Scott D. Haley

Bio: Scott D. Haley is an academic researcher from Colorado State University. The author has contributed to research in topics: Russian wheat aphid & Population. The author has an hindex of 36, co-authored 130 publications receiving 5265 citations. Previous affiliations of Scott D. Haley include Michigan State University & Dakota State University.

Free radical scavenging properties of wheat extracts.

Abstract: Three hard winter wheat varieties (Akron, Trego, and Platte) were examined and compared for their free radical scavenging properties and total phenolic contents (TPC) Free radical scavenging properties of wheat grain extracts were evaluated by spectrophotometric and electron spin resonance (ESR) spectrometry methods against stable 2,2-diphenyl-1-picryhydrazyl radical (DPPH*) and radical cation ABTS*+ (2,2'-azino-di[3-ethylbenzthiazoline sulfonate]) The results showed that the three wheat extracts differed in their capacities to quench or inhibit DPPH* and ABTS*+ Akron showed the greatest activity to quench DPPH radicals, while Platte had the highest capacity against ABTS*+ The ED50 values of wheat extracts against DPPH radicals were 060 mg/mL for Akron, 71 mg/mL for Trego, and 095 mg/mL for Platte under the experimental conditions The trolox equivalents against ABTS*+ were 131 +/- 044, 108 +/- 005, and 191 +/- 006 micromol/g of grain for Akron, Trego, and Platte wheat, respectively ESR results confirmed that wheat extracts directly reacted with and quenched free radicals The TPC were 4879 +/- 9278 microg gallic acid equivalents/g of grain No correlation was observed between TPC and radical scavenging capacities for DPPH* and ABTS*+ (p = 015 and p > 05, respectively)

Antioxidant properties of bran extracts from Trego wheat grown at different locations.

Abstract: The effects of growing conditions during the grain-filling period, including high temperature stress, total solar radiation, and average daily solar radiation, on the antioxidant properties of Trego wheat were evaluated. Bran extracts were prepared from Trego wheat, grown at four nonirrigated and one irrigated location in Colorado, and compared for their radical scavenging activities against ABTS*+ and DPPH*, Fe(2+) chelating capacities, and total phenolic contents. Significant differences in radical scavenging activities, chelating capacities, and total phenolic contents were detected among Trego bran samples grown at different locations, suggesting that growing conditions may influence the antioxidant properties of wheat. The bran sample obtained from Fort Collins had the strongest scavenging activity against either ABTS*+ or DPPH* radicals and the greatest chelating activity, whereas the highest total phenolic content was detected in bran samples from Walsh, indicating that each antioxidant activity may respond to the environmental changes differently. Positive correlations were detected between the DPPH* scavenging activity and either total solar radiation (r = 0.97, p = 0.03) or average daily solar radiation (r = 0.97, p = 0.03). In addition, HPLC analysis detected the presence of ferulic, syringic, vanillic, p-hydroxybenzoic, and coumaric acids in wheat bran. Additional research is needed to further investigate the effects of environmental conditions and the interactions between genotype and environmental factors on the antioxidant properties of wheat to promote the production of wheat with improved antioxidant properties by optimizing the growing conditions for a selected genotype.

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

Abstract: Background: Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. Results: Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). Conclusions: Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.

Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes.

Abstract: A stable QTL that may be used in marker-assisted selection in wheat breeding programs was detected for yield, yield components and drought tolerance-related traits in spring wheat association mapping panel. Genome-wide association mapping has become a widespread method of quantitative trait locus (QTL) identification for many crop plants including wheat (Triticum aestivum L.). Its benefit over traditional bi-parental mapping approaches depends on the extent of linkage disequilibrium in the mapping population. The objectives of this study were to determine linkage disequilibrium decay rate and population structure in a spring wheat association mapping panel (n = 285–294) and to identify markers associated with yield and yield components, morphological, phenological, and drought tolerance-related traits. The study was conducted under fully irrigated and rain-fed conditions at Greeley, CO, USA and Melkassa, Ethiopia in 2010 and 2011 (five total environments). Genotypic data were generated using diversity array technology markers. Linkage disequilibrium decay rate extended over a longer genetic distance for the D genome (6.8 cM) than for the A and B genomes (1.7 and 2.0 cM, respectively). Seven subpopulations were identified with population structure analysis. A stable QTL was detected for grain yield on chromosome 2DS both under irrigated and rain-fed conditions. A multi-trait region significant for yield and yield components was found on chromosome 5B. Grain yield QTL on chromosome 1BS co-localized with harvest index QTL. Vegetation indices shared QTL with harvest index on chromosome 1AL and 5A. After validation in relevant genetic backgrounds and environments, QTL detected in this study for yield, yield components and drought tolerance-related traits may be used in marker-assisted selection in wheat breeding programs.

Occurrence of a New Russian Wheat Aphid Biotype in Colorado

Abstract: Russian wheat aphid [RWA, Diuraphis noxia (Mordvilko)] is a serious pest of wheat (Triticum aestivum L.) in the western USA Great Plains region. While variation in virulence among different RWA isolates has been reported elsewhere, no such variation has been documented among North American RWA isolates. Our objective was to confirm observations in spring 2003 suggesting that a new biotype of RWA was present in southeastern Colorado. The new biotype induced greater injury (leaf rolling and overall plant damage) than the original biotype in standard greenhouse seedling screening tests with a limited collection of resistant and susceptible cultivars. A second experiment with a broader collection of known RWA resistance sources identified only one accession, 94M370 (Dn7 gene), with resistance to the new biotype. Development of wheat cultivars with resistance to this new biotype will depend on rapid identification and deployment of new resistance sources.

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

Abstract: 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.

Genetics of gene expression surveyed in maize, mouse and man

Abstract: 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.

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

Abstract: 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.