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.

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

Registration of CO960293-2 Wheat Germplasm Resistant to Wheat streak mosaic virus and Russian Wheat Aphid

Adoption of a "mini-prep" DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L.).

Drought stress imposes major limits on wheat (Triticum aestivum L.) yield and is predicted to increase in frequency due to climate change. The aim of this study was to explore the potential of synthetic hexaploid wheat (SHW) to improve productivity of winter wheat under drought stress. Six SHW lines and four winter wheat cultivars from the U.S. Great Plains were evaluated in 1 m × 10 cm plastic tubes under drought-stressed and well-watered conditions in a greenhouse study. Root morphology, biomass, stomatal attributes, plant water relations, and the response of these traits to drought stress were measured. Traits significantly (P < 0.05) correlated with a drought tolerance index included root biomass in the bottom third of the tubes, length of the longest root, stomatal conductance, and production of small diameter roots. Plasticity for root biomass allocation to greater depths showed a strong association with maintenance of plant water status. Synthetic line SYN-201 ranked highest for deep root biomass and length of the longest root under stress, and demonstrated plasticity by shifting root biomass production from the upper third to the bottom third of the tubes when stressed. Digital analysis of root morphology indicated that SYN-201, SYN-290, and cultivar Byrd produced large amounts of small diameter roots at depth. SYN-396 showed high stomatal density and reduced stomatal aperture while maintaining leaf growth when stressed despite a lack of deep roots. Trait variation in the SHW lines may contribute beneficial drought tolerance to Great Plains-adapted cultivars through introgression of novel allelic diversity.

Root traits contributing to drought tolerance of synthetic hexaploid wheat in a greenhouse study

Stripe rust resistance was identified in Triticum vavilovii (T. vavilovii Aus22498)-derived Russian wheat aphid (RWA)-resistant germplasm. Inheritance studies indicated monogenic control of resistance. The resistance gene was tentatively designated as Yrvav and was located on chromosome 1B by monosomic analysis. A close association (1.5±0.9% recombination) of Yrvav with a T. vavilovii-derived gliadin allele (Gli-B1vav) placed it in chromosome arm 1BS. Yrvav was allelic with Yr10. Tests with Yr10 avirulent and virulent pathotypes showed that Yrvav and Yr10 possess identical pathogenic specificity. Yrvav and Yr10 showed close genetic associations with alternate alleles at the Xpsp3000 (microsatellite marker), Gli-B1 and Rg1 loci. Based on these observations Yrvav was named as Yr10vav. The close association between Xpsp3000 and Gli-B1 was also confirmed. The Yr10vav-linked Xpsp3000 allele (285 bp) was not present in 65 Australian cultivars, whereas seven Australian wheats lacking Yr10 carried the same Xpsp3000 allele (260 bp) as Yr10 carrying wheat cultivar Moro. Xpsp3000 and/or Gli-B1 could be used in marker-assisted selection for pyramiding Yr10vav or Yr10 with other stripe rust resistance genes. Yr10vav was inherited independently of the T. vavilovii-derived RWA resistance.

Characterisation of Triticum vavilovii-derived stripe rust resistance using genetic, cytogenetic and molecular analyses and its marker-assisted selection.

Russian wheat aphid (RWA) [Diuraphis noxia (Kurdjumov)] is an important pest of wheat (Triticum aestivum L.) in several production areas of the world. The most effective and economical approach for controlling RWA is to use resistant cultivars. A wheat line, ST-ARS 02RWA2414-11 (2414-11), showed a high level of resistance to RWA biotype 2. Our objectives were to map the resistance gene and develop polymerase chain reaction (PCR)-based markers for marker-assisted selection (MAS). A mapping population of 212 F 2 individuals was developed from a cross of 2414-11 and the susceptible cultivar Yuma. The F 2 individuals and F 2:3 families were infested using biotype 2 RWA. The RWA resistance of 2414-11 is controlled by a single major gene, provisionally designated as Dn2414. Using standard PCR, 30 marker loci were found to be linked to Dn2414 with recombination frequencies (θ) of 0.00 to 0.27 and logarithm of the odds to the base 10 (LOD) scores of 7.6 to 66.1. Of the 30 markers, 26 were tightly linked to Dn2414 with θ ≤ 0.05. A genetic map was constructed consisting of 31 loci spanning a region of 34.7 cM. The close link-age of Dn2414 with several rye chromosome 1R short arm (1RS)-specific simple sequence repeat markers and low θ values around the Dn2414 gene indicate that Dn2414 is located on chromosome 1RS.1BL (translocation chromosome with IRS and wheat chromosome 1B long arm). Phenotypic and marker profiles of 2414-11 and its relatives are the same as other lines known to carry Dn7. The Dn2414 gene is thus located on 1RS arm, and the large number of PCR markers will be valuable for MAS of this gene.

Scott D. Haley

Papers

Registration of CO960293-2 Wheat Germplasm Resistant to Wheat streak mosaic virus and Russian Wheat Aphid

Adoption of a "mini-prep" DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L.).

Root traits contributing to drought tolerance of synthetic hexaploid wheat in a greenhouse study

Characterisation of Triticum vavilovii-derived stripe rust resistance using genetic, cytogenetic and molecular analyses and its marker-assisted selection.

Molecular Mapping of the Russian Wheat Aphid Resistance Gene Dn2414 in Wheat