Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)

High-density array-based genome-wide association studies (GWAS) are complemented by exome sequencing and whole-genome resequencing-based association studies. Here we present a composite resequencing-based genome-wide association study (CR-GWAS) strategy that systematically exploits collective biological information and analytical tools for a robust analysis. We showcased the utility of this strategy by using Arabidopsis (Arabidopsis thaliana) resequencing data. Bioinformatic predictions of biological function alteration at each locus were integrated into the process of association testing of both common and rare variants for complex traits with a suite of statistics. Significant signals were then filtered with a priori candidate loci generated from genome database and gene network models to obtain a posteriori candidate loci. A probabilistic gene network (AraNet) that interrogates network neighborhoods of genes was then used to expand the filtering power to examine the significant testing signals. Using this strategy, we confirmed the known true positives and identified several new promising associations. Promising genes (AP1, FCA, FRI, FLC, FLM, SPL5, FY, and DCL2) were shown to control for flowering time through either common variants or rare variants within a diverse set of Arabidopsis accessions. Although many of these candidate genes were cloned earlier with mutational studies, identifying their allele variation contribution to overall phenotypic variation among diverse natural accessions is critical. Our rare allele testing established a greater number of connections than previous analyses in which this issue was not addressed. More importantly, our results demonstrated the potential of integrating various biological, statistical, and bioinformatic tools into complex trait dissection

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

<p>Abstract</p> <p>Background</p> <p>Eight diverse sorghum (<it>Sorghum bicolor </it>L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated.</p> <p>Results</p> <p>Alignment of eight genome equivalents (6 Gb) to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted <it>in silico </it>to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage.</p> <p>Conclusions</p> <p>A sequence quantity of 3 million 50-base reads per accession using a <it>Bsr</it>FI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.</p

Dissection of Leaf Angle Variation in Maize through Genetic Mapping and Meta-Analysis

Maize ( L.) hybrids have transitioned to upright leaf angles (LAs) over the last 50 yr as maize yields and planting densities increased concurrently. Genetic mapping and a meta-analysis were conducted in the present study to dissect genetic factors controlling LA variation. We developed mapping populations using inbred lines B73 (Iowa Stiff Stalk Synthetic), PHW30 (Iodent, expired plant variety protection inbred), and Mo17 (Non-Stiff Stalk) that have distinct LA architectures and represent three important heterotic groups in the United States. These populations were genotyped using genotyping-by-sequencing (GBS), and phenotyped for LA in the F and F generation. Inclusive composite interval mapping across the two generations of the mapping populations revealed 12 quantitative trait loci (QTL), and a consistent QTL on chromosome 1 explained 10 to 17% of the phenotypic variance. To gain a comprehensive understanding of natural variations underlying LA variation, these detected QTL were compared with results from 19 previous studies. In total, 495 QTL were compiled and mapped into 143 genomic bins. A meta-analysis revealed that 58 genomic bins were associated with LA variation. Thirty-three candidate genes were identified in these genomic bins. Together, these results provide evidence of QTL controlling LA variation from inbred lines representing three important heterotic groups in the United States and a useful resource for future research into the molecular variants underlying specific regions of the genome associated with LA variation

Microporous Mesoporous Mat.

Three novel organically templated layered cerium materials, [enH(2)](0.5)[(CeF3)-F-IV(HPO4)] (CeFPO), (enH(2)](0.5)[Ce-III (PO4)(HSO4)(H2O)] (CePSO), and [enH(2)](0.5)[Ce-III (SO4)(2)] (CeSO), have been synthesized by hydrothermal synthesis techniques and characterized by single-crystal and powder XRD, TG-DTA, IR, ICP, CHN, and magnetic susceptibility measurement. These compounds possess unique cerium-centered polyhedra CeO3F5, CeO8(H2O), and CeO9, and their layers are separated by the ethylenediaminium cations. (c) 2006 Elsevier Inc. All rights reserved.Three novel organically templated layered cerium materials, [enH(2)](0.5)[(CeF3)-F-IV(HPO4)] (CeFPO), (enH(2)](0.5)[Ce-III (PO4)(HSO4)(H2O)] (CePSO), and [enH(2)](0.5)[Ce-III (SO4)(2)] (CeSO), have been synthesized by hydrothermal synthesis techniques and characterized by single-crystal and powder XRD, TG-DTA, IR, ICP, CHN, and magnetic susceptibility measurement. These compounds possess unique cerium-centered polyhedra CeO3F5, CeO8(H2O), and CeO9, and their layers are separated by the ethylenediaminium cations. (c) 2006 Elsevier Inc. All rights reserved

Facile molten salt synthesis of ordered perovskite Ba(Sr 1/3Nb 2/3)O3 powders

Extra large Alkaline-earth Sr 2 + cation was successfully introduced into the B′-site of the complex perovskite A(B′ 1/3B″ 2/3)O 3 by a molten salt synthesis method. The crystal structure of the as-synthesized Ba(Sr 1/3Nb 2/3)O 3 was determined by Rietveld refinement of X-ray diffraction and Raman spectrum. The results showed that the as-synthesized Ba(Sr 1/3Nb 2/3)O 3 had the 1:2 order-disorder trigonal perovskite structure, which was also an isometric compound of hexagonal BaTiO 3-type structure Ba 3SrNb 2O 9. The measured dielectric properties on the perovskite Ba(Sr 1/3Nb 2/3)O 3 ceramics showed the good frequency stability and the low dielectric loss

templatefreesynthesisofanovel3dcagelikenanostructuredfe2o3

Synthesis of inorganic nanostructures with specific size and well defined morphologies has attracted considerable attention due to their superior electrical, optical, magnetic, and chemical properties. Up to now, various kinds of metal oxide, sulfide, and hydrate with controlled hierarchical and complex morphologies have been successfully synthesized

Template-free Synthesis of a Novel 3D Cage-like Nanostructured α-Fe2O3

Synthesis of inorganic nanostructures with specific size and well defined morphologies has attracted considerable attention due to their superior electrical, optical, magnetic, and chemical properties. Up to now, various kinds of metal oxide, sulfide, and hydrate with controlled hierarchical and complex morphologies have been successfully synthesized