Post-polyploidisation morphotype diversification associates with gene copy number variation

Genetic models for polyploid crop adaptation provide important information relevant for future breeding prospects. A well-suited model is Brassica napus, a recent allopolyploid closely related to Arabidopsis thaliana. Flowering time is a major adaptation trait determining life cycle synchronization with the environment. Here we unravel natural genetic variation in B. napus flowering time regulators and investigate associations with evolutionary diversification into different life cycle morphotypes. Deep sequencing of 35 flowering regulators was performed in 280 diverse B. napus genotypes. High sequencing depth enabled high-quality calling of single-nucleotide polymorphisms (SNPs), insertion-deletions (InDels) and copy number variants (CNVs). By combining these data with genotyping data from the Brassica 60 K Illumina® Infinium SNP array, we performed a genome-wide marker distribution analysis across the 4 ecogeographical morphotypes. Twelve haplotypes, including Bna.FLC.A10, Bna.VIN3.A02 and the Bna.FT promoter on C02_random, were diagnostic for the diversification of winter and spring types. The subspecies split between oilseed/kale (B. napus ssp. napus) and swedes/rutabagas (B. napus ssp. napobrassica) was defined by 13 haplotypes, including genomic rearrangements encompassing copies of Bna.FLC, Bna.PHYA and Bna.GA3ox1. De novo variation in copies of important flowering-time genes in B. napus arose during allopolyploidisation, enabling sub-functionalisation that allowed different morphotypes to appropriately fine-tune their lifecycle

Targeted deep sequencing of flowering regulators in Brassica napus reveals extensive copy number variation

Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species. Target enrichment was performed using the Agilent SureSelect technology, followed by Illumina sequencing. A bait (probe) pool was developed based on results of a preliminary experiment with representatives from different B. napus morphotypes. A very high mean target coverage of ~670x allowed reliable calling of CNV, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) polymorphisms. No accession exhibited no CNV, and at least one homolog of every gene we investigated showed CNV in some accessions. Some CNV appear more often in specific morphotypes, indicating a role in diversification

Properties of oscillation modes in subgiant stars observed by Kepler

Mixed modes seen in evolved stars carry information on their deeper layers that can place stringent constraints on their physics and on their global properties (mass, age, etc...). In this study, we present a method to identify and measure all oscillatory mode characteristics (frequency, height, width). Analyzing four subgiants stars, we present the first measure of the effect of the degree of mixture on the l=1 mixed modes characteristics. We also show that some stars have measurable l=2 mixed modes and discuss the interest of their measure to constrain the deeper layers of stars.Comment: Accepted to Ap

Vertical structure models of the 1990 equatorial disturbance on Saturn

In September 1990, an atmospheric disturbance in the form of an abnormally high albedo area developed in the equatorial region of Saturn. Events of this nature are exceedingly rare for this planet as they have been detected in the equatorial region on only two other occasions in over a century. In ongoing monitoring of the atmospheres of the outer planets, CCD imaging observations of Saturn by New Mexico State University's Tortugas Mountain Station were made before, during, and after the disturbance's formation through both broad-band filters and narrow-band visible/near-IR filters centered in methane absorption bands. Also, multispectral Hubble Space Telescope observations were made within weeks of the event and later in 1991. These observations were calibrated and scans of reflectivity at constant latitude are being modeled with a vertically inhomogeneous, multiple scattering model previously used to model Jupiter's South Equatorial Belt brightening event in 1989. In addition, the reflectivity of the disturbance as a function of the scattering angles is being obtained so as to model this feature's vertical structure in particular. A preliminary report of the modeling results will be presented

Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle

Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 6834 individuals with birth, weaning and yearling weight records from Cycle VII and advanced generations of the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation (GPE) project. Breeds represented in these data included: Angus, Hereford, Red Angus, Charolais, Gelbvieh, Simmental, Limousin and Composite MARC III. Heterosis was further estimated by proportions of British × British (B × B), British × Continental (B × C) and Continental × Continental (C × C) crosses and by breed-specific combinations. Model 1 fitted fixed covariates for heterosis within biological types while Model 2 fitted random breed-specific combinations nested within the fixed biological type covariates. Direct heritability estimates (SE) for birth, weaning ,and yearling weight for Model 1 were 0.42 (0.04), 0.22 (0.03), and 0.39 (0.05), respectively. The direct heritability estimates (SE) of birth, weaning, and yearling weight for Model 2 were the same as Model 1, except yearling weight heritability was 0.38 (0.05). The B × B, B × C, and C × C heterosis estimates for birth weight were 0.47 (0.37), 0.75 (0.32), and 0.73 (0.54) kg, respectively. The B × B, B × C, and C × C heterosis estimates for weaning weight were 6.43 (1.80), 8.65 (1.54), and 5.86 (2.57) kg, respectively. Yearling weight estimates for B × B, B × C, and C × C heterosis were 17.59(3.06), 13.88 (2.63), and 9.12 (4.34) kg, respectively. Differences did exist among estimates of breed-specific heterosis for weaning and yearling weight, although the variance component associated with breed-specific heterosis was not significant. These results illustrate that there are differences in breed-specific heterosis and exploiting these differences can lead to varying levels of heterosis among mating plans

Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle

Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 6834 individuals with birth, weaning and yearling weight records from Cycle VII and advanced generations of the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation (GPE) project. Breeds represented in these data included: Angus, Hereford, Red Angus, Charolais, Gelbvieh, Simmental, Limousin and Composite MARC III. Heterosis was further estimated by proportions of British × British (B × B), British × Continental (B × C) and Continental × Continental (C × C) crosses and by breed-specific combinations. Model 1 fitted fixed covariates for heterosis within biological types while Model 2 fitted random breed-specific combinations nested within the fixed biological type covariates. Direct heritability estimates (SE) for birth, weaning ,and yearling weight for Model 1 were 0.42 (0.04), 0.22 (0.03), and 0.39 (0.05), respectively. The direct heritability estimates (SE) of birth, weaning, and yearling weight for Model 2 were the same as Model 1, except yearling weight heritability was 0.38 (0.05). The B × B, B × C, and C × C heterosis estimates for birth weight were 0.47 (0.37), 0.75 (0.32), and 0.73 (0.54) kg, respectively. The B × B, B × C, and C × C heterosis estimates for weaning weight were 6.43 (1.80), 8.65 (1.54), and 5.86 (2.57) kg, respectively. Yearling weight estimates for B × B, B × C, and C × C heterosis were 17.59(3.06), 13.88 (2.63), and 9.12 (4.34) kg, respectively. Differences did exist among estimates of breed-specific heterosis for weaning and yearling weight, although the variance component associated with breed-specific heterosis was not significant. These results illustrate that there are differences in breed-specific heterosis and exploiting these differences can lead to varying levels of heterosis among mating plans

The Borexino Thermal Monitoring & Management System and simulations of the fluid-dynamics of the Borexino detector under asymmetrical, changing boundary conditions

A comprehensive monitoring system for the thermal environment inside the Borexino neutrino detector was developed and installed in order to reduce uncertainties in determining temperatures throughout the detector. A complementary thermal management system limits undesirable thermal couplings between the environment and Borexino's active sections. This strategy is bringing improved radioactive background conditions to the region of interest for the physics signal thanks to reduced fluid mixing induced in the liquid scintillator. Although fluid-dynamical equilibrium has not yet been fully reached, and thermal fine-tuning is possible, the system has proven extremely effective at stabilizing the detector's thermal conditions while offering precise insights into its mechanisms of internal thermal transport. Furthermore, a Computational Fluid-Dynamics analysis has been performed, based on the empirical measurements provided by the thermal monitoring system, and providing information into present and future thermal trends. A two-dimensional modeling approach was implemented in order to achieve a proper understanding of the thermal and fluid-dynamics in Borexino. It was optimized for different regions and periods of interest, focusing on the most critical effects that were identified as influencing background concentrations. Literature experimental case studies were reproduced to benchmark the method and settings, and a Borexino-specific benchmark was implemented in order to validate the modeling approach for thermal transport. Finally, fully-convective models were applied to understand general and specific fluid motions impacting the detector's Active Volume.Comment: arXiv admin note: substantial text overlap with arXiv:1705.09078, arXiv:1705.0965

Evaluating a New Shade for Feedlot Cattle Performance and Heat Stress

Heat stress in cattle results in decreased feed intake, lower daily gain, and potentially death in susceptible animals under intense conditions. A study was carried out during the summer of 2013 at the USDA-ARS U.S. Meat Animal Research Center feedlot evaluating the impact of shade on environmental conditions and cattle performance. A novel two-tiered shade was used in half of the 14 pens, each holding 30 animals. The shades were designed to reduce solar heat load by 40% to 60% and to provide traveling shade across the pen, providing varied amounts of shade area as well as varied solar reduction potential. The objective of this study was to determine if the shade was effective at improving performance (evaluated as average daily gain, feed intake, and feed to gain ratio) and reducing environmental conditions that cause heat stress. A group of mixed-breed cattle with varied genetics including both and were selected, penned on the basis of sex, and blocked by color. Production parameters of pen feed usage were measured daily, and individual body weights were taken monthly. Environmental conditions including air temperature, relative humidity, wind speed, ground temperature, and black globe temperature with and without shade were measured. Solar load on the pens was reduced when shade was provided, with both ground temperature and black globe temperature showing reductions. Cattle showed nominally better performance; however, no significant differences were found in gain or feed intake. Panting scores were significantly lower with shade provided; slopes of cattle respiration rate versus ambient temperature were significantly lower with shade during the afternoon period

Singularity in the boundary resistance between superfluid 4^4He and a solid surface

We report new measurements in four cells of the thermal boundary resistance $R$ between copper and $^4$He below but near the superfluid-transition temperature $T_\lambda$. For $10^{-7} \leq t \equiv 1 - T/T_\lambda \leq 10^{-4}$ fits of $R = R_0 t^{x_b} + B_0$ to the data yielded $x_b \simeq 0.18$, whereas a fit to theoretical values based on the renormalization-group theory yielded $x_b = 0.23$. Alternatively, a good fit of the theory to the data could be obtained if the {\it amplitude} of the prediction was reduced by a factor close to two. The results raise the question whether the boundary conditions used in the theory should be modified.Comment: 4 pages, 4 figures, revte