Further studies on the occurrence and inheritance of resistance in red raspberry to a resistance-breaking strain of raspberry bushy dwarf virus

A strain of raspberry bushy dwarf virus (RBDV-RB), discovered in England in 1981, readily infects by grafting many raspberry cvs that have gene Bu, which confers strong resistance or immunity to isolates of the common strain. Haida is one of two cultivars that are highly resistant or immune from RBDV-RB, but both its parents, cvs Creston and Malling Promise, are infectible. Studies of the segregation of resistance to both RBDV-RB and a common strain of RBDV (D200) in four progenies related to cv. Haida or its two parents, showed that resistance to RBDV-RB was heritable and occurred when gene Bu was present with a second resistance component whose inheritance is probably multigenic. There was some indication that the second component might be a form of partial resistance to graft inoculation of varying expression, and that cv. Haida possesses this resistance at a high level that has not been distinguished from immunity in the graft inoculations used. Cultivars Creston and Malling Promise possibly have this resistance to a lesser degree, while resistance in cv. Heritage has been distinguished from immunity only by extensive graft tests. Some possible implications for breeding RBDV-RB resistant cultivars are discussed.     

Common resistance in red raspberry to Botrytis cinerea and Didymella applanata, two pathogens occupying the same ecological niche

Comparisons were made between Botrytis cinerea and Didymella applanata, which occupy the same ecological niche on canes of red raspberry. Isolates of B. cinerea from diverse localities within the British Isles were pathogenic to the SCRI selection M30 when internodal wounds on young canes were inoculated. A single inoculation frequently caused the buds at several nodes to fail the following spring. Differences in the lengths of the stem lesions that formed indicated differences in isolate pathogenicity, but these were not related to isolate origin. Bud suppression and lateral shoot failure also occurred when petioles of cvs Mailing Orion, Mailing Jewel and Glen Clova were wound inoculated with B. cinerea up to late August. The relative resistance of seven cultivars to three isolates of each pathogen was determined. Principal components analysis of data from five estimates of resistance to each pathogen showed that 40% of the variation described a common resistance to the two diseases. Further analysis showed that cvs Chilcotin and Meeker had the strongest common resistance and that cvs Glen Prosen and Mailing Jewel had the weakest. The remaining variation described cultivar differences in relative bud length after petiole inoculation with either pathogen, and differences in the relative importance of spring and autumn symptoms. Only 7% of the variation indicated independent resistance to the two pathogens and this was not influenced by cultivar differences.     

A genetic ensemble approach for gene-gene interaction identification

Background  

It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging.     

Use of hair tubes to survey for shrews: new methods for identification and quantification of abundance

• 1 Accurate and sensitive survey and monitoring methods are needed for shrews. We present a new design of hair tube and a new, simple method of species identification from multivariate analysis of four parameters measured from shrew guard hairs using a binocular microscope with incident light.
• 2 Multivariate analysis of these parameters measured from hairs of known identity showed that they can be used to identify hair to the species level with 85% accuracy.
• 3 We compared our indices of abundance from hair tubes (the hair tube index) with those from live trapping in 40 field margins. Capture‐mark‐recapture methods showed that capture rate did not vary systematically across sites, so that number of individuals captured was used as an index of abundance.
• 4 The hair tube index showed a significant association with the number of individuals captured for Sorex araneus and Neomys fodiens. The lack of a significant association for Sorex minutus may be because hair tubes are more sensitive in detecting this species than live trapping.
• 5 Hair tubes have additional advantages over live trapping, since they do not require frequent checking, are much lighter and cheaper than live traps, and no licence is required for their use in the UK. We therefore recommend consideration of their use in future surveys and monitoring studies of shrews. We provide an equation so that other researchers can use our multivariate method.

     

Gene-gene interaction filtering with ensemble of filters

BACKGROUND: Complex diseases are commonly caused by multiple genes and their interactions with each other. Genome-wide association (GWA) studies provide us the opportunity to capture those disease associated genes and gene-gene interactions through panels of SNP markers. However, a proper filtering procedure is critical to reduce the search space prior to the computationally intensive gene-gene interaction identification step. In this study, we show that two commonly used SNP-SNP interaction filtering algorithms, ReliefF and tuned ReliefF (TuRF), are sensitive to the order of the samples in the dataset, giving rise to unstable and suboptimal results. However, we observe that the 'unstable' results from multiple runs of these algorithms can provide valuable information about the dataset. We therefore hypothesize that aggregating results from multiple runs of the algorithm may improve the filtering performance. RESULTS: We propose a simple and effective ensemble approach in which the results from multiple runs of an unstable filter are aggregated based on the general theory of ensemble learning. The ensemble versions of the ReliefF and TuRF algorithms, referred to as ReliefF-E and TuRF-E, are robust to sample order dependency and enable a more informative investigation of data characteristics. Using simulated and real datasets, we demonstrate that both the ensemble of ReliefF and the ensemble of TuRF can generate a much more stable SNP ranking than the original algorithms. Furthermore, the ensemble of TuRF achieved the highest success rate in comparison to many state-of-the-art algorithms as well as traditional χ2-test and odds ratio methods in terms of retaining gene-gene interactions.     

云南省米虾属一新种(十足目：匙指虾科)

报道了米虾属一新种-昆明米虾Caridina kunmingensis Wang et Liang,sp.nov.。昆明米虾与石林米虾Caridina shilinica Liang et Cai2000有相似之处,但前者额角较短,前两对步足腕节和螯短而粗,雄性第1腹肢内肢、雄附肢形态和结构均与后者不同。