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.
We report a detection of the baryon acousticoscillation (BAO) feature in the flux-correlation function of the Lyα forest of high-redshift quasars with a statistical significance of five standard ...deviations. The study uses 137 562 quasars in the redshift range 2.1 ≤ z ≤ 3.5 from the data release 11 (DR11) of the Baryon Oscillation Spectroscopic Survey (BOSS) of SDSS-III. This sample contains three times the number of quasars used in previous studies. The measured position of the BAO peak determines the angular distance, DA(z = 2.34) and expansion rate, H(z = 2.34), both on a scale set by the sound horizon at the drag epoch, rd. We find DA/rd = 11.28 ± 0.65(1σ)+2.8-1.2 (2σ) and DH/rd = 9.18 ± 0.28(1σ) ± 0.6(2σ) where DH = c/H. The optimal combination, ~DH0.7DA0.3/rd is determined with a precision of ~2%. For the value rd = 147.4 Mpc, consistent with the cosmic microwave background power spectrum measured by Planck, we find DA(z = 2.34) = 1662 ± 96(1σ) Mpc and H(z = 2.34) = 222 ± 7(1σ) km s-1 Mpc-1. Tests with mock catalogs and variations of our analysis procedure have revealed no systematic uncertainties comparable to our statistical errors. Our results agree with the previously reported BAO measurement at the same redshift using the quasar-Lyα forest cross-correlation. The autocorrelation and cross-correlation approaches are complementary because of the quite different impact of redshift-space distortion on the two measurements. The combined constraints from the two correlation functions imply values of DA/rd that are 7% lower and 7% higher for DH/rd than the predictions of a flat ΛCDM cosmological model with the best-fit Planck parameters. With our estimated statistical errors, the significance of this discrepancy is ≈2.5σ.
Fertilization is commonly used to increase growth in forest plantations, but it may also affect tree water relations and responses to drought. Here, we measured changes in biomass, transpiration, ...sapwood‐to‐leaf area ratio (As:Al) and sap flow driving force (ΔΨ) during the 6‐year rotation of tropical plantations of Eucalyptus grandis under controlled conditions for throughfall and potassium (K) fertilization. K fertilization increased final tree height by 8 m. Throughfall exclusion scarcely affected tree functioning because of deep soil water uptake. Tree growth increased in K‐supplied plots and remained stable in K‐depleted plots as tree height increased, while growth per unit leaf area increased in all plots. Stand transpiration and hydraulic conductance standardized per leaf area increased with height in K‐depleted plots, but remained stable or decreased in K‐supplied plots. Greater Al in K‐supplied plots increased the hydraulic constraints on water use. This involved a direct mechanism through halved As:Al in K‐supplied plots relative to K‐depleted plots, and an indirect mechanism through deteriorated water status in K‐supplied plots, which prevented the increase in ΔΨ with tree height. K fertilization in tropical plantations reduces the hydraulic compensation to growth, which could increase the risk of drought‐induced dieback under climate change.
Potassium fertilization in Eucalyptus grandis plantations reduces tree hydraulic compensation to growth through its effects on Huber value and soil‐to‐leaves sap flow driving force.
We present a tentative detection of the large-scale structure of Ly α emission in the Universe at redshifts z = 2–3.5 by measuring the cross-correlation of Ly α surface brightness with quasars in ...Sloan Digital Sky Survey/Baryon Oscillation Spectroscopic Survey. We use a million spectra targeting luminous red galaxies at z < 0.8, after subtracting a best-fitting model galaxy
spectrum from each one, as an estimate of the high-redshift Ly α surface brightness. The quasar–Ly α emission cross-correlation is detected on scales 1 ∼ 15 h
−1 Mpc, with shape consistent with a ΛCDM model with
$\Omega _{\rm m} =0.30^{+0.10}_{-0.07}$
. The predicted amplitude of this cross-correlation is proportional to the product of the mean Ly α surface brightness, 〈μα〉, the amplitude of mass fluctuations and the quasar and Ly α emission bias factors. We infer 〈μα〉 (b
α/3) = (3.9 ± 0.9) × 10−21 erg s−1 cm−2 Å−1 arcsec−2, where b
α is the Ly α emission bias. If star-forming galaxies dominate this emission, we find ρSFR = (0.28 ± 0.07)(3/b
α) yr−1 Mpc−3. For b
α = 3, this value is ∼30 times larger than previous estimates from individually detected Ly α emitters, but consistent with the total ρSFR derived from dust-corrected, continuum UV galaxy surveys, if most of the Ly α photons from these galaxies avoid dust absorption and are reemitted after diffusing in large gas haloes. Heating of intergalactic gas by He ii photoionization from quasar radiation or jets may alternatively explain the detected correlation, and cooling radiation from gas in galactic haloes may also contribute. We also detect redshift space anisotropy of the quasar–Ly α emission cross-correlation, finding evidence at the 3.0σ level that it is radially elongated, which may be explained by radiative-transfer effects. Our measurements represent the first application of the intensity mapping technique to optical observations.
We analyse the density field of galaxies observed by the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS) included in the SDSS Data Release Nine (DR9). DR9 includes ...spectroscopic redshifts for over 400 000 galaxies spread over a footprint of 3275 deg2. We identify, characterize and mitigate the impact of sources of systematic uncertainty on large-scale clustering measurements, both for angular moments of the redshift-space correlation function, ξℓ(s), and the spherically averaged power spectrum, P(k), in order to ensure that robust cosmological constraints will be obtained from these data. A correlation between the projected density of stars and the higher redshift (0.43 < z < 0.7) galaxy sample (the approximately constant stellar mass threshold 'CMASS' sample) due to imaging systematics imparts a systematic error that is larger than the statistical error of the clustering measurements at scales s > 120 h
−1 Mpc or k < 0.01 h Mpc−1. We find that these errors can be ameliorated by weighting galaxies based on their surface brightness and the local stellar density. The clustering of CMASS galaxies found in the Northern and Southern Galactic footprints of the survey generally agrees to within 2σ. We use mock galaxy catalogues that simulate the CMASS selection function to determine that randomly selecting galaxy redshifts in order to simulate the radial selection function of a random sample imparts the least systematic error on ξℓ(s) measurements and that this systematic error is negligible for the spherically averaged correlation function, ξ0. We find a peak in ξ0 at s∼ 200 h
−1 Mpc, with a corresponding feature with period ∼0.03 h Mpc−1 in P(k), and find features at least as strong in 4.8 per cent of the mock galaxy catalogues, concluding this feature is likely to be a consequence of cosmic variance. The methods we recommend for the calculation of clustering measurements using the CMASS sample are adopted in companion papers that locate the position of the baryon acoustic oscillation feature, constrain cosmological models using the full shape of ξ0 and measure the rate of structure growth.
We analyse the density field of 264 283 galaxies observed by the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS) and included in the SDSS Data Release 9 (DR9). In ...total, the SDSS DR9 BOSS data include spectroscopic redshifts for over 400 000 galaxies spread over a footprint of more than 3000 deg2. We measure the power spectrum of these galaxies with redshifts 0.43 < z < 0.7 in order to constrain the amount of local non-Gaussianity, , in the primordial density field, paying particular attention to the impact of systematic uncertainties. The BOSS galaxy density field is systematically affected by the local stellar density and this influences the ability to accurately measure . In the absence of any correction, we find (erroneously) that the probability that is greater than zero, P( > 0), is 99.5 per cent. After quantifying and correcting for the systematic bias and including the added uncertainty, we find − 45 < < 195 at 95 per cent confidence and P( > 0) = 91.0 per cent. A more conservative approach assumes that we have only learnt the k dependence of the systematic bias and allows any amplitude for the systematic correction; we find that the systematic effect is not fully degenerate with that of , and we determine that −82 < < 178 (at 95 per cent confidence) and P( > 0) = 68 per cent. This analysis demonstrates the importance of accounting for the impact of Galactic foregrounds on measurements. We outline the methods that account for these systematic biases and uncertainties. We expect our methods to yield robust constraints on for both our own and future large-scale structure investigations.
Potassium (K) is generally considered as being closely linked to plant water dynamics. Consequently, reinforcing K nutrition, which theoretically favors root growth and specific surface, extends leaf ...lifespan, and regulates stomatal functioning, is often used to tackle water stress. We designed a greenhouse pot-scale device to test these interactions on corn (Zea mays L.), and to analyze their links to plant transpiration. Three levels of K nutrition were combined with two water-supply treatments. Shoot and root development and growth were continuously measured during a 60-day-long experiment. Individual plant transpiration was measured by weighing pots and by calculating water mass balances. The results showed that, although K deficiency symptoms resembled those caused by water shortage, there was no advantage to over-fertilizing water-stressed plants. K failed to decrease either the transpiration per unit leaf surface or to improve water use efficiency. The link between K nutrition and plant transpiration appears solely attributable to the effect of K on leaf area. We conclude that K over-fertilization could ultimately jeopardize crops by enhancing early-stage water transpiration to the detriment of later developmental stages.
We present the BOSS Lyman- alpha (Ly alpha ) Forest Sample from SDSS Data Release 9, comprising 54,468 quasar spectra with z sub(qso) > 2.15 suitable for Ly alpha forest analysis. This data set ...probes the intergalactic medium with absorption redshifts 2.0 < z sub( alpha ) < 5.7 over an area of 3275 deg super(2), and encompasses an approximate comoving volume of 20 h super(-3) Gpc super(3). With each spectrum, we have included several products designed to aid in Ly alpha forest analysis: improved sky masks that flag pixels where data may be unreliable, corrections for known biases in the pipeline estimated noise, masks for the cores of damped Ly alpha systems and corrections for their wings, and estimates of the unabsorbed continua so that the observed flux can be converted to a fractional transmission. The continua are derived using a principal component fit to the quasar spectrum redward of rest-frame Ly alpha (lambda. > 1216 A), extrapolated into the forest region and normalized by a linear function to fit the expected evolution of the Ly alpha forest mean flux. The estimated continuum errors are lap 5% rms. We also discuss possible systematics arising from uncertain spectrophotometry and artifacts in the flux calibration; global corrections for the latter are provided. Our sample provides a convenient starting point for users to analyze clustering in BOSS Ly alpha forest data, and it provides a fiducial data set that can be used to compare results from different analyses of baryon acoustic oscillations in the Ly alpha forest. The full data set is available from the SDSS-III DR9 Web site.
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