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

The Russian wheat aphid, Diuraphis noxia (Mordvilko) (Homoptera: Aphididae), has been a major economic pest of small grains in the western United States since its introduction in 1986. Recently, a new Russian wheat aphid biotype was discovered in southeastern Colorado that damaged previously resistant wheat, Triticum aestivum L. Biotype development jeopardizes the durability of plant resistance, which has been a cornerstone for Russian wheat aphid management. Our objective was to assess the relative amount of biotypic diversity among Russian wheat aphid populations collected from cultivated wheat and barley, Hordeum vulgare L. We conducted field surveys from May through June 2002 and August 2003 from seven counties within Texas, Kansas, Nebraska, and Wyoming. Based upon a foliar chlorosis damage rating, three new Russian wheat aphid biotypes were identified, one of which was virulent to all characterized sources of Russian wheat aphid resistance. The future success of Russian wheat aphid resistance breeding programs will depend upon the continual monitoring of extant biotypic diversity and determination of the ecological and genetic factors underlying the development of Russian wheat aphid biotypes.

https://bioone.org/journals/Journal-of-Economic-Entomology/volume-99/issue-5/0022-0493-99.5.1862/Biotypic-Variation-Among-North-American-Russian-Wheat-Aphid-Homoptera/10.1603/0022-0493-99.5.1862.pdf

Biotypic Variation Among North American Russian Wheat Aphid (Homoptera: Aphididae) Populations

Achieving acceptable end-use (milling and baking) quality is a fundamental objective of wheat (Triticum aestivum L.) breeding programs throughout the U.S. hard winter wheat region. Numerous analytical methods have been developed to measure quality. Few tools are available to assist in the decision-making process when faced with a large number of parameters from comprehensive milling and baking tests. Our objective was to develop a relational database system for summarization and interpretation of wheat end-use quality data from the USDA-ARS Hard Winter Wheat Quality Laboratory. The database system uses a graphical interface with a series of layouts that require input from the user, guide the user to a successive layout, or provide a data report. The database system provides simultaneous assessment of multiple quality traits on a standardized scale, user-specified prioritization of end-use quality traits for numerical and qualitative ratings of genotypes. tabulation of major quality deficiencies of genotypes, and summarization of quality ratings for a genotype across multiple nurseries. The database system has specific application to the hard winter wheat regional testing program; however, the basic principle and design could be readily extended to nursery-based end-use quality testing programs in other wheat regions and market classes.

Relational Database System for Summarization and Interpretation of Hard Winter Wheat Regional Quality Data

Gene pyramiding in Phaseolus vulgaris is being utilized to develop more effective resistance to the temperature-insensitive-necrosis-inducing (TINI) strains of Bean Common Mosaic Virus (BCMV) present in the USA. Our data indicate that contrary to previous work, the bc-3 gene is effective against these strains in the absence of the strain unspecific bc-u gene in genotypes possessing the I gene. The epistatic bc-3 gene interferes with traditional efforts to pyramid the other recessive resistance genes by masking their activity. Indirect selection based on markers linked to the other recessive resistance genes would likewise be ineffective without the ability to also select for the bc-u gene which is required for expression of the bc-2
2 gene in germplasm carrying the I gene. Because the most resistant genotype (I, bc-u, bc-I
2, bc-22, bc-3) can only be introduced into a wide range of germplasm through the use of molecular markers linked to the different resistance genes, the search for a marker linked to the strain unspecific bc-u gene should also be given priority.

Pyramiding genes for resistance to bean common mosaic virus

Reduced height alleles at the Rht-Bl and Rht-D1 loci have been widely incorporated into wheat (Triticum aestivum L.) cultivars with the intent of improving partitioning of assimilates to grain. Although generally effective at increasing yield in high yield environments, their effects under heat and drought stress have been variable. We undertook this study to evaluate the effects of the Rht-Bl b and Rht-D1b dwarfing alleles in a recombinant inbred line (RIL) spring wheat population under a range of soil moisture conditions. Rht-B1 and Rht-D1 genotypes of 140 RILs derived from a cross between 'Kauz' and MTRWA116 were determined by polymerase chain reactions (PCR). The population was evaluated for yield and agronomic traits in four Colorado environments under fully irrigated, partially irrigated, and rainfed conditions in 2001 and 2002. Lines with both dwarfing alleles were significantly (P 0.05). Desirable values for most traits occurred across a relatively wide range of plant heights, with the best performing lines either shorter lines in the tall class or taller lines in the semidwarf classes.

Agronomic Performance of Rht Alleles in a Spring Wheat Population across a Range of Moisture Levels

The random amplified polymorphic DNA (RAPD) assay has recently provided a marker system that may be useful for indirect selection and pyramiding of monogenic pest resistance traits in crop species. Our objective was to investigate the efficiency of marker-assisted selection with RAPD markers linked in coupling and in repulsion with a single resistance allele. Common bean (Phaseolus vulgaris L.) near-isogenic lines differing for the recessive bean common mosaic virus (BCMV) resistance allele bc-3 were screened to identify linked RAPD markers [...]

Scott D. Haley

Papers

Biotypic Variation Among North American Russian Wheat Aphid (Homoptera: Aphididae) Populations

Relational Database System for Summarization and Interpretation of Hard Winter Wheat Regional Quality Data

Pyramiding genes for resistance to bean common mosaic virus

Agronomic Performance of Rht Alleles in a Spring Wheat Population across a Range of Moisture Levels

Selection for Monogenic Pest Resistance Traits with Coupling- and Repulsion-Phase RAPD Markers