A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

(0) Save to: more options A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation Author(s): Howe, GT (Howe, Glenn T.)[ 1 ] ; Yu, JB (Yu, Jianbin)[ 1 ] ; Knaus, B (Knaus, Brian)[ 2 ] ; Cronn, R (Cronn, Richard)[ 2 ] ; Kolpak, S (Kolpak, Scott)[ 1 ] ; Dolan, P (Dolan, Peter)[ 3 ] ; Lorenz, WW (Lorenz, W. Walter)[ 4 ] ; Dean, JFD (Dean, Jeffrey F. D.)[ 4 ] Source: BMC GENOMICS Volume: 14 Article Number: 137 DOI: 10.1186/1471-2164-14-137 Published: FEB 28 2013 Times Cited: 0 (from Web of Science) Cited References: 81 [ view related records ] Citation Map Abstract: Background: Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. Results: We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Conclusions: Based on our validation efficiency, our SNP database may contain as many as similar to 200,000 true SNPs, and as many as similar to 69,000 SNPs that could be genotyped at similar to 20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.Keywords: Genome wide association, Pseudotsuga menziesii, Seed orchard, Complex traits, Pinus taeda. L., Population, Generation, Database, Selection, White spruc

Discovery of a Radio Source following the 27 December 2004 Giant Flare from SGR 1806-20

Over a decade ago it was established that the remarkable high energy transients, known as soft gamma-ray repeaters (SGRs), are a Galactic population and originate from neutron stars with intense (<~ 10^15 G) magnetic fields ("magnetars"). On 27 December 2004 a giant flare (fluence >~ 0.3 erg/cm^2) was detected from SGR 1806-20. Here we report the discovery of a fading radio counterpart. We began a monitoring program from 0.2GHz to 250GHz and obtained a high resolution 21-cm radio spectrum which traces the intervening interstellar neutral Hydrogen clouds. Analysis of the spectrum yields the first direct distance measurement of SGR 1806-20. The source is located at a distance greater than 6.4 kpc and we argue that it is nearer than 9.8 kpc. If true, our distance estimate lowers the total energy of the explosion and relaxes the demands on theoretical models. The energetics and the rapid decay of the radio source are not compatible with the afterglow model that is usually invoked for gamma-ray bursts. Instead we suggest that the rapidly decaying radio emission arises from the debris ejected during the explosion.Comment: 16 pages, 2 figures, submitted to Nature (substantial revisions

MALT90 Kinematic Distances to Dense Molecular Clumps

Using molecular-line data from the Millimetre Astronomy Legacy Team 90 GHz Survey (MALT90), we have estimated kinematic distances to 1905 molecular clumps identified in the ATLASGAL 870 μm continuum survey over the longitude range 295° < l < 350°. The clump velocities were determined using a flux-weighted average of the velocities obtained from Gaussian fits to the HCO+, HNC, and N2H+ (1–0) transitions. The near/far kinematic distance ambiguity was addressed by searching for the presence or absence of absorption or self-absorption features in 21 cm atomic hydrogen spectra from the Southern Galactic Plane Survey. Our algorithm provides an estimation of the reliability of the ambiguity resolution. The Galactic distribution of the clumps indicates positions where the clumps are bunched together, and these locations probably trace the locations of spiral arms. Several clumps fall at the predicted location of the far side of the Scutum–Centaurus arm. Moreover, a number of clumps with positive radial velocities are unambiguously located on the far side of the Milky Way at galactocentric radii beyond the solar circle. The measurement of these kinematic distances, in combination with continuum or molecular-line data, now enables the determination of fundamental parameters such as mass, size, and luminosity for each clump

Jennings_POC_PopInfo

This comma-delimited file provides location and genotype data for individuals from four populations of Oregon Port-Orford cedar that were surveyed with 11 microsatellite loci. The file shows individual numbers, population names, population latitudes, population longitudes, and the microsatellite allele length for diploid loci. Missing genotypes are indicated by the value "0, 0"

Data from: Microsatellite primers for the Pacific Northwest endemic conifer Chamaecyparis lawsoniana (Cupressaceae)

Microsatellite primers were developed for the Pacific Northwest conifer, Chamaecyparis lawsoniana (A. Murray) Parl. (Cupressaceae), to enhance efficiencies in disease-resistance breeding and germplasm screening for gene conservation of this rare species. Using multiplexed massively parallel Illumina sequencing, we identified over 300,000 microsatellite-containing sequences from 2 million paired-end microreads. After stringent filtering and primer evaluation, we selected 11 primer pairs and used these to screen variation in 4 populations of C. lawsoniana. Loci show between three and ten repeats per locus, with an average of eight. Screening of these markers in the North American relative Callitropsis nootkatensis demonstrated limited marker transferability, but these markers could have utility in Asian species of Chamaecyparis. These genetic markers show high polymorphism and should provide a high level of individual discrimination for paternity analysis in defined pedigrees, and routine screening of wild variation in Chamaecyparis lawsoniana

Jennings_POC_PrimerSeqs

This comma-delimited file provides information for 144 primers that were screened the Port-Orford populations. Included are the primer name, forward and reverse primer sequence, the original sequence name from Illumina sequencing, and the nucleotide sequence of the microread (2 x 80 bp, with read 1 and read 2 separated by 8 N's)

Developing high biofuel coastal, Douglas-fir feedstocks by genetic selection

This report describes the development of a state-of-the-science genotyping array based on SNP technology for marker-based selection of phenotypes conducive to production of biofuels from woody residuals