Measuring and Predicting Individual Differences in Executive Functions at 14 Months: A Longitudinal Study.

This study of 195 (108 boys) children seen twice during infancy (Time 1: 4.12 months; Time 2: 14.42 months) aimed to investigate the associations between and infant predictors of executive function (EF) at 14 months. Infants showed high levels of compliance with the EF tasks at 14 months. There was little evidence of cohesion among EF tasks but simple response inhibition was related to performance on two other EF tasks. Infant attention (but not parent-rated temperament) at 4 months predicted performance on two of the four EF tasks at 14 months. Results suggest that EF skills build on simpler component skills such as attention and response inhibition.ESR

A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57–.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection

The generation challenge programme platform: semantic standards and workbench for crop science.

doi:10.1155/2008/369601

Fabrication Of An 8:1 Ellipsoidal Mirror For A Synchrotron X-Ray Microprobe

The fabrication of an 8:1 demagnifying ellipsoidal mirror to be used for an x-ray microprobe at the National Synchrotron Light Source X-26 beam port is described. The design aim was to produce a mirror that could be used over the photon energy range from about 3 to 17 keV. The 300-mm long mirror was required to operate at a grazing angle of 5 mr. The semimajor axis was 4500 mm and the semiminor axis 14.142 mm. Surface roughness of 1 nm or less and slope errors of 1 arc second parallel to the long axis and 200 arc seconds parallel to the short direction were specified. Production of the first electroless nickel-coated aluminum mirror using a diamond-turning technique has been completed. The mirror meets the 1 arc sec surface figure specification except for areas near the ends of the mirror. The reasons for these deviations arise from subtle details of the diamond-turning process which have not been fully incorporated in to the computer program that controls the diamond-turning machines. Further work in computer correction of repeatable errors of the diamond-turning machine can eliminate the waviness at the ends of the mirror. The diamond-turned mirror surface was not fully polished under this effort and therefore does not meet the roughness specification; however, surface smoothness of a fully polished cylindrical mirror manufactured using the same techniques does not meet the specification. It can be concluded that it is now technically feasible to meet the required specifications for the mirror and that the x-ray microprobe based on its use can be achieved

TASSEL: software for association mapping of complex traits in diverse samples

Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components. Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www.maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel. Contact: [email protected]

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.

Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, TASSEL-GBS, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs. We describe the TASSEL-GBS pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the TASSEL-GBS pipeline provide robust tools for studying genomic diversity

ORIC stripping foil positioner for tandem beam injection

The Oak Ridge Isochronous Cyclotron (ORIC) is used as an energy booster for heavy ions from a 25 MV tandem accelerator. This operation requires precise placement of a stripping foil in the cyclotron for capture of the injected ions into an acceleration orbit. The mechanical design and control of the foil positioning device are described

Comprehensive genotyping of the USA national maize inbred seed bank

Background: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results: The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions: The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity