bluuebunny/crossref_metadata_2025 huggingface dataset:
Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies
Authors: Homer Nils , Tembe Waibhav D. , Szelinger Szabolcs , Redman Margot , Stephan Dietrich A. , Pearson John V. , Nelson Stanley F. , Craig David
Published: July 2008

Summary: For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Pooling-based GWA studies could benefit significantly by utilizing this redundancy to reduce noise, improve the accuracy of the observations and increase genomic coverage. We introduce a measure of correlation between individual genotyping and pooling, under the same framework that r2 provides a measure of linkage disequilibrium (LD) between pairs of SNPs. We then report a new non-haplotype multimarker multi-loci method that leverages the correlation structure between SNPs in the human genome to increase the efficacy of pooling-based GWA studies. We first give a theoretical framework and derivation of our multimarker method. Next, we evaluate simulations using this multimarker approach in comparison to single marker analysis. Finally, we experimentally evaluate our method using different pools of HapMap individuals on the Illumina 450S Duo, Illumina 550K and Affymetrix 5.0 platforms for a combined total of 1 333 631 SNPs. Our results show that use of multimarker analysis reduces noise specific to pooling-based studies, allows for efficient integration of multiple microarray platforms and provides more accurate measures of significance than single marker analysis. Additionally, this approach can be extended to allow for imputing the association significance for SNPs not directly observed using neighboring SNPs in LD. This multimarker method can now be used to cost-effectively complete pooling-based GWA studies with multiple platforms across over one million SNPs and to impute neighboring SNPs weighted for the loss of information due to pooling.

Contact:  dcraig@tgen.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Synthetics for the Shah: DuPont and the Challenges to Multinationals in 1970s Iran
Authors: Blaszczyk Regina Lee
Published: July 2008

In the 1960s and 1970s, the largest U.S. chemical firm, E.I. du Pont de Nemours & Company, established an international presence in synthetic fibers by building plants to make nylon, polyester, and acrylic in Latin America and Europe. DuPont managers also looked to the Middle East, specifically to Iran, which was fast industrializing under Shah Mohammad Reza Pahlavi. The Shah's pro-Western stance and his country's rich oil fields made Iran appealing to a petrochemical giant like DuPont, which used petroleum feed stocks to make fibers and other products. In the 1970s, DuPont partnered with the Behshahr Industrial Group, a conglomerate run by the Ledjavardi clan, one of Iran's leading families, to build a high-tech fiber facility that would help modernize the Iranian textile industry. The story of this short-lived joint venture, a victim of the Islamic Revolution, demonstrates the challenges to multinationals operating in imperial Iran, and shows how the daily experience of dealing with cultural differences often masked larger political and economic troubles.
Transmission of Activated-Episomal Banana streak OL (badna)virus (BSOLV) to cv. Williams Banana (Musa sp.) by Three Mealybug Species
Authors: Meyer J. B. , Kasdorf G. G. F. , Nel L. H. , Pietersen G.
Published: July 2008

Four different mealybug species (Dysmicoccus brevipes, Planococcus citri, P. ficus, and Pseudococcus longispinus) were evaluated for their ability to transmit putative activated-episomal Banana streak OL (badna)virus (BSOLV) to banana cv. Williams (Cavendish subgroup, AAA). Expressible endogenous sequences of banana streak viruses (BSVs) have been reported to be present in the DNA of various Musa hybrids, including FHIA-21 (AAAB). To obtain activated episomal BSOLV for this experimental transmission study, intentional stress by tissue culture propagation was applied to indexed FHIA-21 which, while free of other viruses, can contain activated episomal BSOLV. Immunocapture polymerase chain reaction and triple-antibody sandwich enzyme-linked immunosorbent assay results revealed that 13.4% of the derived progeny of the mother plants were infected with episomal BSOLV. Four of these BSOLV-infected progeny were used as sources of episomal virus for transmission studies. D. brevipes, Planococcus citri, and P. ficus mealybugs were able to transmit the putative activated episomal BSOLV. Control plants for the transmission experiments included FHIA-21 corms with no background history of tissue culture, as well as virus-free Williams plants. Episomal Banana streak GF (badna)virus (BSGFV) was transmitted from asymptomatic corm-derived FHIA-21 plants by P. citri and P. ficus. This is the first report of P. ficus as a vector of BSVs.
Incidence, Distribution, and Association of Spongospora subterranea and Potato mop-top virus in Costa Rica
Authors: Montero-Astúa Mauricio , Vasquéz Viviana , Turechek William W. , Merz Ueli , Rivera Carmen
Published: July 2008

A survey was conducted in 39 potato (Solanum tuberosum) fields in Costa Rica to determine incidence and association of Spongospora subterranea f. sp. subterranea and Potato mop-top pomovirus (PMTV). The fields were located in Costa Rica's two major potato-production regions and were further characterized by their altitude. In all, 633 paired samples of leaf tissue and corresponding tubers were collected, assessed visually for disease, and subsequently assayed by enzyme-linked immunosorbent assay (ELISA). S. subterranea presence in tuber tissue was tested by double-antibody sandwich (DAS)-ELISA and PMTV presence in leaf and tuber tissues was tested by triple-antibody sandwich (TAS)-ELISA. Moreover, soil samples were collected from 10 fields surveyed and were evaluated for both pathogens via ELISA and bioassay. The incidence of both diseases ranged from 0 to 100% within individual fields, with incidences lower than 40% occurring in more than 70% of the fields. Higher incidences were found in fields located at higher altitudes. Of the 633 paired samples, 179 and 146 were positive for PMTV and S. subterranea, respectively, according to ELISA in either the foliage or tubers. A low correlation was found for PMTV visual symptoms and ELISA test results. Only 14 of the 81 foliar samples testing positive for PMTV had visual symptoms; the remaining 67 samples were asymptomatic. Conversely, comparison of visual evaluation with detection of S. subterranea by ELISA on tubers showed that 70% of the results were coincident. S. subterranea was detected in 4 of 10 soil samples tested by ELISA. Soilborne PMTV was detected by ELISA in roots of bait plants sown in these soil samples. Co-occurrence of both pathogens was detected in 64 samples. A significant but low degree of association for vector and virus was determined, and data suggests that S. subterranea is participating in the transmission of PMTV in Costa Rica in low frequency.
Virulence and Fungicide Sensitivity of Phytophthora cactorum Isolated from American Ginseng Gardens in Wisconsin and Michigan
Authors: Hill S. N. , Hausbeck M. K.
Published: July 2008

Phytophthora cactorum causes foliar blight and root rot on cultivated ginseng (Panax quinquefolium). Commercial ginseng gardens in Wisconsin and Michigan and research gardens at Michigan State University were sampled and P. cactorum isolated. In all, 114 and 96 P. cactorum isolates were recovered in 2003 and 2004, respectively. The majority (82%) of the isolates screened (210 in total) were resistant to the fungicide mefenoxam. P. cactorum isolates were screened for pathogenicity using ‘McIntosh’ apple fruit (206 isolates) and ginseng seedlings (38 isolates). Most isolates (98%) produced necrotic lesions on apple fruit and nearly all (97%) isolates resulted in 40 to 100% plant death. Apple fruit and ginseng seedlings were also used to test fungicide efficacy against P. cactorum. Mefenoxam, the industry standard, was ineffective in both the apple fruit and seedling studies when using a mefenoxam-resistant P. cactorum isolate. Only copper hydroxide provided consistent control against P. cactorum when tested on apple fruit and ginseng seedlings.
Adaptation of an Apple Sooty Blotch and Flyspeck Warning System for the Upper Midwest United States
Authors: Duttweiler K. B. , Gleason M. L. , Dixon P. M. , Sutton T. B. , McManus P. S. , Monteiro J. E. B. A.
Published: July 2008

A warning system for sooty blotch and flyspeck (SBFS) of apple, developed in the southeastern United States, uses cumulative hours of leaf wetness duration (LWD) to predict the timing of the first appearance of signs. In the Upper Midwest United States, however, this warning system has resulted in sporadic disease control failures. The purpose of the present study was to determine whether the warning system's algorithm could be modified to provide more reliable assessment of SBFS risk. Hourly LWD, rainfall, relative humidity (RH), and temperature data were collected from orchards in Iowa, North Carolina, and Wisconsin in 2005 and 2006. Timing of the first appearance of SBFS signs was determined by weekly scouting. Preliminary analysis using scatterplots and boxplots suggested that cumulative hours of RH ≥ 97% could be a useful predictor of SBFS appearance. Receiver operating characteristic curve analysis was used to compare the predictive performance of cumulative LWD and cumulative hours of RH ≥ 97%. Cumulative hours of RH ≥ 97% was a more conservative and accurate predictor than cumulative LWD for 15 site years in the Upper Midwest, but not for four site years in North Carolina. Performance of the SBFS warning system in the Upper Midwest and climatically similar regions may be improved if cumulative hours of RH ≥ 97% were substituted for cumulative LWD to predict the first appearance of SBFS.
Survival of Didymella bryoniae in Infested Muskmelon Crowns in South Carolina
Authors: Keinath Anthony P.
Published: July 2008

The crowns of muskmelon (Cucumis melo subsp. melo) plants are susceptible to cankers caused by the fungal pathogen Didymella bryoniae. The objective of this study was to compare the length of time D. bryoniae survived in infested crowns that were buried or left on the soil surface. Dried crowns with cankers were buried 12.5 cm deep, placed on the soil surface, or placed on top of raised beds covered with white-on-black polyethylene mulch from July 2002 to June 2003, December 2003 to October 2004, July 2004 to November 2005, and November 2005 to November 2007. At regular intervals, crowns or crown debris were retrieved, washed, cut into pieces, and cultured on semiselective medium to recover D. bryoniae. D. bryoniae was not recovered from crowns buried 35 and 45 weeks in 2003 and 2004 but was recovered from 2.5% of crowns buried 66 weeks in 2005. In contrast, D. bryoniae was recovered after 48, 45, 66, and 103 weeks from 66, 6.3, 2.5, and 10% of crowns on the soil surface in 2003, 2004, 2005, and 2007, respectively. D. bryoniae also was recovered after 66 and 103 weeks from 12.5 and 8% of crowns on mulched beds in 2005 and 2007. In two additional experiments, the pathogen was recovered from 15.0 and 20.1% of infested muskmelon debris left in place for 42 and 38 weeks on polyethylene-mulched beds. To reduce the time D. bryoniae survives after a cucurbit crop, crop debris should be incorporated into soil promptly after harvest.
Occurrence, Prevalence, and Distribution of Viruses Infecting Peanut in Argentina
Authors: de Breuil S. , Nievas M. S. , Giolitti F. J. , Giorda L. M. , Lenardon S. L.
Published: July 2008

This is the first survey to determine the occurrence, prevalence, and distribution of peanut (Arachis hypogaea) viral diseases in Argentina. It was conducted in the province of Córdoba, which has 92% of the country's peanut production. It included the main peanut viruses Peanut mottle virus (PeMoV), Peanut stripe virus (PStV), Cucumber mosaic virus (CMV), Peanut stunt virus (PSV), Tomato spotted wilt virus (TSWV), and Groundnut ringspot virus (GRSV). Leaf samples from 1,028 individual peanut plants with virus-like symptoms and 986 samples from asymptomatic plants were collected in six counties of Córdoba over 3 years and serologically tested for the presence of viruses. PeMoV was the most frequently detected virus, found in 58.8, 34.2, and 23.4% of samples from the 2003–04, 2004–05, and 2005–06 growing seasons, respectively, and it was found in all sampled counties. Also, it was the only virus detected in asymptomatic plants. Less than 4% of symptomatic plants were infected with CMV or GRSV; 0.5, 3.6, and 2% of samples were positive for CMV; and 0.5, 3.1, and 1.6% were positive for GRSV in the 2003–04, 2004–05 and 2005–06 seasons, respectively. Some mixed infections were found: CMV-PeMoV and GRSV-PeMoV. During this survey, PSV, PStV, and TSWV were not detected in any peanut samples.
First Report of Begonia Chlorotic Ringspot Caused by Zucchini yellow mosaic virus in Taiwan
Authors: Chen Y. K. , Hong Y. H.
Published: July 2008

Begonia (Begonia semperflorens) showing symptoms of systemic chlorotic ringspots were observed in the central part of Taiwan in May 2006. Infected begonia plants showed faint ringspots in leaves at the early stage of infection. Symptoms turned chlorotic and coalesced as the disease progressed. Electron microscopic examination revealed filamentous virus particles approximately 750 × 13 nm in the crude sap of infected begonia. Typical pinwheel inclusion bodies of potyvirus infection were observed in the ultrathin sections of infected begonia. A virus culture was isolated via mechanical inoculations in Chenopodium quinoa and serologically identified as Zucchini yellow mosaic virus (ZYMV) (1) by ELISA, western blotting, and immunoelectron microscopy. Complementary DNA fragments of viral genomic RNA were cloned, sequenced, and the full-length sequence was submitted to the EMBL database (Accession No. AM422386). The genomic RNA consists of 9,591 nucleotides excluding the poly-A tail and has an identical genome organization to that reported for members of the genus, Potyvirus. The nucleotide sequence of the full-length genome and the deduced amino acid sequence of coat protein share 98% identity to those of ZYMV-CU (Accession No. AJ307036), ZYMV-SG (Accession No. AJ316228), and ZYMV-TW-TN3 (Accession No. AF127929). The virus caused local lesions on the inoculated leaves of C. quinoa, systemic mosaic in cucumber (Cucumis sativus), zucchini (Cucurbita pepo), and Cucumis metuliferus, and chlorotic ringspots in begonia. Symptoms caused by the begonia isolate in cucurbits were much milder than those caused by ZYMVs of cucurbit origin. A ringspot disease with symptoms similar to those caused by ZYMV is also produced on begonia by an Ilarvirus, Prunus necrotic ringspot virus (PNRSV), which was previously identified in begonia (2). To our knowledge, this is the first report of natural infection of ZYMV in begonia.

References: (1) V. Lisa et al. Phytopathology 71:667, 1981. (2) N. Verma et al. Plant Pathol. 51:800, 2002.
First Report of Anthracnose Fruit Rot Caused by Colletotrichum acutatum on Strawberry in Korea
Authors: Nam M. H. , Kim T. I. , Gleason M. L. , Song J. Y. , Kim H. G.
Published: July 2008

Symptoms typical of anthracnose fruit rot; sunken, dark brown lesions on maturing fruits, were found in a commercial field of strawberry (Fragaria × ananassa) cv. Cal Giant in Yangyang County, Korea in May 2007. Masses of conidia were produced in acervuli in the center of lesions. The fungus was isolated on potato dextrose agar (PDA). Colonies grown on PDA were pale to mouse gray and became dark green to black in reverse. Conidia were formed in orange-to-salmon pink masses in the center of the culture. The average size of conidia on PDA was 15.2 × 4.6 μm, and they were hyaline, straight, cylindrical, with pointed ends, and aseptate (1). The fungus did not form an ascigerous stage in culture. Mycelial growth rate was 7.5 mm per day at 25°C on PDA. The identity of two isolates was confirmed as Colletotrichum acutatum J.H. Simmonds by PCR amplification using species-specific primers TBCA and TB5 (2), resulting in a characteristic 330-bp band on agarose gel. Morphological characters were in accordance with previous reports on C. acutatum. A pathogenicity test was conducted with five healthy plants of cvs. Cal Giant, Maehyang, Seolhyang, Kumhyang, Akihime, and Redpearl. After fruits and flowers were sprayed with a conidia suspension (105 conidia per ml), the plants were maintained at 10 to 25°C and 100% relative humidity in a greenhouse. As a control, five healthy plants were sprayed with sterile distilled water and incubated under the same conditions. Dark brown, water-soaked spots appeared on mature fruits of all cultivars after 5 days, and lesions on green fruits appeared on individual achenes. Flowers developed dark lesions, dried out, and died. No symptoms were found on the control plants. After the pathogen was reisolated from fruits and flowers lesions, the morphological characters developed in culture as described above. To our knowledge, this is the first report of C. acutatum causing strawberry anthracnose in Korea.

References: (1) B. J. Smith and L. L. Black. Plant Dis. 74:69, 1990. (2) P. Talhinhas et al. Appl. Environ. Microbiol. 71:2987, 2005.
First Report of Xylella fastidiosa in Nerium oleander in Costa Rica
Authors: Montero-Astúa M. , Saborío-R. G. , Chacón-Díaz C. , Villalobos W. , Rodríguez C. M. , Moreira L. , Rivera C.
Published: July 2008

Oleander (Nerium oleander L.) shrubs presenting mottling, leaf tip and margin scorch, short internodes, defoliation, and branch dieback were observed at different localities in the Central Valley in Costa Rica. Severity of the symptoms ranged widely, and most plants showed both diseased and healthy branches. In severe cases, entire sections of the plant were defoliated. Symptoms resembled those described for oleander leaf scorch (OLS) caused by the bacterium Xylella fastidiosa in the United States (3). This bacterium has been reported in coffee and citrus plants in Costa Rica. Sixty plants from five different places were sampled and tested using ELISA (Agdia Inc., Elkhart, IN) against X. fastidiosa. Thirty-five plants showed absorbance mean value of duplicate wells greater than the mean of control wells plus three times the standard deviation, and therefore were considered positive. Thirty-three of the sixty samples were processed for an immunofluorescence assay modified from Carbajal et al. (1) with antibody to X. fastidiosa (Agdia Inc.). Thirteen samples showed fluorescent rod-shaped bacilli with morphology similar to those observed from a pure culture of X. fastidiosa obtained from coffee. Ten of these thirteen samples were positive by ELISA. DNA extracts (2) from three of the oleander plants with high ELISA absorbance values were tested by nested PCR with primer pair 272-1/272-2 followed by the pair 272-1 int/272-2 int (4). Two of the samples were positive for the bacterium and one of the PCR products was cloned and sequenced in both directions (GenBank Accession No. EU009615). The negative (PCR mix) and positive (pure culture of X. fastidiosa isolated from grapevine) controls for nested-PCR were indeed negative and positive, respectively. The BLAST program was used to compare the sequence to the nucleotide collection (nr/nt) and Microbe Assembled Genomes databases in GenBank. All matches corresponded to X. fastidiosa sequences. The sequence showed 97% similarity with strains Found-4 (coffee strain from Brazil) and Found-5 (citrus strain from Brazil) and 96% similarity with strain Ann-1 from oleander in California. On the basis of serological, microscopic, and molecular detection of X. fastidiosa from oleander exhibiting symptoms of OLS similar to those reported in the literature, this pathogen likely is causing the symptoms we observed in Costa Rica.

References: (1) D. Carbajal et al. Curr. Microbiol. 49:372, 2004. (2) M. J. Green et al. Plant Dis. 83:482, 1999. (3) Q. Huang et al. Plant Dis. 88:1049, 2004. (4) M. R. Pooler and J. S. Hartung. Curr. Microbiol. 31:377, 1995.
First Report of the Occurrence of Grapevine fanleaf virus in Washington State Vineyards
Authors: Mekuria T. , Martin R. R. , Naidu R. A.
Published: July 2008

Grapevine fanleaf virus (GFLV; genus Nepovirus, family Comoviridae), responsible for fanleaf degeneration disease, is one of the most important viruses of grapevines worldwide (1). During our reconnaissance studies during 2007, dormant wood cuttings from individual grapevines of wine grape cv. Chardonnay were collected randomly from two geographically separate vineyards in eastern Washington State. Extracts made from cambial scrapings of these cuttings were tested separately for different viruses by single-tube reverse transcription (RT)-PCR using virus-specific primers. Two of the thirty-one grapevines in one vineyard tested positive for GLFV as mixed infection with Grapevine leafroll-associated virus (GLRaV)-3. In another vineyard, six of the twenty-six grapevines tested positive for GFLV as mixed infection with GLRaV-1, GLRaV-3, and Grapevine virus A (GVA) A forward primer (5′-ACCGGATTGACGTGGGTGAT, corresponding to nucleotides [nt] 2231–2250) and reverse primer (5′-CCAAAGTTGGTTTCCCAAGA, complementary to nt 2533–2552) specific to RNA-2 of GFLV-F13 isolate (GenBank Accession No. X16907) were used in RT-PCR assays for the detection of GFLV (4). Primers used for RT-PCR detection of GLRaV-1, GLRaV-2, and GVA were described in Martin et al (2) and Minafra et al (3). The RT-PCR results indicated mixed infection of GFLV with GLRaV-1, GLRaV-3, and GVA. To confirm the presence of GFLV, the 322-bp sequence representing a portion of the coat protein encoded by RNA-2 genomic segment was cloned into pCR2.1 (Invitrogen Corp., Carlsbad, CA). Amplicons obtained from six individual grapevines in the two vineyards were used for cloning. Three independent clones per amplicon were sequenced from both orientations. Pairwise comparison of these sequences showed 99 to 100% nucleotide sequence identity among themselves, indicating that GFLV isolates from the two vineyards may be identical. A comparison of the consensus sequence (GenBank Accession No. EU573307) with corresponding sequences of other GFLVs deposited in GenBank showed 89 to 91% identity at the nucleotide level and 95 to 99% identity at the amino acid level. However, mixed infection of GFLV with different viruses in the two vineyards suggests separate introduction of the planting material. ELISA with GFLV-specific antibodies further confirmed the presence of the virus in samples that were positive in RT-PCR. To our knowledge, this is the first report of GFLV in grapevines grown in the Pacific Northwest states of the United States. Further investigations are being carried out on the distribution, symptoms, molecular variability, and nematode vector transmission of GFLV.

References: (1) P. Andret-Link et al. J. Plant Pathol. 86:183, 2004. (2) R. R. Martin et al. Plant Dis. 89:763, 2005. (3) A. Minafra et al. Arch. Virol. 142:417, 1997 (4) A. Rowhani et al. Phytopathology 83:749, 1993.
First Report of Sclerotinia sclerotiorum on Argyranthemum frutescens in Italy
Authors: Garibaldi A. , Pensa P. , Gullino M. L.
Published: July 2008

Paris daisy (Argyranthemum frutescens (L.) Sch. Bip.) is an economically important crop on the Riviera Ligure (northern Italy), where approximately 10 million plants per year are produced for export. In the winter of 2007, extensive wilting was observed on 5-month-old potted plants of A. frutescens grown in a commercial greenhouse near Albenga. First symptoms included stem necrosis, darkening and withering of leaves, and wilting of young buds. As stem and foliar necrosis progressed, infected plants wilted and died. Wilt occurred a few days after the appearance of the first symptoms. Infected plants were characterized by the presence of soft, watery tissues. Lesions became covered with a whitish mycelium and dark sclerotia were produced on the mycelium. Diseased stem tissue was surface sterilized for 1 min in 1% NaOCl and plated on potato dextrose agar (PDA) amended with 100 mg/l streptomycin sulfate. Sclerotinia sclerotiorum (Lib.) de Bary (2) was consistently recovered from infected stem pieces. Sclerotia produced on PDA measured 1.4 to 5.2 × 2.3 to 6.7 (average 3.3 to 4.2) mm. The internal transcribed spacer (ITS) region of rDNA was amplified using primers ITS4/ITS6 and then sequenced. BLAST analysis (1) of the 531-bp segment showed a 100% homology with the sequence of S. sclerotiorum. The nucleotide sequence has been assigned GenBank Accession No. EU 556701. Pathogenicity of two isolates obtained from infected plants was confirmed by inoculating 10 90-day-old plants for each isolate. Plants were grown singly in 18-cm-diameter pots maintained in a greenhouse under shade and were regularly irrigated and fertilized. Mycelium plugs 1 cm2 were excised from a 10-day-old PDA culture of both isolates and placed on the soil surface around the base of each plant. Ten noninoculated plants served as controls. Plants were maintained in a greenhouse under shade at temperatures ranging between 6 and 22°C (average 18°C) and relative humidity at >90%. The inoculation trial was carried out twice. All inoculated plants developed leaf yellowing by 22 days after inoculation. White, cottony mycelium and black sclerotia developed on stems and at the base of all inoculated plants. Eventually, infected plants wilted. Control plants remained symptomless. S. sclerotiorum was reisolated from the stems of inoculated plants. To our knowledge, this is the first report of S. sclerotiorum causing white mold on A. frutescens in Italy as well as worldwide. The economic importance of this disease can be considered limited at the moment.

References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997 (2) N. F. Buchwald. Kongl. Veterisk Landb. Aarssk. 75, 1949.
First Record of Bacterial Blight Caused by Pseudomonas syringae pv. syringae on Pyracantha coccinea and an Amelanchier sp. in Bulgaria
Authors: Bobev S. G. , Baeyen S. , Van Vaerenbergh J. , Maes M.
Published: July 2008

During the spring and summer months of 2004 and 2005, sporadic damage on individual shrubs of Pyracantha coccinea and an Amelanchier sp. were observed at two locations in the region of Plovdiv, Bulgaria. Symptoms initially were expressed as blossom blight and subsequently expanded to the shoots and branches, forming cankers on the supplying wood. In both years, a fluorescent gram-negative bacterium was isolated from diseased tissues onto King's B medium. The bacterial strains were levan positive and oxidase and arginine dihydrolase negative. They were able to induce a typical hypersensitive response on tobacco plants (cv. Samsun), but failed to rot potato slices. Pathogenicity of the strains was confirmed by puncture-inoculating detached shoots from both hosts and immature cherry and pear fruits with a bacterial suspension (108 CFU/ml, 50 μl per wound, and 3 replicates). Controls were punctured with sterile water. The inoculated plant material was maintained at room temperature (22 to 25°C) in plastic pots and covered with polyethylene bags for the first 48 h after inoculation. The inoculated and control subjects were kept under the same conditions as before inoculation. Except for the controls, slowly expanding but well defined necrotic lesions around the inoculation points were observed within the next 5 to 7 days. Bacteria reisolated from symptomatic tissue were identical to the initial cultures. On the basis of the symptoms and results from all laboratory tests, the bacterium was considered to be Pseudomonas syringae pv. syringae (1). PCR amplification of the 752-bp syrB fragment (2) confirmed the identification. To our knowledge, this is the first occurrence of P. syringae pv. syringae on Pyracantha coccinea and an Amelanchier sp. in Bulgaria, and most probably, this pathogen will play a more significant role within the rosaceous group because of a rising number of the cultivated ornamental species.

References: (1) N. W. Schaad et al., eds. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2001. (2) K. N. Sorensen et al. Appl. Environ. Microbiol. 64:226, 1998.
First Report of Apium virus Y on Cilantro, Celery, and Parsley in California
Authors: Tian T. , Liu H.-Y. , Koike S. T.
Published: July 2008

Recently, Apium virus Y (ApVY) was detected in field-grown cilantro (Coriandrum sativum), celery (Apium graveolens), and parsley (Petroselinum crispum) in California. In 2003, cilantro plants growing in three different fields in California (Monterey, San Joaquin, and San Luis Obispo counties) expressed symptoms of mosaic, vein clearing, and stunting. When plant sap was examined by transmission electron microscopy, flexuous, rod-shaped virus particles were observed. Total RNA was extracted from the symptomatic cilantro plants and used as a template in reverse transcription (RT)-PCR using universal potyvirus primers according to Chen et al. (1). The RT-PCR product was cloned into pGEM-T (Promega, Madison, WI) and the insert of 1,713 bp was sequenced (GenBank Accession No. EU515125). Nucleotide sequences from clones derived from three different infected cilantro plants were 89 to 97% identical to ApVY sequences encoding partial sequence of polyprotein in GenBank (Accession Nos. AY049716, EU127499, AF207594, AF203529, and EU255632). In 2007, celery plants showing necrotic line patterns and necrotic lesions on lower leaves and petioles were observed in several fields in two coastal counties in California (Monterey and Santa Clara counties). Flexuous, rod-shaped virus particles were also observed in the sap of those plants. ELISA for Cucumber mosaic virus and RT-PCR for Celery mosaic virus were negative. ApVY specific primers were designed on the basis of a consensus sequence of ApVY identified from cilantro in 2003; reverse primer 5′-GGCTCTTGCTATAGACAAATAGT-3′ and forward primer 5′-GAAGACCAAGCCAATGTGTGTA-3′. The sequence of RT-PCR products (GenBank Accession No. EU515126) amplified from infected celery had 90 to 98% nucleotide identity to ApVY. When the deduced amino acid sequences of NIb and CP regions from both cilantro and celery were used for comparison, they showed 95 to 99% identity with the known ApVY GenBank sequences mentioned above. More than 10 asymptomatic parsley plants growing in fields adjacent to the infected celery were also tested for ApVY and found to be infected. ApVY was previously identified in three Apiaceae weeds in Australia (2) and in celery in New Zealand (3). To our knowledge, this is the first report of ApVY on cilantro, celery, and parsley in California.

References: (1) J. Chen et al. Arch. Virol. 146:757, 2001. (2) J. Moran et al. Arch. Virol. 147:1855, 2002. (3) J. Tang et al. Plant Dis. 91:1682, 2007.
Characterization of Iris yellow spot virus from Onion in Arizona
Authors: Pappu Hanu , Matheron Michael
Published: July 2008

Iris yellow spot virus is an economically important pathogen affecting both bulb and seed onion crops in the US and several parts of the world. In January 2008, two commercial onion fields in Yuma County, Arizona, had plants with symptoms suggestive of IYSV infection. IYSV infection was confirmed by ELISA, and the virus infection was further verified by reverse transcription-polymerase chain reaction.

Accepted for publication 29 May 2008. Published 11 July 2008.
Recombinant Inbred Line Differential Identifies Race-Specific Resistance to Phytophthora Root Rot in Capsicum annuum
Authors: Sy O. , Steiner R. , Bosland P. W.
Published: July 2008

A differential series is the normal method for identification of races within a plant pathogen and a host interaction. A host differential is extremely useful for phytopathological as well as breeding purposes. A set of recombinant inbred lines (RILs) were developed and characterized for race differentiation of Phytophthora root rot caused by Phytophthora capsici. The highly resistant Capsicum annuum accession Criollo de Morelos-334 was hybridized to a susceptible cultivar, Early Jalapeno, to generate the RIL population. The host differential characterized 17 isolates of P. capsici into 13 races. The establishment of a stable host differential for the P. capsici and C. annuum interaction will assist researchers in understanding the complex inheritance of resistance to Phytophthora root rot and to develop resistant cultivars.
Allele Sequencing of the Barley Stem Rust Resistance Gene Rpg1 Identifies Regions Relevant to Disease Resistance
Authors: Mirlohi A. , Brueggeman R. , Drader T. , Nirmala J. , Steffenson B. J. , Kleinhofs A.
Published: July 2008

The stem rust resistance gene Rpg1 has protected North American barley cultivars from significant yield losses for over 65 years. The remarkable durability of this gene warrants further study as to its possible origin and allelic variation. Eight Swiss barley (Hordeum vulgare) landraces and eight wild barley (H. vulgare subsp. spontaneum) accessions from diverse geographic regions were analyzed to uncover new alleles of Rpg1 and learn about its possible origin. The two germplasm groups included accessions that were resistant and susceptible to Puccinia graminis f. sp. tritici pathotype MCCF. Allele-specific primers were utilized to amplify 1 kbp overlapping fragments spanning the Rpg1 gene and sequenced if a polymerase chain reaction (PCR) fragment was generated. Variation among the PCR products revealed significant polymorphisms among these Hordeum accessions. Landraces and wild barley accessions susceptible to pathotype MCCF exhibited the highest degree of Rpg1 polymorphism. One resistant landrace (Hv672) and one resistant wild barley accession (WBDC040) yielded all seven Rpg1-specific PCR fragments, but only landrace Hv672 coded for an apparently functional Rpg1 as determined by comparison to previously characterized resistant and susceptible alleles and also resistance to HKHJ, a stem rust pathotype that can specifically detect Rpg1 in the presence of other resistance genes. Accessions resistant to stem rust pathotype MCCF, but completely lacking Rpg1-specific PCR amplification and hybridization with an Rpg1-specific probe, suggested the presence of stem rust resistant gene(s) different from Rpg1 in the Hordeum germplasm pool. Some Rpg1 alleles that retained the ability to autophosphorylate did not confer resistance to Puccinia graminis f. sp. tritici pathotype MCCF, confirming our previous observations that autophosphorylation is essential, but not sufficient for disease resistance. Thus, the RPG1 protein plays a complex role in the stem rust disease resistance-signaling pathway.
Polyphasic Characterization of Xanthomonas axonopodis pv. allii Associated with Outbreaks of Bacterial Blight on Three Allium Species in the Mascarene Archipelago
Authors: Picard Y. , Roumagnac P. , Legrand D. , Humeau L. , Robène-Soustrade I. , Chiroleu F. , Gagnevin L. , Pruvost O.
Published: July 2008

Based on the number of new reports during the last two decades, bacterial blight of onion (Allium cepa) is considered an emerging disease. The causal agent, Xanthomonas axonopodis pv. allii, is pathogenic to several Allium species after inoculation, but outbreaks worldwide have been primarily reported on onion. We describe a unique epidemiological situation in Réunion Island, France, with concomitant outbreaks on three Allium species, onion, leek (A. porrum), and garlic (A. sativum). There was no host specialization within Allium spp. among strains associated with the three host species. Based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism, strains associated with these outbreaks in Réunion Island were highly related genetically to strains isolated from diseased plant samples and contaminated seed lots in the neighboring island of Mauritius, where the disease has occurred since 1984. All AFLP haplotypes were identified as X. axonopodis pv. allii based on polymerase chain reaction analysis using specific primers, biochemical tests, and/or pathogenicity tests. Two genetically related groups of strains (A and B) that can be distinguished by AFLP, differential utilization of three carbon sources, and xanthomonadin pigment production were detected initially after establishment of the pathogen. In less than 10 years after the establishment of the pathogen there was nearly an extinction of group A strains in Réunion Island, suggesting differences in fitness between strains in the two groups.
Spatial Distribution of the Dagger Nematode Xiphinema index and Its Associated Grapevine fanleaf virus in French Vineyard
Authors: Villate L. , Fievet V. , Hanse B. , Delemarre F. , Plantard O. , Esmenjaud D. , van Helden M.
Published: July 2008

The nematode Xiphinema index is, economically, the major virus vector in viticulture, transmitting specifically the Grapevine fanleaf virus (GFLV), the most severe grapevine virus disease worldwide. Increased knowledge of the spatial distribution of this nematode, both horizontally and vertically, and of correlative GFLV plant infections, is essential to efficiently control the disease. In two infested blocks of the Bordeaux vineyard, vertical distribution data showed that the highest numbers of individuals occurred at 40 to 110 cm depth, corresponding to the two layers where the highest densities of fine roots were observed. Horizontal distribution based on a 10 × 15 m grid sampling procedure revealed a significant aggregative pattern but no significant neighborhood structure of nematode densities. At a finer scale (≈2 × 2 m), nematode sampling performed in a third block confirmed a significant aggregative pattern, with patches of 6 to 8 m diameter, together with a significant neighborhood structure of nematode densities, thus identifying the relevant sampling scale to describe the nematode distribution. Nematode patches correlate significantly with those of GFLV-infected grapevine plants. Finally, nematode and virus spread were shown to extend preferentially parallel to vine rows, probably due to tillage during mechanical weeding.
Confounding between recombination and selection, and the Ped/Pop method for detecting selection
Authors: O’Reilly Paul F. , Birney Ewan , Balding David J.
Published: July 2008

In recent years, there have been major developments of population genetics methods to estimate both rates of recombination and levels of natural selection. However, genomic variants subject to positive selection are likely to have arisen recently and, consequently, had less opportunity to be affected by recombination. Thus, the two processes have an intimately related impact on genetic variation, and inference of either may be vulnerable to confounding by the other. We illustrate here that even modest levels of positive selection can substantially reduce population-based recombination rate estimates. We also show that genome-wide scans to detect loci under recent selection in humans have tended to highlight loci in regions of low recombination, suggesting that confounding by recombination rate may have reduced the power of these studies. Motivated by these findings, we introduce a new genome-wide approach for detecting selection, based on the ratio of pedigree-based to population-based estimates of recombination rate. Simulations suggest that our “Ped/Pop” method, which is designed to capture completed sweeps, has good power to discriminate between neutral and adaptive evolution. Unusually for a multimarker method, our approach performs well in regions of high recombination and also has good power for many generations after the fixation of an advantageous variant. We apply the method to human HapMap and Perlegen data sets, finding confirmation of reported candidates as well as identifying new loci that may have undergone recent intense selection.
A molecular phylogeny of fleas (Insecta: Siphonaptera): origins and host associations
Authors: Whiting Michael F. , Whiting Alison S. , Hastriter Michael W. , Dittmar Katharina
Published: July 2008

Siphonaptera (fleas) is a highly specialized order of holometabolous insects comprising ∼2500 species placed in 16 families. Despite a long history of extensive work on flea classification and biology, phylogenetic relationships among fleas are virtually unknown. We present the first formal analysis of flea relationships based on a molecular matrix of four loci (18S ribosomal DNA, 28S ribosomal DNA, Cytochrome Oxidase II, and Elongation Factor 1‐alpha) for 128 flea taxa from around the world representing 16 families, 25 subfamilies, 26 tribes, and 83 flea genera with eight outgroups. Trees were reconstructed using direct optimization and maximum likelihood techniques. Our analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas. Pygiopsyllomorpha is monophyletic, as are the constituent families Lycopsyllidae, Pygiopsyllidae, and Stivaliidae, with a sister group relationship between the latter two families. Macropsyllidae is resolved as sister group to Coptopsyllidae with moderate nodal support. Stephanociricidae is monophyletic, as are the two constituent subfamilies Stephanocircinae and Craneopsyllinae. Vermipsyllidae is placed as sister group to Jordanopsylla. Rhopalopsyllidae is monophyletic as are the two constituent subfamilies Rhopalopsyllinae and Parapsyllinae. Hystrichopsyllidae is paraphyletic with Hystrichopsyllini placed as sister to some species of Anomiopsyllini and Ctenopariini placed as sister to Carterettini. Ctenophthalmidae is grossly paraphyletic with the family broken into seven lineages dispersed on the tree. Most notably, Anomiopsyllini is paraphyletic. Pulicidae and Chimaeropsyllidae are both monophyletic and these families are sister groups. Ceratophyllomorpha is monophyletic and includes Ischnopsyllidae, Ceratophyllidae, and Leptopsyllidae. Leptopsyllidae is paraphyletic as are its constituent subfamilies Amphipsyllinae and Leptopsyllinae and the tribes Amphipsyllini and Leptopsyllini. Ischnopsyllidae is monophyletic. Ceratophyllidae is monophyletic, with a monophyletic Dactypsyllinae nested within Ceratophyllinae, rendering the latter group paraphyletic. Mapping of general host associations on our topology reveals an early association with mammals with four independent shifts to birds.

© The Willi Hennig Society 2008.
Finding an upper limit for gap costs in direct optimization parsimony
Authors: Spagna Joseph C. , Álvarez‐Padilla Fernando
Published: July 2008

Exploring a large number of parameter sets in sensitivity analyses of direct optimization parsimony can be costly in terms of time and computing resources, and there is little a priori guidance available for reasonable limits to these search parameters. For this reason, we sought a general‐purpose upper limit for gap costs in the direct optimization program POY to streamline this process. To test the performance of POY as gap costs increase, we simulated data onto a pre‐set topology using a GTR + I + G model modified to include gaps by adding them according to a negative‐binomial model. Gaps were then removed and the data were analysed in POY at increasing gap costs. Increasing gap costs consistently resulted in reduced phylogenetic accuracy across trees of different relative branch lengths. Decoupling gap insertion and gap extension costs recovered a fraction of the accuracy lost by having both high gap insertion and gap extension costs, but only in trees with long internal nodes. To determine whether loss of phylogenetic accuracy was node‐specific, we designed a small dataset with a constrained node, where all possible combinations of cost substitution and different percentages of gap versus nucleotide changes were explored. These analyses showed that the effects of gap insertion and extension are node‐specific, and the minimum threshold for convergence on gap‐supported nodes is similar to the threshold for accuracy loss found in the larger simulated datasets. Subsequent analyses of empirical data revealed that a similar pattern of loss with gap cost increase can occur with ribosomal genes (18S, 28S, 16S and 12S) but this pattern was not seen in the intron data (myoglobin II) examined. In conjunction with previously published congruence‐based studies, the results suggest that POY sensitivity analyses can be streamlined and made more accurate if gap insertion and extension costs follow, as a guideline, a limit of four times the highest base‐transformation cost.

© The Willi Hennig Society 2008.
Parsimony and explanatory power
Authors: Farris James S.
Published: July 2008

Parsimony can be related to explanatory power, either by noting that each additional requirement for a separate origin of a feature reduces the number of observed similarities that can be explained as inheritance from a common ancestor; or else by applying Popper’s formula for explanatory power together with the fact that parsimony yields maximum likelihood trees under No Common Mechanism (NCM). Despite deceptive claims made by some likelihoodists, most maximum likelihood methods cannot be justified in this way because they rely on unrealistic background assumptions. These facts have been disputed on the various grounds that ad hoc hypotheses of homoplasy are explanatory, that they are not explanatory, that character states are ontological individuals, that character data do not comprise evidence, that unrealistic theories can be used as background knowledge, that NCM is unrealistic, and that likelihoods cannot be used to evaluate explanatory power. None of these objections is even remotely well founded, and indeed most of them do not even seem to have been meant seriously, having instead been put forward merely to obstruct the development of phylogenetic methods.

© The Willi Hennig Society 2008.
Large genetic divergence of new, morphologically similar species of sterile lichens from Europe (Lepraria, Stereocaulaceae, Ascomycota): concordance of DNA sequence data with secondary metabolites
Authors: Fehrer Judith , Slavíková‐Bayerová Štěpánka , Orange Alan
Published: July 2008

Lichenized fungi of the genus Lepraria are known for their paucity of morphological characters. Species identification is therefore largely based on secondary chemistry. We investigated different chemotypes of the morphologically highly similar L. jackii species complex by internal transcribed spacer (ITS) sequencing. In phylogenetic analyses including all available Lepraria species, samples belonging to different chemotypes of the L. jackii agg. corresponded to four highly divergent clusters. While true L. jackii was genetically uniform, the other three clades represented previously unrecognized species. They originated from different major speciation events, and two of them were not closely related to any other species. Assessment of intraspecific genetic variability revealed four different patterns with respect to geographic scale. ITS sequences proved to be the most reliable and distinctive characters for species recognition in the Lepraria jackii complex and were in accordance with chemical and ecogeographic data. Frequent occurrence of long branches, relatively few resolved relationships despite high genetic variability, and the discovery and description of a considerable part of the Lepraria species within the last 10 years suggest that the genus is probably much larger than currently known. The diversification of this asexual group in the potential absence of recombination is discussed.

© The Willi Hennig Society 2008.