Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within-and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.Asian cultivated rice is grown worldwide and comprises the staple food for half of the global population. It is envisaged that by the year 2035 1 feeding this growing population will necessitate that an additional 112 million metric tons of rice be produced on a smaller area of land, using less water and under more fluctuating climatic conditions, which will require that future rice cultivars be higher yielding and resilient to multiple abiotic and biotic stresses. The foundation of the continued improvement of rice cultivars is the rich genetic diversity within domesticated populations and wild relatives [2][3][4] . For over 2,000 years, two major types of O. sativa-O. sativa Xian group (here referred to as Xian/Indica (XI) and also known as , Hsien or Indica) and O. sativa Geng Group (here referred to as Geng/Japonica (GJ) and also known as , Keng or Japonica)-have historically been recognized [5][6][7] . Varied degrees of post-reproductive barriers exist between XI and GJ rice accessions 8 ; this differentiation between XI and GJ rice types and the presence of different varietal groups are well-documented at isozyme and DNA levels 6,9 . Two other distinct groups have also been recognized using molecular markers 10 ; one of these encompasses the Aus, Boro and Rayada ecotypes from Bangladesh and India (which we term the circum-Aus group (cA)) and the other comprises the famous Basmati and Sadri aromatic varieties (which we term the circum-Basmati group (cB)).Approximately 780,000 rice accessions are available in gene banks worldwide 11 . To enable the more efficient use of these accessions in future rice improvement, the Chinese Academy of Agricultural Sciences, BGI-Shenzhen and International Rice Research Institute sequenced over 3,000 rice genomes (3K-RG) as part of the 3,000 Rice Genomes Project 12. Here we present analyses of genetic variation in the 3K-RG that focus on important aspects of O. sativa diversity, single nucleotide polymorphisms (SNPs) and structural variation (deletions, duplications, inversions and translocations). We also construct a species pangenome consisting of 'core...

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The rice (Oryza sativa) floral homeotic C-class gene, MADS3, was previously shown to be required for stamen identity determination during early flower development. Here, we describe a role for MADS3 in regulating late anther development and pollen formation. Consistent with this role, MADS3 is highly expressed in the tapetum and microspores during late anther development, and a newly identified MADS3 mutant allele, mads3-4, displays defective anther walls, aborted microspores, and complete male sterility. During late anther development, mads3-4 exhibits oxidative stress-related phenotypes. Microarray analysis revealed expression level changes in many genes in mads3-4 anthers. Some of these genes encode proteins involved in reactive oxygen species (ROS) homeostasis; among them is MT-1-4b, which encodes a type 1 small Cys-rich and metal binding protein. In vivo and in vitro assays showed that MADS3 is associated with the promoter of MT-1-4b, and recombinant MT-1-4b has superoxide anion and hydroxyl radical scavenging activity. Reducing the expression of MT-1-4b causes decreased pollen fertility and an increased level of superoxide anion in transgenic plants. Our findings suggest that MADS3 is a key transcriptional regulator that functions in rice male reproductive development, at least in part, by modulating ROS levels through MT-1-4b.

We present the results from a detailed analysis of photometric and spectrophotometric data on five Seyfert 1 galaxies observed as a part of a recent reverberation mapping program. The data were collected at several observatories over a 140-day span beginning in 2010 August and ending in 2011 January. We obtained high sampling-rate light curves for Mrk 335, Mrk 1501, 3C 120, Mrk 6, and PG 2130+099, from which we have measured the time lag between variations in the 5100Å continuum and the Hβ broad emission line. We then used these measurements to calculate the mass of the supermassive black hole at the center of each of these galaxies. Our new measurements substantially improve previous measurements of M BH and the size of the broad line-emitting region for four sources and add a measurement for one new object. Our new measurements are consistent with photoionization physics regulating the location of the broad line region in active galactic nuclei.

SUMMARY Antagonistic pleiotropy (AP) or genetic tradeoff is an important concept invoked frequently in theories of aging, cancer, genetic disease, and other common phenomena. But, it is unclear how prevalent AP is, which genes are subject to AP, and to what extent and how AP may be resolved. By measuring the fitness difference between the wild-type and null alleles of ~5000 nonessential genes in yeast, we find that, in any given environment, yeast expresses hundreds of genes that harm rather than benefit the organism, demonstrating widespread AP. Nonetheless, under sufficient selection, AP is often resolvable through regulatory evolution, primarily by trans-acting changes, although in one case we also detect a cis-acting change and localize its causal mutation. AP resolution, however, is slower in smaller populations, predicting more unresolved AP in multicellular organisms than in yeast. These findings provide the empirical foundation for AP-dependent theories and have broad biomedical and evolutionary implications.

We present velocity-resolved reverberation results for five active galactic nuclei. We recovered velocity-delay maps using the maximum entropy method for four objects: Mrk 335, Mrk 1501, 3C 120, and PG 2130+099. For the fifth, Mrk 6, we were only able to measure mean time delays in different velocity bins of the Hβ emission line. The four velocity-delay maps show unique dynamical signatures for each object. For 3C 120, the Balmer lines show kinematic signatures consistent with both an inclined disk and infalling gas, but the He ii λ4686 emission line is suggestive only of inflow. The Balmer lines in Mrk 335, Mrk 1501, and PG 2130+099 show signs of infalling gas, but the He ii emission in Mrk 335 is consistent with an inclined disk. We also see tentative evidence of combined virial motion and infalling gas from the velocity-binned analysis of Mrk 6. The maps for 3C 120 and Mrk 335 are two of the most clearly defined velocity-delay maps to date. These maps constitute a large increase in the number of objects for which we have resolved velocity-delay maps and provide evidence supporting the reliability of reverberation-based black hole mass measurements.

Context. Dust is expected to be ubiquitous in extrasolar planetary systems owing to the dynamical activity of minor bodies. Inner dust populations are, however, still poorly known because of the high contrast and small angular separation with respect to their host star, and yet, a proper characterisation of exozodiacal dust is mandatory for the design of future Earth-like planet imaging missions. Aims. We aim to determine the level of near-infrared exozodiacal dust emission around a sample of 42 nearby main sequence stars with spectral types ranging from A to K and to investigate its correlation with various stellar parameters and with the presence of cold dust belts. Methods. We use high-precision K-band visibilities obtained with the FLUOR interferometer on the shortest baseline of the CHARA array. The calibrated visibilities are compared with the expected visibility of the stellar photosphere to assess whether there is an additional, fully resolved circumstellar emission source. Results. Near-infrared circumstellar emission amounting to about 1% of the stellar flux is detected around 13 of our 42 target stars. Follow-up observations showed that one of them (eps Cep) is associated with a stellar companion, while another one was detected around what turned out to be a giant star (kap CrB). The remaining 11 excesses found around single main sequence stars are most probably associated with hot circumstellar dust, yielding an overall occurrence rate of 28 +8 −6 % for our (biased) sample. We show that the occurrence rate of bright exozodiacal discs correlates with spectral type, K-band excesses being more frequent around A-type stars. It also correlates with the presence of detectable far-infrared excess emission in the case of solar-type stars. Conclusions. This study provides new insight into the phenomenon of bright exozodiacal discs, showing that hot dust populations are probably linked to outer dust reservoirs in the case of solar-type stars. For A-type stars, no clear conclusion can be made regarding the origin of the detected near-infrared excesses.

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