the NS may be tidally disrupted before it is swallowed by the BH. In this case, the amplitude of the merger and ringdown waveforms is very low, and thus, gravitational waves are characterized by the inspiral waveform and subsequent quick damping. The difference in the merger and ringdown waveforms is clearly reflected in the spectrum shape and in the "cut-off" frequency above which the spectrum amplitude steeply decreases. When an NS is not tidally disrupted (e.g., for Q = 5), kick velocity, induced by asymmetric gravitational wave emission, agrees approximately with that derived for the merger of BH-BH binaries, whereas for the case that the tidal disruption occurs, the kick velocity is significantly suppressed.

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BackgroundTo create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.ResultsThe total 5.89-Gb sequence for Koshihikari, equivalent to 15.7× the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversityConclusionsDetection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.

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