Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)

Background Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments

Allelic richness and diversity in global composite collection and reference sets in chickpea (Cicer arietinum L.)

Chickpea is the fourth largest grain legume crop globally. A composite collection of 3000 accessions was formed and genotyped using 50 SSR markers. The accessions were also field evaluated for seven qualitative traits. Analysis of 48 SSR markers data on 2915 accessions detected 1683 alleles, of which 935 were rare and 748 common. Gene diversity varied from 0.533 to 0.975. Kabuli chickpea as a group were genetically more diverse than other seed types. Several group-specific unique alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in West Asia and Mediterranean, 117 in South and South East Asia, and 10 in African region accessions. A genotype-based reference set captured 1315 alleles compared to 1237 alleles in the reference set based on qualitative traits or 1354 alleles based on SSRs and qualitative traits data. The relative usefulness of these reference sets in chickpea breeding and genomics studies are being further investigated

Predictions from Quantum Cosmology

The world view suggested by quantum cosmology is that inflating universes with all possible values of the fundamental constants are spontaneously created out of nothing. I explore the consequences of the assumption that we are a `typical' civilization living in this metauniverse. The conclusions include inflation with an extremely flat potential and low thermalization temperature, structure formation by topological defects, and an appreciable cosmological constant.Comment: (revised version), 15 page

The Close AGN Reference Survey (CARS) A massive multi-phase outflow impacting the edge-on galaxy HE 1353-1917

Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Open Access funding provided by Max Planck Society.Context. Galaxy-wide outflows driven by star formation and/or an active galactic nucleus (AGN) are thought to play a crucial rule in the evolution of galaxies and the metal enrichment of the inter-galactic medium. Direct measurements of these processes are still scarce and new observations are needed to reveal the nature of outflows in the majority of the galaxy population. Aims. We combine extensive, spatially-resolved, multi-wavelength observations, taken as part of the Close AGN Reference Survey (CARS), for the edge-on disc galaxy HE 1353-1917 in order to characterise the impact of the AGN on its host galaxy via outflows and radiation. Methods. Multi-color broad-band photometry was combined with spatially-resolved optical, near-infrared (NIR) and sub-mm and radio observations taken with the Multi-Unit Spectroscopy Explorer (MUSE), the Near-infrared Integral Field Spectrometer (NIFS), the Atacama Large Millimeter Array (ALMA), and the Karl G. Jansky Very Large Array (VLA) to map the physical properties and kinematics of the multi-phase interstellar medium. Results. We detect a biconical extended narrow-line region ionised by the luminous AGN orientated nearly parallel to the galaxy disc, extending out to at least 25 kpc. The extra-planar gas originates from galactic fountains initiated by star formation processes in the disc, rather than an AGN outflow, as shown by the kinematics and the metallicity of the gas. Nevertheless, a fast, multi-phase, AGN-driven outflow with speeds up to 1000 km s(-1) is detected close to the nucleus at 1 kpc distance. A radio jet, in connection with the AGN radiation field, is likely responsible for driving the outflow as confirmed by the energetics and the spatial alignment of the jet and multi-phase outflow. Evidence for negative AGN feedback suppressing the star formation rate (SFR) is mild and restricted to the central kpc. But while any SFR suppression must have happened recently, the outflow has the potential to greatly impact the future evolution of the galaxy disc due to its geometrical orientation. Conclusions.. Our observations reveal that low-power radio jets can play a major role in driving fast, multi-phase, galaxy-scale outflows even in radio-quiet AGN. Since the outflow energetics for HE 1353-1917 are consistent with literature, scaling relation of AGN-driven outflows the contribution of radio jets as the driving mechanisms still needs to be systematically explored.© B. Husemann et al. 2019We thank the referee for providing very valuable comments, which significantly improved the quality of the manuscript. MK acknowledges support from DLR grant 50OR1802. GRT acknowledges support from the NASA through Einstein Postdoctoral Fellowship Award Number PF-150128, issued by the Chandra X-ray Observatory Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS8-03060. MG is supported by the Lyman Spitzer Jr. Fellowship (Princeton University) and by NASA Chandra grants GO7-18121X/GO8-19104X. SMC acknowledges support from the Australian Research Council (DP190102714). We thank Alex Markowitz for helpful discussions on the RGS data in the context of warm absorbers. The work of SAB, CPO and MS was supported by a generous grant from the Natural Sciences and Engineering Research Council of Canada. Based on observations collected at the European Organization for Astronomical Research in the Southern Hemisphere under ESO programme 095. B-0015(A). Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), National Research Council (Canada), CONICYT (Chile), Ministerio de Ciencia, Tecnologia e Innovacion Productiva (Argentina), Ministerio da Ciencia, Tecnologia e Inovacao (Brazil), and Korea Astronomy and Space Science Institute (Republic of Korea). Based on observations obtained at the Southern Astrophysical Research (SOAR) telescope, which is a joint project of the Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC) do Brasil, the U.S. National Optical Astronomy Observatory (NOAO), the University of North Carolina at Chapel Hill (UNC), and Michigan State University (MSU). Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut fur Astronomie Heidelberg and the Instituto de Astrofiica de Andaluci (CSIC). This paper makes use of the following ALMA data: ADS/JAO.ALMA#2016.1.00952. S. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. This work is based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member States and NASA. The VLA is operated by the National Radio Astronomy Observatory, a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA. This publication makes use of data products from the Wide-field Infrared Survey Explorer, which is a joint project of the University of California, Los Angeles, and the Jet Propulsion Laboratory/California Institute of Technology, funded by the National Aeronautics and Space Administration. This research has made use of the NASA/IPAC Infrared Science Archive, which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. The Pan-STARRS1 Surveys (PS1) and the PS1 public science archive have been made possible through contributions by the Institute for Astronomy, the University of Hawaii, the Pan-STARRS Project Office, the Max-Planck Society and its participating institutes, the Max Planck Institute for Astronomy, Heidelberg and the Max Planck Institute for Extraterrestrial Physics, Garching, The Johns Hopkins University, Durham University, the University of Edinburgh, the Queen's University Belfast, the Harvard-Smithsonian Center for Astrophysics, the Las Cumbres Observatory Global Telescope Network Incorporated, the National Central University of Taiwan, the Space Telescope Science Institute, the National Aeronautics and Space Administration under Grant No. NNX08AR22G issued through the Planetary Science Division of the NASA Science Mission Directorate, the National Science Foundation Grant No. AST-1238877, the University of Maryland, Eotvos Lorand University (ELTE), the Los Alamos National Laboratory, and the Gordon and Betty Moore Foundation. This work is based in part on observations made with the Galaxy Evolution Explorer (GALEX). GALEX is a NASA Small Explorer, whose mission was developed in cooperation with the Centre National d'Etudes Spatiales (CNES) of France and the Korean Ministry of Science and Technology. GALEX is operated for NASA by the California Institute of Technology under NASA contract NAS5-98034

Interacting New Agegraphic Dark Energy in a Cyclic Universe

The main goal of this work is investigation of NADE in the cyclic universe scenario. Since, cyclic universe is explained by a phantom phase ($\omega<-1$), it is shown when there is no interaction between matter and dark energy, ADE and NADE do not produce a phantom phase, then can not describe cyclic universe. Therefore, we study interacting models of ADE and NADE in the modified Friedmann equation. We find out that, in the high energy regime, which it is a necessary part of cyclic universe evolution, only NADE can describe this phantom phase era for cyclic universe. Considering deceleration parameter tells us that the universe has a deceleration phase after an acceleration phase, and NADE is able to produce a cyclic universe. Also it is found valuable to study generalized second law of thermodynamics. Since the loop quantum correction is taken account in high energy regime, it may not be suitable to use standard treatment of thermodynamics, so we turn our attention to the result of \citep{29}, which the authors have studied thermodynamics in loop quantum gravity, and we show that which condition can satisfy generalized second law of thermodynamics.Comment: 8 pages, 3 figure

Cosmology at the Millennium

One hundred years ago we did not know how stars generate energy, the age of the Universe was thought to be only millions of years, and our Milky Way galaxy was the only galaxy known. Today, we know that we live in an evolving and expanding Universe comprising billions of galaxies, all held together by dark matter. With the hot big-bang model, we can trace the evolution of the Universe from the hot soup of quarks and leptons that existed a fraction of a second after the beginning to the formation of galaxies a few billion years later, and finally to the Universe we see today 13 billion years after the big bang, with its clusters of galaxies, superclusters, voids, and great walls. The attractive force of gravity acting on tiny primeval inhomogeneities in the distribution of matter gave rise to all the structure seen today. A paradigm based upon deep connections between cosmology and elementary particle physics -- inflation + cold dark matter -- holds the promise of extending our understanding to an even more fundamental level and much earlier times, as well as shedding light on the unification of the forces and particles of nature. As we enter the 21st century, a flood of observations is testing this paradigm.Comment: 44 pages LaTeX with 14 eps figures. To be published in the Centennial Volume of Reviews of Modern Physic

Categorizing Different Approaches to the Cosmological Constant Problem

We have found that proposals addressing the old cosmological constant problem come in various categories. The aim of this paper is to identify as many different, credible mechanisms as possible and to provide them with a code for future reference. We find that they all can be classified into five different schemes of which we indicate the advantages and drawbacks. Besides, we add a new approach based on a symmetry principle mapping real to imaginary spacetime.Comment: updated version, accepted for publicatio

An improved method for measuring muon energy using the truncated mean of dE/dx

The measurement of muon energy is critical for many analyses in large Cherenkov detectors, particularly those that involve separating extraterrestrial neutrinos from the atmospheric neutrino background. Muon energy has traditionally been determined by measuring the specific energy loss (dE/dx) along the muon's path and relating the dE/dx to the muon energy. Because high-energy muons (E_mu > 1 TeV) lose energy randomly, the spread in dE/dx values is quite large, leading to a typical energy resolution of 0.29 in log10(E_mu) for a muon observed over a 1 km path length in the IceCube detector. In this paper, we present an improved method that uses a truncated mean and other techniques to determine the muon energy. The muon track is divided into separate segments with individual dE/dx values. The elimination of segments with the highest dE/dx results in an overall dE/dx that is more closely correlated to the muon energy. This method results in an energy resolution of 0.22 in log10(E_mu), which gives a 26% improvement. This technique is applicable to any large water or ice detector and potentially to large scintillator or liquid argon detectors.Comment: 12 pages, 16 figure

Dark Energy and Gravity

I review the problem of dark energy focusing on the cosmological constant as the candidate and discuss its implications for the nature of gravity. Part 1 briefly overviews the currently popular `concordance cosmology' and summarises the evidence for dark energy. It also provides the observational and theoretical arguments in favour of the cosmological constant as the candidate and emphasises why no other approach really solves the conceptual problems usually attributed to the cosmological constant. Part 2 describes some of the approaches to understand the nature of the cosmological constant and attempts to extract the key ingredients which must be present in any viable solution. I argue that (i)the cosmological constant problem cannot be satisfactorily solved until gravitational action is made invariant under the shift of the matter lagrangian by a constant and (ii) this cannot happen if the metric is the dynamical variable. Hence the cosmological constant problem essentially has to do with our (mis)understanding of the nature of gravity. Part 3 discusses an alternative perspective on gravity in which the action is explicitly invariant under the above transformation. Extremizing this action leads to an equation determining the background geometry which gives Einstein's theory at the lowest order with Lanczos-Lovelock type corrections. (Condensed abstract).Comment: Invited Review for a special Gen.Rel.Grav. issue on Dark Energy, edited by G.F.R.Ellis, R.Maartens and H.Nicolai; revtex; 22 pages; 2 figure

Fitting the integrated Spectral Energy Distributions of Galaxies

Fitting the spectral energy distributions (SEDs) of galaxies is an almost universally used technique that has matured significantly in the last decade. Model predictions and fitting procedures have improved significantly over this time, attempting to keep up with the vastly increased volume and quality of available data. We review here the field of SED fitting, describing the modelling of ultraviolet to infrared galaxy SEDs, the creation of multiwavelength data sets, and the methods used to fit model SEDs to observed galaxy data sets. We touch upon the achievements and challenges in the major ingredients of SED fitting, with a special emphasis on describing the interplay between the quality of the available data, the quality of the available models, and the best fitting technique to use in order to obtain a realistic measurement as well as realistic uncertainties. We conclude that SED fitting can be used effectively to derive a range of physical properties of galaxies, such as redshift, stellar masses, star formation rates, dust masses, and metallicities, with care taken not to over-interpret the available data. Yet there still exist many issues such as estimating the age of the oldest stars in a galaxy, finer details ofdust properties and dust-star geometry, and the influences of poorly understood, luminous stellar types and phases. The challenge for the coming years will be to improve both the models and the observational data sets to resolve these uncertainties. The present review will be made available on an interactive, moderated web page (sedfitting.org), where the community can access and change the text. The intention is to expand the text and keep it up to date over the coming years.Comment: 54 pages, 26 figures, Accepted for publication in Astrophysics & Space Scienc