Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids

Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.

Mutational analysis identifies functional Rap1, Su(Hw), and CTCF insulator sites in Arabidopsis thaliana

Genetic analysis identifies multiple, potential protein binding sites important for insulator function in Arabidopsis thaliana: Rap1 site in UASrpg, Su(Hw) site in UASrpg, and CTCF site in BEAD1c. Three non-plant insulators UASrpg, BEAD1c, and gypsy isolated from Ashbya gossypii, Homo sapiens and Drosophila melanogaster gypsy retrotransposon, respectively, demonstrate insulator function in transgenic Arabidopsis thaliana. Here, the hypothesis that DNA sequences functional in A. thaliana are the same as those in the original host as previously assumed, was tested. Genetic analyses of the cloned fragments in an enhancer blocking assay system was performed through deletions and mutations to identify more precisely which sequences within the cloned fragments function as insulators. Significant loss of insulator activity was observed when the UASrpg Rap1 binding site R2 was mutated but not R1. Cloned fragments containing BEAD1c are effective insulators in our assay system and the previously investigated gypsy insulator is non-functional. Further analyses identified potential Su(Hw) and CTCF sites within UASrpg, of which only the Su(Hw) site was functional. Thus, the activity of non-plant insulators in A. thaliana is context dependent. These results support the hypothesis that insulator function is conserved across kingdoms.

Advocacy, Strategy and Tactics Used to Confront Corporate Power: The Nestlé Boycott and International Code of Marketing of Breast-milk Substitutes

Douglas A. Johnson began his career as a human rights activist while earning his undergraduate degree in philosophy (1975) at Macalester College in the United States. He lived at Gandhi's ashram in India to study nonviolent organizing (1969 to 1970). He served as the director of the Third World Institute in Minneapolis, MN, USA (1973-1979), which functioned as the international social justice program of the Archdiocese of Minneapolis and St. Paul. Johnson's work included creating and running a political collective; leading development study tours into villages in Guatemala and Honduras; and investigating how transnational companies (e.g., Nestlé) were penetrating the developing world. He was the co-founder of the Infant Formula Action Coalition (INFACT), elected national chairperson (1977-1985), and appointed as Executive Director (1978-1984). His role included representing INFACT before national and international organizations, the human milk substitute industry, the US Congress and Executive Branch, and the press. He initiated and coordinated the first international grass-roots consumer boycott (against Nestlé) in ten nations. He was also a co-founder of the International Nestlé Boycott Committee and the International Baby Food Action Network (IBFAN). He earned a Master's in Public and Private Management at Yale University (1988). Then he became the first Executive Director of the Center for Victims of Torture, in Minneapolis (1988-2012), the first treatment center for torture victims in the US. Since 2013, he has been teaching human rights theory and practice, and sharing lessons he has learned, as a Lecturer in Public Policy at the Harvard Kennedy School, Harvard University (US). (This interview was conducted via Zoom and transcribed verbatim. It has been edited for ease of readability. DJ refers to Doug Johnson and LD refers to Laura Duckett.).

Suboptimal sleep and incident cardiovascular disease among African Americans in the Jackson Heart Study (JHS)

BACKGROUND

Suboptimal sleep, including insufficient/long sleep duration and poor sleep quality, is a risk factor for cardiovascular disease (CVD) common but there is little information among African Americans, a group with a disproportionate CVD burden. The current study examined the association between suboptimal sleep and incident CVD among African Americans.

METHODS

This study included 4,522 African Americans without CVD at baseline (2000-2004) of the Jackson Heart Study (JHS). Self-reported sleep duration was defined as very short (<6 h/night), short (6 h/night), recommended (7-8 h/night), and long (≥9 h/night). Participants' self-reported sleep quality was defined as "high" and "low" quality. Suboptimal sleep was defined by low quality sleep and/or insufficient/long sleep duration. Incident CVD was a composite of incident coronary heart disease and stroke. Associations between suboptimal sleep and incident CVD were examined using Cox proportional hazards models over 15 follow-up years with adjustment for predictors of CVD risk and obstructive sleep apnea.

RESULTS

Sample mean age was 54 years (SD = 13), 64% female and 66% reported suboptimal sleep. Suboptimal sleep was not associated with incident CVD after covariate adjustment [HR(95% CI) = 1.18(0.97-1.46)]. Long [HR(95%CI) = 1.32(1.02-1.70)] and very short [HR(95% CI) = 1.56(1.06-2.30)] sleep duration were associated with incident CVD relative to recommended sleep duration. Low quality sleep was not associated with incident CVD (p = 0.413).

CONCLUSIONS

Long and very short self-reported sleep duration but not self-reported sleep quality were associated with increased hazard of incident CVD.

0784 Associations Of Sleep Regularity And Chronotype With Hypertension Among African Americans In The Jackson Heart Sleep Study

Introduction

Emerging evidence suggests that disparities in sleep regularity, a marker of circadian disruption, contributes to hypertension disparities; however, data among African Americans are limited. We examined associations of sleep regularity and chronotype with hypertension among African Americans in the Jackson Heart Sleep Study (JHSS).

Methods

Participants underwent 7-day actigraphy, completed questionnaires, and had seated blood pressure (BP) measured as part of the JHSS (2012 - 2016). Sleep regularity was defined as the standard deviation (SD) of actigraphy-measured sleep onset timing or sleep duration. Chronotype was assessed by the Morningness-Eveningness Questionnaire. Prevalent hypertension was defined as either a systolic BP ≥ 130 mmHg or diastolic BP ≥ 80mmHg, antihypertensive medication use, or self-report of diagnosed hypertension. Multivariable logistic regression models were fit to estimate the prevalence odds ratio (OR) and 95% confidence intervals for the associations of hypertension with sleep regularity measures (SD of sleep onset timing and sleep duration) and chronotype adjusted for covariates.

Results

Participants (n=830) on average were 63.4 years (SD:10.7), mostly female (66.3%) and hypertensive (85.8%). Compared to individuals with sleep onset SD &lt; 30 minutes, higher adjusted odds of hypertension was observed with increasing variability: OR:1.87 (CI:0.99-3.56); OR:2.16 (1.06-4.39), and OR:2.41 (1.12-5.20), for SD &gt; 30 & ≤ 60, &gt; 60 & ≤ 90 and &gt; 90 minutes, respectively. Among non-shift workers, definite morning and evening types compared to intermediates had higher adjusted odds of hypertension, OR:1.71 (1.04-2.83) and OR:2.56 (1.12-5.84), respectively. There were no observed associations for the SD of sleep duration with hypertension.

Conclusion

Increased sleep onset variability and extreme chronotypes were associated with prevalent hypertension, supporting interventions targeting sleep hygiene recommendations promoting regular sleep. Future research is needed to understand sleep patterns and risk of cardiovascular disease according to chronotype.

Support

NHLBI K01HL138211 and HL110068-03S1

1097 Sleep Disturbances, Sleep Burden, And Depressive Symptoms In US Hispanics/Latinos: Results From The HCHS/SOL Sueño Study

Introduction

While sleep disturbances and depression often co-occur, these associations are understudied among Hispanics/Latinos. We examined the associations of sleep disturbances and sleep burden with depressive symptoms among Hispanic/Latino adults in the United States.

Methods

We used cross-sectional data from the Hispanic Community Health Study/Study of Latinos Sueño Ancillary study (2010-2013). The study enrolled 2072 adults (ages 18-64; 51.5% females) who completed one-week wrist-actigraphy and sleep questionnaires. Sleep burden was operationalized as the total count of sleep disturbances across six domains (duration, efficiency, midpoint, variability, insomnia, sleepiness). Depressive symptoms were assessed using the Center for Epidemiological Studies Depression scale (CESD-10). We used weighted survey linear regressions to evaluate the association of sleep disturbances and sleep burden with elevated depressive symptoms (CESD≥10) in individual models adjusted for age, gender, site, heritage, nativity, education, income, and employment. Sensitivity analyses further adjusted for behavioral health risk factors and apnea-hypopnea index.

Results

An estimated 28.3% had elevated depressive symptoms, 8.0% had short sleep duration (&lt;6 hours of sleep), 10.9% had long sleep duration (&gt;9 hours), 45.2% exhibited a later sleep midpoint (≥4:00AM), 38.4% had high sleep timing variability (upper third tertile for between day sleep midpoint), 15.3% had insomnia (ISI≥10), 17.3% had excessive daytime sleepiness (ESS ≥10), 21.5% had poor sleep efficiency (&lt;85%), and 77.4% had a total sleep burden count of ≥0. Insomnia (ß=0.49,95%CI:.43,.56), later sleep timing (ß=0.10,95%CI:.04,.16), excessive daytime sleepiness (ß=0.19,95%CI:.11,.27), poor sleep efficiency (ß=0.09,95%CI:.02,.17), high variability (ß=0.07, 95%CI:.01,.12), and sleep burden (ß=0.11,95%CI:.09,.13), were each positively associated with elevated depressive symptoms in individual adjusted models and sensitivity analyses. Extreme sleep durations were not associated with elevated depressive symptoms.

Conclusion

Multiple inter-related sleep disturbances, particularly those pertaining to sleep quality and timing, are associated with depression and may be targets for future interventions aimed at improving mood among Hispanics/Latinos.

Support

HL127307, HL098927, HL125748

1007 Sociodemographic, Lifestyle and Dietary Correlates of Actigraphy-Measured Irregular Sleep Schedules in the Multi-Ethnic Study of Atherosclerosis

Introduction

Increasing evidence links daily variability in sleep schedules to increased cardiometabolic risk. Little is known, however, regarding sociodemographic and behavioral correlates of irregular sleep schedules that may help identify causes or consequences of irregular sleep.

Methods

Among 1,946 participants from the Multi-Ethnic Study of Atherosclerosis, we examined the cross-sectional associations of irregular sleep schedules with sociodemographic, lifestyle, dietary factors, and actigraphy-based indices of rest-wake rhythms using multiple linear regression with adjustment for age, sex, race/ethnicity, education, income, marital status and work schedules. Sleep regularity was assessed using standard deviations (SD) in actigraphy-measured sleep duration and sleep onset timing across 7 days.

Results

Compared to Whites, the 7-day sleep duration SD (95% CI) was 17.4min (12.6, 22.2) higher in African-Americans, 10.4min (4.8, 16.0) higher in Hispanics and 7.9min (1.3, 14.4) higher in Chinese. Shift versus regular work was associated with 11.4min (5.1, 17.7) higher sleep duration SD. Irregular sleep duration was associated with lower income (p=0.006), higher depressive symptoms (p&lt;0.0001), higher BMI (p=0.004) and current smoking (p=0.06). Higher sleep duration variability was associated with lower Alternative Healthy Eating Index (p=0.01), mainly due to suboptimal intakes of fruits, whole grains and nuts/legumes. No associations were observed for age, sex, education, marital status or number of meals per day. While sleep duration variability was not associated with self-reported physical activity level or actigraphy-measured 7-day mean activity count, sleep duration SD was inversely associated with relative amplitude (difference between the most versus the least active period; p&lt;0.0001) and inter-daily stability (synchronization between rest-activity patterns and environmental zeitgebers; p&lt;0.0001) of 24-h rest-activity patterns. Similar results were observed for sleep onset timing SD.

Conclusion

Substantial differences by sociodemographic factors exist regarding the consistency of day-to-day sleep schedules. Irregular sleep schedules are associated with overall circadian disruption across the day and some unhealthy lifestyle behaviors. Future studies are needed to understand temporal relationships of the observed associations.

Support

NIH grants K01HL143034, R35HL135818

Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea

BACKGROUND AND AIMS

Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here.

METHODS

Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry.

KEY RESULTS

Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis.

CONCLUSIONS

Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.

Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea

BACKGROUND AND AIMS

Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here.

METHODS

Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry.

KEY RESULTS

Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis.

CONCLUSIONS

Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.

Susceptibility of Weedy Hosts from Pacific Northwest Potato Production Systems to Crop-Aggressive Isolates of Verticillium dahliae

Verticillium wilt, caused by Verticillium dahliae, is a disease of dicotyledonous crops such as potato and has a wide host range and persistent, long-term survival structures called microsclerotia that can persist in soil for up to 14 years. Some V. dahliae isolates are particularly aggressive on a specific plant host while retaining the ability to infect a wide range of other hosts. Weeds can serve as hosts for V. dahliae but whether they serve as sources of inoculum for aggressive isolates of V. dahliae to crop hosts is unknown. The goal of this research was to quantify V. dahliae microsclerotia obtained from 16 weeds which were grown in the greenhouse. Potting medium was infested with one of eight V. dahliae isolates from potato, mint, sugar beet, sunflower, tomato, and watermelon. The isolates from mint and potato were aggressive on the host from which they were originally isolated. All 16 weeds were infected by at least one V. dahliae isolate, although the number of microsclerotia produced from some infections was relatively low (≤5 microsclerotia/g of dry plant). Black nightshade yielded greater numbers of microsclerotia of the V. dahliae potato isolate than any other isolate in three of four trials in the greenhouse (second trial false discovery rate, adjusted P ≤ 0.0158; third trial, P ≤ 0.0264; and fourth trial, P ≤ 0.0193). Litchi tomato yielded greater numbers of microsclerotia of the V. dahliae potato isolate than any other isolate in one of four trials (first trial, P ≤ 0.0149). A V. dahliae isolate from tomato yielded greater numbers of microsclerotia in large crabgrass and wild oat in a second trial (P ≤ 0.0158). Weeds, depending on the species, grown during and between potato crop rotations may increase the number of microsclerotia of the potato-aggressive isolates of V. dahliae.

Evaluation of Solanum sisymbriifolium as a Potential Inoculum Source of Verticillium dahliae and Colletotrichum coccodes

Solanum sisymbriifolium, the litchi tomato, is a perennial herbaceous plant from South America that is used as a trap crop to reduce soilborne populations of the pale cyst nematode Globodera pallida, an important potato pathogen. Possible interactions of soilborne potato pathogens Verticillium dahliae and Colletotrichum coccodes with litchi tomato are unknown, yet important for potato production if litchi tomato is to be planted as a trap crop. The goal of this research was to quantitatively assess if litchi tomato is a potential inoculum source for C. coccodes and V. dahliae by comparing colony forming units (CFU) observed in litchi tomato to susceptible and resistant potato cultivars. The potato cvs. Alturas (P = 0.0003), Ranger Russet (P = 0.0193), and Russet Norkotah (P = 0.0022) produced more CFUs of the potato pathotype of V. dahliae than litchi tomato the first of two years of greenhouse trials. Significantly more CFUs of the potato pathotype of V. dahliae were quantified from stems and roots of only cv. Russet Norkotah compared with litchi tomato (P = 0.0001) in the second year. The CFUs for C. coccodes varied between litchi tomato and the potato cvs., perhaps due to varying levels of resistance since litchi tomato is from a selected intermated seed source. Based on these data, the effect of litchi tomato in rotation with potato is likely to have limited effect on the proliferation of V. dahliae or C. coccodes populations in the soil when compared with a susceptible potato cultivar.

Protein engineering of Saccharomyces cerevisiae transporter Pdr5p identifies key residues that impact Fusarium mycotoxin export and resistance to inhibition

Cereal infection by the broad host range fungal pathogen Fusarium graminearum is a significant global agricultural and food safety issue due to the deposition of mycotoxins within infected grains. Methods to study the intracellular effects of mycotoxins often use the baker's yeast model system (Saccharomyces cerevisiae); however, this organism has an efficient drug export network known as the pleiotropic drug resistance (PDR) network, which consists of a family of multidrug exporters. This study describes the first study that has evaluated the potential involvement of all known or putative ATP-binding cassette (ABC) transporters from the PDR network in exporting the F. graminearum trichothecene mycotoxins deoxynivalenol (DON) and 15-acetyl-deoxynivalenol (15A-DON) from living yeast cells. We found that Pdr5p appears to be the only transporter from the PDR network capable of exporting these mycotoxins. We engineered mutants of Pdr5p at two sites previously identified as important in determining substrate specificity and inhibitor susceptibility. These results indicate that it is possible to alter inhibitor insensitivity while maintaining the ability of Pdr5p to export the mycotoxins DON and 15A-DON, which may enable the development of resistance strategies to generate more Fusarium-tolerant crop plants.

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia

Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

Verticillium dahliae Infects, Alters Plant Biomass, and Produces Inoculum on Rotation Crops

Verticillium wilt, caused by Verticillium dahliae, reduces yields of potato and mint. Crop rotation is a potential management tactic for Verticillium wilt; however, the wide host range of V. dahliae may limit the effectiveness of this tactic. The hypothesis that rotation crops are infected by V. dahliae inoculum originating from potato and mint was tested by inoculation of mustards, grasses, and Austrian winter pea with eight isolates of V. dahliae. Inoculum density was estimated from plants and soil. Typical wilt symptoms were not observed in any rotation crop but plant biomass of some crops was reduced, not affected, or increased by infection of specific isolates. Each isolate was host-specific and infected a subset of the rotation crops tested but microsclerotia from at least one isolate were observed on each rotation crop. Some isolates were host-adapted and differentially altered plant biomass or produced differential amounts of inoculum on rotation crops like arugula and Austrian winter pea, which supported more inoculum of specific isolates than potato. Evidence of asymptomatic and symptomatic infection and differential inoculum formation of V. dahliae on rotation crops presented here will be useful in designing rotations for management of Verticillium wilt.

Feedback facilitates transfer of training with US Hispanic workers in a healthcare laundry linen facility

BACKGROUND

This study aimed to increase safety knowledge and behaviour of US Hispanic custodial workers in healthcare through a culturally appropriate training and monitoring process.

METHOD

A single-group, repeated-measures, pre-test and post-test design was used to examine training effectiveness across four sets of behaviours with 23 Spanish-speaking workers.

RESULTS

Small group, lecture-style training in Spanish with pictures and video resulted in significant improvements in knowledge and behaviour. However, additional analyses show that behavioural feedback was the critical component in improving safety behaviour during transfer of training.

DISCUSSION

Findings from reaction, knowledge, behaviour and results measures suggest that group training and graphic feedback is culturally appropriate and effective with Hispanic workers. Further investigation is needed to understand cultural factors that facilitate effective development and delivery of safety training and feedback to US Hispanic workers.

Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen

Phytophthora infestans has been a named pathogen for well over 150 years and yet it continues to "emerge", with thousands of articles published each year on it and the late blight disease that it causes. This review explores five attributes of this oomycete pathogen that maintain this constant attention. First, the historical tragedy associated with this disease (Irish potato famine) causes many people to be fascinated with the pathogen. Current technology now enables investigators to answer some questions of historical significance. Second, the devastation caused by the pathogen continues to appear in surprising new locations or with surprising new intensity. Third, populations of P. infestans worldwide are in flux, with changes that have major implications to disease management. Fourth, the genomics revolution has enabled investigators to make tremendous progress in terms of understanding the molecular biology (especially the pathogenicity) of P. infestans. Fifth, there remain many compelling unanswered questions.

Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for 12 microsatellite markers, resulting in multiple polymorphic markers on three chromosomes. Each isolate was homokaryotic for the 12 loci. Pairwise LD was estimated using three methods: Fisher's exact test, index of association (IA) and Hedrick's D'. For most of the populations, pairwise LD decayed with increasing physical distance between loci in two of the three chromosomes. Therefore, the observed recombination of alleles cannot be simply attributed to mutation alone. Different recombination rates in various DNA regions (recombination hot/cold spots) and different evolutionary histories of the populations could explain the observed differences in rates of LD decay among the chromosomes and among populations. The majority of the isolates exhibited mycelial incompatibility, minimizing the possibility of heterokaryon formation and mitotic recombination. Thus, the observed high intrachromosomal recombination is due to meiotic recombination, suggesting frequent outcrossing in these populations, supporting the view that homothallism favors universal compatibility of gametes instead of traditionally believed haploid selfing in S. sclerotiorum. Frequent outcrossing facilitates emergence and spread of new traits such as fungicide resistance, increasing difficulties in managing Sclerotinia diseases.

What does the nr5S DNA multigene family tell us about the genomic relationship between Dasypyrum breviaristatum and D. villosum (Triticeae: Poaceae)?

The genus Dasypyrum contains two species: the annual and widespread D. villosum (2x = 2n = 14) and the perennial and generally rare D. breviaristatum (2x = 2n = 14 and 4x = 2n = 28). The origin of the latter and its genome constitution have been subject of several studies. There is agreement that the genome of the diploid D. villosum (VV) is different from the diploid cytotype of D. breviaristatum (VbVb), but there is no agreement of the constitution of the tetraploid cytotype, specifically whether is it an autotetraploid or an allotetraploid. This is a long-standing disagreement that this study aims to resolve using the 5S nrDNA as a genomic marker. Our studies suggest that the 4x D. breviaristatum is an allotetraploid (VVVbVb).

What does the 5S rRNA multigene family tell us about the origin of the annual Triticeae (Poaceae)?

We have investigated the complex relationships among the annual genera within the tribe Triticeae through phylogenetic analyses of the 5S rRNA multigene family. Cloned sequences were assigned to groups of orthologous sequences, called unit classes, that were subjected to several analyses including BLAST (Basic Local Alignment Search Tool) searches to assess possible ancestral relationships with perennial genera; phylogenetic analyses using parsimony (Pars), maximum likelihood (ML), and Bayesian methods; and minimum reticulation networks from the Pars, ML, and Bayesian trees. In this study, we included genera with both annual and perennial species, such as Dasypyrum, Hordeum, and Secale. BLAST pointed to Pseudoroegneria (carrier of the St genome) and possibly Thinopyrum (carrier of the J genome) as the potential next of kin. However, Thinopyrum and Pseudoroegneria have never fallen together on the individual trees with the former generally associated with Crithopsis, Aegilops, Triticum, and Dasypyrum, while the latter is usually associated with the rest of the genera within Triticeae. The "long" unit classes placed Dasypyrum breviaristatum together with Dasypyrum villosum, whereas the "short" unit classes put them far apart on the trees. None of the gene trees alone was able to summarize the complex relationships among the genera, in line with previous results in the Triticeae. However, the application of tools designed to display phylogenetic networks was able to depict the complex links among the genera based on the short and the long gene trees, including the close link between Thinopyrum and Pseudoroegneria suggested by the phylogenetic analyses. In addition, our analyses provide support for the hypothesis that at least some annual Triticeae taxa are derived from their perennial relatives.

First Report of Blackleg Caused by Leptosphaeria maculans on Canola in Idaho

Canola (Brassica napus L.) is produced in the dryland agriculture areas of eastern Washington State and northern Idaho, often in rotation with cereal cropping systems. Canola is also used as a rotation crop in irrigated circles in the Columbia Basin of Washington and southern Idaho, where potato is the main cash crop. In 2011, 7,700 ha of canola were harvested in Idaho and 4,200 ha in Washington. One of the major diseases of canola around the world is blackleg, caused by Leptosphaeria maculans (aggressive) and L. biglobosa (non-aggressive). Both Washington and Idaho have been considered blackleg-free, and production of canola in Idaho is subject to government regulations. Canola seed originating from outside of Washington and Idaho should have a phytosanitary certificate. This disease is widespread in Canada and the U.S. Northern Plains, Midwest, and South, and is the major disease of canola in these areas. In August 2011, a sample from a canola field in Bonners Ferry, Idaho, was brought for diagnosis to Washington State University. The canola stems showed the typical gray to dark grey lesions with black pycnidia. The pycnidia and conidia were examined microscopically, and found to be similar to descriptions of Phoma lingam, the anamorph of L. maculans (2). Samples were sent to the University of Manitoba for confirmation with PCR. The pathogen was cultured out of stems on V8 juice agar amended with streptomycin and 22 single pynidiospore isolates were made from the cultures. DNA was extracted from the cultures using methods described in Fernando et al. (1) and a multiplex PCR was performed with species-specific primers for L. maculans and L. biglobosa. The reaction should produce a 330-bp amplicon for L. maculans and a 440-bp amplicon for L. biglobosa. Based on this, all 22 isolates were identified as L. maculans. The susceptible cultivar Westar was inoculated with the isolates, by wound inoculating 7-day-old cotyledons with a concentration of 10⁷ spores/ml. Plants were kept in a moist chamber at 23°C. After 14 days, plants were rated for disease with a 0 to 9 scale, where 0 = no infection and 9 = tissue collapse and appearance of pycnidiospores. Isolates with rating ≥5 are considered virulent. All isolates produced a rating of 7 to 9, indicating a high level of virulence. The source of the seed used in the infested fields is not known at this time. This disease is seedborne, and may pose a threat to the two major vegetable and oilseed brassica seed production areas of Washington: the Skagit River valley of western Washington and the Columbia Basin area of central Washington. In addition, the susceptibility of Pacific Northwest varieties of canola and other brassica oilseeds is largely unknown. References: (1) W. G. D. Fernando et al. Plant Dis. 90:1337, 2006. (2) S. Roger Rimmer et al. Compendium of Brassica Diseases, APS Press, 2007.

First Report of Pectobacterium wasabiae Causing Aerial Stem Rot of Potato in Washington State

Aerial stem rot of potato (Solanum tuberosum), also known as bacterial stem rot, is often caused by the pectolytic bacteria Pectobacterium (Erwinia) carotovorum subsp. carotovorum, P. atrosepticum, or Dickeya spp. (3). A survey was carried out in August 2008 in 'Russet Burbank' potato fields exhibiting aerial stem rot symptoms in the Columbia Basin of Washington State. One bacterial strain isolated during the survey, PwO405, exhibited pectolytic ability on crystal violet pectate (CVP) agar and potato slices and failed to grow at 37°C, but physiological tests did not conclusively distinguish the bacterium as P. atrosepticum (1). The bacterium was positive for ONPG, N-acetylglucosaminyl transferase, gelatin liquefaction, and acid production from D-galactose, lactose, melibiose, raffinose, citrate, and trehalose. The bacterium was negative for indole production and acid production from maltose, α-methyl-D-glucoside, sorbitol, D-arabitol, inositol, inulin, and melezitose. Molecular identification of the bacterium was performed with 16S rRNA, aconitase (acnA), and malate dehydrogenase (mdh) coding sequences as previously described (2,4). Partial sequences of 16S rRNA (1,408 bp) and acnA (412 bp) genes (GenBank Accession Nos. JQ723958 and JQ723959, respectively) exhibited 99% shared identities with P. wasabiae strain WPP163, while the mdh sequence (435 bp) (GenBank Accession No. JQ723960) exhibited 100% shared identity with mdh sequences from three P. wasabiae strains (NZEC9, NZEC10, and NZEC8974). Maximum parsimony analysis using concatenated acnA and mdh sequences from this study and Pectobacterium sequences previously deposited in GenBank (2,4) clustered strain PwO405 with other P. wasabiae strains. Three 7-week-old 'Russet Norkotah' potato plants were wound-inoculated by inserting a sterile 23 gauge needle just above a central leaf axil at a depth of 1 mm. A 10-μl drop of inoculum (10⁴ CFU) was placed on the wound. Plants were exposed to a 24-h leaf wetness period (90 to 100% RH in a mist chamber) and lesions were measured. All three inoculated plants exhibited aerial stem rot symptoms similar to those observed in the field, including brown water-soaked lesions that spread acropetally and basipetally. Upon drying, the lesions became shriveled and turned dark brown to black. Some plants exhibited hollowing of the stems and unilateral wilt on the side of the lesion. Symptoms were not observed on water-inoculated controls. The bacteria that were reisolated into pure culture from all three inoculated stems caused pitting on CVP and exhibited the same morphology as the original culture and were confirmed as P. wasabiae using 16S rRNA, acnA, and mdh coding sequences, fulfilling Koch's postulates. Stem rot ability of the bacterium was also confirmed on four potato cultivars: 'Ranger Russet,' 'Russet Burbank,' 'Russet Norkotah,' and 'Umatilla Russet' by wound-inoculating six single-stem plants of each cultivar as described above. To our knowledge, this is the first report of aerial stem rot of potato caused by P. wasabiae in Washington State. References: (1) S. De Boer and A. Kelman. Page 56 in: Laboratory Guide for Identification of Plant Pathogenic Bacteria, 3rd ed. N. Schaad et al., ed. APS Press, St. Paul, 2001. (2) A. Pitman et al. Eur. J. Plant Pathol. 32:211, 2010. (3) M. Powelson and G. Franc. Page 10 in: Compendium of Potato Diseases. W. Stevenson et al., ed. APS Press, St. Paul, 2002. (4) M. Yap et al. Appl. Environ. Microbiol. 70:3013, 2004.