Positive Darwinian selection at single amino acid sites conferring plant virus resistance

Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of amino acid substitutions in the plant gene eIF4E to evaluate the performance of these methods in detecting site-specific positive selection. We documented for the first time a molecular signature of positive selection within a recessive resistance gene in plants. We then used two statistical platforms, Phylogenetic Analysis Using Maximum Likelihood and Hypothesis Testing Using Phylogenies (HyPhy), to look for site-specific positive selection. Their relative power and accuracy are assessed by comparing the sites they identify as being positively selected with those of resistance-determining amino acids. Our results indicate that although both methods are surprisingly accurate in their identification of resistance sites, HyPhy appears to more accurately identify biologically significant amino acids using our data set.

Resistance conferred against bean common mosaic virus by the incompletely dominant I locus of Phaseolus vulgaris is active at the single cell level

A protoplast transfection system was used in Phaseolus vulgaris to study the incompletely dominant resistance locus I. The genetic materials in the study were cultivar 'Black Turtle Soup' lines nearly isogenic for I and their F1. Accumulation of bean common mosaic virus (BCMV; genus Potyvirus) RNA and virions was assayed following BCMV RNA electrotransfection of protoplasts from each genotype. BCMV RNA and virions accumulated in all genotypes tested but the relative rates of RNA accumulation differed. This suggests that the I allele is active at the single cell level and in a dosage-dependent fashion and supports previous work in this area.

Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper

Phytophthora capsici causes devastating disease on many crop species, including Capsicum. Resistance in Capsicum annuum is genetically and physiologically complex. A panel of Capsicum germplasm that included genotypes from both C. annuum and C. chinense showing highly resistant, highly susceptible and intermediate or tolerant responses to the pathogen, respectively, was screened with a series of randomly amplified polymorphic sequence primers to determine which genomic regions contribute to the highest level of resistance. One primer, OpD04, amplified a single band only in those C. annuum and C. chinense genotypes showing the highest level of resistance. The amplified product was cloned, sequenced and used to design longer primers in order to generate a sequence characterized amplified region marker which was then mapped in a reference mapping population and a screened population segregating for resistance to P. capsici. These primers were observed to define a locus on pepper chromosome 5 tightly linked to Phyto.5.2, one of six quantitative trait loci (QTL) previously reported to contribute to P. capsici resistance. These results indicate that the Phyto.5.2 QTL may be widely distributed in highly resistant germplasm and provide improved resolution for this QTL. This work also defines the first breeding tools for this system, allowing for the rapid selection of genotypes likely to be highly resistant to P. capsici.

Five independent loci each control monogenic resistance to gummy stem blight in melon ( Cucumis melo L.)

Inheritance and segregation analysis demonstrated that five independent genes in melon confer monogenic resistance to foliar infection by the fungal pathogen Didymella bryoniae, resulting in the disease known as gummy stem blight (GSB). In this study, two new monogenic sources of GSB resistance were characterized. Resistance in Cucumis melo PI 482398 was monogenic dominant based on segregation analysis of F(1), F(2) and backcross populations, while resistance in C. melo PI 482399 showed monogenic recessive inheritance. Four accessions, PI 482398, PI 157082, PI 511890, and PI 140471, each previously known to carry monogenic dominant resistance to GSB, were intercrossed to determine genetic relationships among these resistance sources. Recovery of susceptible individuals in F(2) populations confirmed that these accessions possess different resistance genes. Resistance loci were designated Gsb-1 (formerly Mc, monogenic dominant resistance from PI 140471), Gsb-2 (monogenic dominant resistance from PI 157082), Gsb-3 (monogenic dominant resistance from PI 511890), Gsb-4 (monogenic dominant resistance from PI 482398) and gsb-5 (monogenic recessive resistance from PI 482399).

Production of haploid and doubled haploid plants of melon ( Cucumis melo L) for use in breeding for multiple virus resistance

We have developed improved procedures for recovery of haploid and doubled haploid (DH) melon plants, using hybrids derived from crosses of lines with multiple virus resistance. Seeds formed after pollination with irradiated pollen were cultured in liquid medium for 10 days before excision of the embryos for further culture. This made it easier to identify the seeds containing parthenogenetic embryos, thereby reducing the effort required and increasing the percentage of plants recovered. The plants obtained (approximately 175) were transferred to a greenhouse for evaluation. Three fertile lines were identified, and selfed seeds were obtained for evaluating virus resistance. Flow cytometry of leaf tissues showed that two of these lines were spontaneous DH and the third was a mixoploid containing haploid and diploid cells. The other plants remained sterile through the flowering stage. Flow cytometry of 20 sterile plants showed that all were haploid. Attempts to induce chromosome doubling by applying colchicine to greenhouse-grown plants were unsuccessful. Shoot tips from the haploid plants were used to establish new in vitro cultures. In vitro treatment of 167 micropropagated haploid shoots with colchicine produced 10 diploid plants as well as 100 mixoploid plants. Pollen from male flowers that formed in vitro on the colchicine-treated plants was examined. High percentages of viable pollen that stained with acetocarmine were found not only in the diploids but also in >60% of the plants scored as mixoploid or haploid by flow cytometry. Efficient recovery of DH from hybrid melon lines carrying combinations of important horticultural traits will be a valuable tool for melon breeders.

A new gene, Ny (tbr), for hypersensitivity to Potato virus Y from Solanum tuberosumMaps to Chromosome IV

A diploid backcross population derived from a cross between Solanum tuberosum and Solanum berthaultiisegregated for monogenic dominant hypersensitivity to Potato virus Y(PVY). We propose the symbol Ny (tbr) for this locus because plants carrying this gene develop necrosis after inoculation with PVY and the allele originated in S. tuberosum. The gene mapped to chromosome IV between TG316 and TG208 at LOD=2.72. This location does not correspond to any other mapped resistance genes in potato.