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Modern Applied Statistics With S

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Half of all insect species are dependent on living plant tissues, consuming about 10% of plant annual production in natural habitats and an even greater percentage in agricultural systems, despite sophisticated control measures. Plants are generally remarkably well-protected against insect attack, with the result that most insects are highly specialized feeders. The mechanisms underlying plant resistance to invading herbivores on the one side, and insect food specialization on the other, are the main subjects of this book. For insects these include food-plant selection and the complex sensory processes involved, with their implications for learning and nutritional physiology, as well as the endocrinological spects of life cycle synchronization with host plant phenology. In the case of plants exposed to insect herbivores, they include the activation of defence systems in order to minimize damage, as well as the emission of chemical signals that may attract natural enemies of the invading herbivores and maybe exploited by neighbouring plants that mount defences as well.

Insect-plant biology

A compilation was made of 307 studies using nuclear DNA markers for evaluating among- and within-population diversity in wild angiosperms and gymnosperms. Estimates derived by the dominantly inherited markers (RAPD, AFLP, ISSR) are very similar and may be directly comparable. STMS analysis yields almost three times higher values for within-population diversity whereas among-population diversity estimates are similar to those derived by the dominantly inherited markers. Number of sampled plants per population and number of scored microsatellite DNA alleles are correlated with some of the population genetics parameters. In addition, maximum geographical distance between sampled populations has a strong positive effect on among-population diversity. As previously verified with allozyme data, RAPD- and STMS-based analyses show that long-lived, outcrossing, late successional taxa retain most of their genetic variability within populations. By contrast, annual, selfing and/or early successional taxa allocate most of the genetic variability among populations. Estimates for among- and within-population diversity, respectively, were negatively correlated. The only major discrepancy between allozymes and STMS on the one hand, and RAPD on the other hand, concerns geographical range; within-population diversity was strongly affected when the former methods were used but not so in the RAPD-based studies. Direct comparisons between the different methods, when applied to the same plant material, indicate large similarities between the dominant markers and somewhat lower similarity with the STMS-based data, presumably due to insufficient number of analysed microsatellite DNA loci in many studies.

Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants.

http://envismadrasuniv.org/Bioremediation/pdf/Phytoremediation%20of%20heavy%20metal.pdf

Phytoremediation of heavy metal-contaminated land by trees--a review.

The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis. The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley.

/pdf/a-novel-qtl-for-powdery-mildew-resistance-in-nordic-spring-42fwy68ft7.pdf

A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study.

Aphids such as the bird cherry-oat aphid (Rhopalosiphum padi L.) are serious pests in agriculture worldwide. Partially resistant barley genotypes have been produced in a breeding program for resistance to R. padi. The resistance is manifested as smaller aphids after a certain period of nymphal growth on the test plants. A large number of doubled haploid breeding lines thereby characterized as partially resistant or susceptible to R. padi are available from this breeding program. In the present study a selection of these lines, spanning four generations and 23 genotypes, was used for the evaluation of the constitutive transcript abundance of gene sequences in young barley plants. The genes were selected from an earlier microarray study where they had been identified as being up-regulated by aphids in all four barley genotypes studied or differentially up-regulated or constitutively expressed in the two resistant as compared to the two susceptible barley genotypes. The prediction for constitutive transcript abundance across the selection of genotypes was here confirmed for five out of eight investigated genes. Two of these were, as predicted, expressed at equal levels in all genotypes. Two gene sequences exhibited higher transcript abundance in resistant than in susceptible offspring; one coding for a thionin and another for a proteinase inhibitor. A lipoxygenase gene had higher transcript abundance in the susceptible lines. The study thus gives further support for putative constitutive roles of three genes previously identified as significant in the barley-R. padi interaction.

Transcript abundance of resistance- and susceptibility-related genes in a barley breeding pedigree with partial resistance to the bird cherry-oat aphid (Rhopalosiphum padi L.)

Recent studies have shown that volatile chemical interaction between certain barley (Hordeum vulgare) cultivars can cause reduced host plant acceptance by the aphid Rhopalosiphum padi, and that certain cultivars can induce this effect while others can respond. In this study, we tested whether inducing and responding capabilities are linked to year of release in Swedish two-rowed spring barley. Eighteen cultivars released between 1897 and 1992 were tested in randomly selected subsets with pairwise combinations of volatile emitters and receivers. Significantly reduced aphid acceptance as a result of exposure to volatiles from plants of a different cultivar were found in 24% of the cultivar combinations. In general, older cultivars had a higher degree of aphid resistance after barley volatile treatment than did younger cultivars. The inducing effect of the emitter was also related to date of emitter cultivar release but the time relationship was reversed. Combinations with a younger volatile emitter and an older volatile receiver gave the strongest reduction in aphid acceptance of treated plants. Linear relationships between microsatellite diversity of emitting cultivars and their efficiency as inducers indicated that younger cultivars might have a more unique odour, whereas older cultivars may be more sensitive to induction.

Plant volatile-induced aphid resistance in barley cultivars is related to cultivar age

Many of the pre-requisites necessary for breeding plants with inducible resistance to pests are no different from breeding for constitutive resistance. In both cases it is necessary to have resistance genes giving high enough yield gains from pest protection, efficient selection methods and means of introducing resistance genes into agronomically acceptable plant material. In addition, resistance traits need to be neutral or positive to non-target organisms. In inducible resistance, there is also the need for proper timing and specificity of induction. Tentatively the ideal inducible resistance is triggered by specific cues which rapidly induce specific resistance traits with long duration relative to the sensitive period of the crop and which give a systemic plant response. It takes knowledge to develop appropriate selection methods for resistance and in the case of inducible resistance we also need knowledge about how the inducing factors are operating. Inducing cues may come from insect activities on the plant (e.g. feeding, oviposition), from neighbouring plants or from manmade chemical formulations of elicitors. Plant selections can be based on plant damage levels, insect numbers, insect responses, plant resistance traits and/or molecular characteristics of the plant genome. Breeding for insect-inducible resistance to insects has been applied in the form of rapidly induced highly specific resistance in insect - crop combinations where there are gene-for-gene relationships, such as with the Hessian fly and the Russian wheat aphid in wheat. To my knowledge there are no examples of traditional breeding where less specific types of resistance; induced by insects, by neighbouring plants or by chemical formulations; have been deliberately bred into commercial cultivars. It is likely that the accumulating knowledge about the mechanisms of induced resistance will find applications in cultivars produced by genetic engineering.

/pdf/breeding-for-inducible-resistance-against-insects-applied-cphtmsb6nx.pdf

Breeding for inducible resistance against insects – applied plant breeding aspects

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Adult pollen beetles were exposed to three transgenic lines of Brassica napus L. expressing pea lectin up to 0.7% of total soluble protein in anthers. Two lines not expressing the pea lectin were used as controls. Adult responses were recorded in two experiments where beetles were fed either racemes or anthers. There was no effect of plant line on feeding rate, weight change or oviposition rate. A slightly reduced egg size was recorded when beetles were feeding on one of the plant lines with high concentration of pea lectin. Previous studies on the effect of pea lectin on pollen beetles have only focused on larval performance. The results of this study suggest that pea lectin has no adverse effect on the pest in its most damaging life stage.

Inger Åhman

Papers

A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study.

Transcript abundance of resistance- and susceptibility-related genes in a barley breeding pedigree with partial resistance to the bird cherry-oat aphid (Rhopalosiphum padi L.)

Plant volatile-induced aphid resistance in barley cultivars is related to cultivar age

Breeding for inducible resistance against insects – applied plant breeding aspects

Influence of pea lectin expressed transgenically in oilseed rape (Brassica napus) on adult pollen beetle (Meligethes aeneus)