Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Phenolic compounds in plants and agri-industrial by-products: Antioxidant activity, occurrence, and potential uses

Treating messenger RNA transcript abundances as quantitative traits and mapping gene expression quantitative trait loci for these traits has been pursued in gene-specific ways. Transcript abundances often serve as a surrogate for classical quantitative traits in that the levels of expression are significantly correlated with the classical traits across members of a segregating population. The correlation structure between transcript abundances and classical traits has been used to identify susceptibility loci for complex diseases such as diabetes and allergic asthma. One study recently completed the first comprehensive dissection of transcriptional regulation in budding yeast, giving a detailed glimpse of a genome-wide survey of the genetics of gene expression. Unlike classical quantitative traits, which often represent gross clinical measurements that may be far removed from the biological processes giving rise to them, the genetic linkages associated with transcript abundance affords a closer look at cellular biochemical processes. Here we describe comprehensive genetic screens of mouse, plant and human transcriptomes by considering gene expression values as quantitative traits. We identify a gene expression pattern strongly associated with obesity in a murine cross, and observe two distinct obesity subtypes. Furthermore, we find that these obesity subtypes are under the control of different loci.

Genetics of gene expression surveyed in maize, mouse and man

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

/pdf/characterization-of-polyploid-wheat-genomic-diversity-using-2k5bjm1mv0.pdf

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

Diallel Analysis of Resistance in Winter Wheat

The present invention provides for compositions and methods for producing crop plants that are resistant to herbicides. In particular, the present invention provides for wheat plants, plant tissues and plant seeds that contain altered acetyl-CoA carboxylase (ACCase) genes and proteins that are resistant to inhibition by herbicides that normally inhibit the activity of the ACCase protein.

Acetyl co-enzyme a carboxylase herbicide resistant plants

Darrell' (Reg. No. CV-1024, PI 644224) hard red winter wheat (Triticum aestivum L.) was developed by the South Dakota State University-Agricultural Experiment Station and released in 2006 to seed producers by the South Dakota State University-Agricultural Experiment Station and the University of Nebraska Agricultural Experiment Station. Darrell was selected from the cross 2076-W12-11/'Karl 92' (PI 564245)//NE89526. NE89526 is an experimental line from the University of Nebraska with the pedigree 'Lancota' (CI 17389) selection/'Siouxland' (PI 483469)//TX792729. 2076-W12-11 is an unreleased experimental line that originated from a population with an unidentifi ed pedigree. Darrell was selected as an F3:4 line in 1998 and was assigned experimental line number SD98102. Darrell was released on the basis of its good disease resistance and excellent yield potential in the northern Great Plains.

/pdf/registration-of-darrell-wheat-4rtarakrzo.pdf

Registration of 'Darrell' Wheat

‘Sunshine’ (Reg. No. CV-1129, PI 674741) hard white winter wheat (Triticum aestivum L.) was developed by the Colorado Agricultural Experiment Station and released in August 2014 through a marketing agreement with the Colorado Wheat Research Foundation. In addition to researchers at Colorado State University, USDA-ARS researchers at Manhattan, KS, St. Paul, MN, and Pullman, WA participated in its development. Sunshine was developed with the objective of making available a hard white winter wheat cultivar with improved grain yield and straw strength and similar milling and baking qualities to ‘Snowmass’ hard white winter wheat. Both Snowmass and Sunshine are grown in Colorado and adjacent areas of the west-central Great Plains in an identity-preserved marketing system whereby a grower premium is paid through a contract with a flour milling company. Sunshine was developed with a modified-bulk breeding method from the cross KS01HW152-6/HV9W02-267W made in 2005 at Fort Collins, CO. Following two generations (F₂ and F₃) of bulk-population evaluation, Sunshine was selected as an F₃:₄ line in July 2009, assigned experimental line number CO09W293, and evaluated in replicated yield trials from 2012 to 2014 in eastern Colorado.

Scott D. Haley

Papers

Diallel Analysis of Resistance in Winter Wheat

Acetyl co-enzyme a carboxylase herbicide resistant plants

Registration of 'Darrell' Wheat

Registration of ‘Sunshine’ Hard White Winter Wheat

Registration of 'Harding' wheat.