solGS: a web-based tool for genomic selection

Background

Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders.

Results

We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs.

Conclusions

solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0398-7) contains supplementary material, which is available to authorized users.     

InSatDb: A Genomic Tool for Insect Geneticists

Microsatellites show tremendous variation between genomes in terms of their occurrence and composition. Availability of whole genome sequences allows us to study microsatellite characteristics of fully sequenced insect genomes to understand the evolution and biological significance of microsatellites. InSatDb is an insect microsatellite database that provides an interactive interface to query information on microsatellites annotated with size (in base pairs and repeat units); genomic location (exon, intron, up-stream or transposon); nature (perfect or imperfect); and sequence composition (repeat motif and GC%). Here, we present a snap shot of the distribution and composition of microsatellites in introns and exons of insect genomes. The data present interesting observations regarding the microsatellite life-cycle and genome flux.     

Physiology of larval diapause: a tool for insect pest management

Summary

Two major pests cause damage of economic importance to maize crops in France: the European corn borer (Ostrinia nubilalis), which has a worldwide distribution, and the pink maize stalk borer (Sesamia nonagrioides), which is present all around the Mediterranean. During winter, last instar larvae of these species exhibit a facultative diapause. Early forecasting of the field emergence period and a good knowledge of the overwintering survival (both strongly dependent on conditions controlling diapause maintenance and termination) are key features for effective management of these pests. In this connection physiological studies of diapause provide us with useful information. Special emphasis is given to variations of carbohydrate metabolism, particularly glycogen, trehalose and glycerol in both species. In the European corn borer the presence of glycerol and trehalose makes it possible to forecast diapause termination 2–3 months before the first field pupal molts. These data are used for the construction of a model of the population dynamics, developed by the National Institute of Agronomic Research. In the pink maize stalk borer we demonstrate the great sensibility of this pest to low temperatures, and we propose a novel cultural pest-suppressing method which is now being tested in collaboration with the General Association of Maize Producers.     

Rare genomic changes as a tool for phylogenetics

DNA sequence data have offered valuable insights into the relationships between living organisms. However, most phylogenetic analyses of DNA sequences rely primarily on single nucleotide substitutions, which might not be perfect phylogenetic markers. Rare genomic changes (RGCs), such as intron indels, retroposon integrations, signature sequences, mitochondrial and chloroplast gene order changes, gene duplications and genetic code changes, provide a suite of complementary markers with enormous potential for molecular systematics. Recent exploitation of RGCs has already started to yield exciting phylogenetic information.     

GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations

A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods. The program and data can be downloaded from http://pondside.uchicago.edu/~lilab/ and http://webcollab.iis.sinica.edu.tw/~biocom.     

siRNA as a tool for streamlining functional genomic studies

RNA interference (RNAi) has the potential to accelerate greatly the pace of discovery biology. The active RNAi intermediate is the small interfering RNA (siRNA), a discrete nucleic acid duplex that can be generated by several methods and used to directly silence gene expression. The choice of methods employed depends largely on the research or therapeutic objective. In most cases, rational design offers several advantages over random design, including greater predictability of function, higher silencing potency and longer duration of suppression. Of the production methods, chemical synthesis provides the fastest production capability, the highest purity and the easiest scalability for high-throughput strategies. Effective coupling of several methods gives the greatest potential for the application of RNAi across functional genomic and target validation studies. Furthermore, the coupling of RNAi with cellular profiling technologies will provide opportunities to streamline drug discovery significantly.     

DNannotator: Annotation software tool kit for regional genomic sequences

Sequence annotation is essential for genomics-based research. Investigators of a specific genomic region who have developed abundant local discoveries such as genes and genetic markers, or have collected annotations from multiple resources, can be overwhelmed by the difficulty in creating local annotation and the complexity of integrating all the annotations. Presenting such integrated data in a form suitable for data mining and high-throughput experimental design is even more daunting. DNannotator, a web application, was designed to perform batch annotation on a sizeable genomic region. It takes annotation source data, such as SNPs, genes, primers, and so on, prepared by the end-user and/or a specified target of genomic DNA, and performs de novo annotation. DNannotator can also robustly migrate existing annotations in GenBank format from one sequence to another. Annotation results are provided in GenBank format and in tab-delimited text, which can be imported and managed in a database or spreadsheet and combined with existing annotation as desired. Graphic viewers, such as Genome Browser or Artemis, can display the annotation results. Reference data (reports on the process) facilitating the user's evaluation of annotation quality are optionally provided. DNannotator can be accessed at http://sky.bsd.uchicago.edu/DNannotator.htm.     

DNAlive: a tool for the physical analysis of DNA at the genomic scale

SUMMARY: DNAlive is a tool for the analysis and graphical display of structural and physical characteristics of genomic DNA. The web server implements a wide repertoire of metrics to derive physical information from DNA sequences with a powerful interface to derive 3D information on large sequences of both naked and protein-bound DNAs. Furthermore, it implements a mesoscopic Metropolis code which allows the inexpensive study of the dynamic properties of chromatin fibers. In addition, our server also surveys other protein and genomic databases allowing the user to combine and explore the physical properties of selected DNA in the context of functional features annotated on those regions. AVAILABILITY: http://mmb.pcb.ub.es/DNAlive/ ; http://www.inab.org/     

Essential oil formulations useful as a new tool for insect pest control

This study investigated the effects of some essential oils onLimantria dispar (Lepidoptera: Lymantridae, gypsy moth) larvae, one of the most serious pests of cork oak forests. The essential oils were first formulated as oil in water (o/w) emulsions and used in laboratory bioassays to assess their lethal concentration (LC50). Microcapsules containing the most promising, oils (Rosmarinus officinalis andThymus herba-barona) were then prepared by a phase separation process, followed by freeze-drying. The formulations thus obtained, characterized in terms of essential oil content and composition, morphology, storage stability, and release profile, were tested on gypsy moth larvae. The results showed that the tested oils possess interesting larvicidal effects that make them suitable for application in integrated control strategies. The microencapsulation process gave high encapsulation yields (over 98%) with both essential oils, which have different chemical compositions. The microcapsules had toxic effects at a concentration similar to that usually employed for localized treatments with microgranular synthetic pesticides. Toxicity appeared to be maximized when the microparticles adhered to the typical hair structures of several defoliator families. These formulations seem to be able to protect the core material against environmental agents and could be considered for use in controlled drug release systems. The natural active principles they contain could provide an alternative system in insect pest control.     

Snat: a SNP annotation tool for bovine by integrating various sources of genomic information

Background

Genome-wide association (GWA) study has recently become a powerful approach for detecting genetic variants for common diseases without prior knowledge of the variant's location or function. Generally, in GWA studies, the most significant single-nucleotide polymorphisms (SNPs) associated with top-ranked p values are selected in stage one, with follow-up in stage two. The value of selecting SNPs based on statistically significant p values is obvious. However, when minor allele frequencies (MAFs) are relatively low, less-significant p values can still correspond to higher odds ratios (ORs), which might be more useful for prediction of disease status. Therefore, if SNPs are selected using an approach based only on significant p values, some important genetic variants might be missed. We proposed a hybrid approach for selecting candidate SNPs from the discovery stage of GWA study, based on both p values and ORs, and conducted a simulation study to demonstrate the performance of our approach.

Results

The simulation results showed that our hybrid ranking approach was more powerful than the existing ranked p value approach for identifying relatively less-common SNPs. Meanwhile, the type I error probabilities of the hybrid approach is well-controlled at the end of the second stage of the two-stage GWA study.

Conclusions

In GWA studies, SNPs should be considered for inclusion based not only on ranked p values but also on ranked ORs.     

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

Background  

Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these transitions preferentially affect CpA di-nucleotides thus altering the frequency of certain di-nucleotides in the affected sequences. The majority of previously published in silico analyses were limited to the comparison of ratios of pre- and post-RIP di-nucleotides in putatively RIP-affected sequences – so-called RIP indices. The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, however, a dearth of bioinformatics tools available to the fungal research community for alignment-based RIP analysis of repeat families.     

Fluorescent insect growth regulators (FIGR's): A new tool for insect physiologists

A compound was synthesized that fluoresces in the visible spectrum and has the properties of an insect juvenile hormone. When it was assayed against Aedes aegypti larvae, it produced larval-pupal and pupal-adult intermediates; when injected into allatectomized adult females, it restored normal egg development. The fluorescent insect growth regulator (5-[[[5-(dimethylamino)-1-naphthalenyl]sulfonyl]amino]-1,3-benzodioxole) when injected into females, could be traced into eggs and newly hatched larvae. Microspectrofluorometric and chromatographic studies indicate that it is metabolically stable. Fluorescent insect growth regulators constitute new tools for the investigation of the action of insect growth regulators in general.