2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative

OBJECTIVES

This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available.

DATA DESCRIPTION

The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data.

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition

OBJECTIVES

The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data.

DATA DESCRIPTION

This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.

2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project

OBJECTIVES

This report provides information about the public release of the 2018-2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions.

DATA DESCRIPTION

Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. Collaborators in the G2F initiative collected data for each location and year; members of the group responsible for coordination and data processing combined all the collected information and removed obvious erroneous data. The collaborators received the data before the DOI release to verify and declare that the data generated in their own locations was accurate. ReadMe and description files are available for each dataset. Previous years of evaluation are already publicly available, with common hybrids present to connect across all locations and years evaluated since this project's inception.

The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment

High-dimensional and high-throughput genomic, field performance, and environmental data are becoming increasingly available to crop breeding programs, and their integration can facilitate genomic prediction within and across environments and provide insights into the genetic architecture of complex traits and the nature of genotype-by-environment interactions. To partition trait variation into additive and dominance (main effect) genetic and corresponding genetic-by-environment variances, and to identify specific environmental factors that influence genotype-by-environment interactions, we curated and analyzed genotypic and phenotypic data on 1918 maize (Zea mays L.) hybrids and environmental data from 65 testing environments. For grain yield, dominance variance was similar in magnitude to additive variance, and genetic-by-environment variances were more important than genetic main effect variances. Models involving both additive and dominance relationships best fit the data and modeling unique genetic covariances among all environments provided the best characterization of the genotype-by-environment interaction patterns. Similarity of relative hybrid performance among environments was modeled as a function of underlying weather variables, permitting identification of weather covariates driving correlations of genetic effects across environments. The resulting models can be used for genomic prediction of mean hybrid performance across populations of environments tested or for environment-specific predictions. These results can also guide efforts to incorporate high-throughput environmental data into genomic prediction models and predict values in new environments characterized with the same environmental characteristics.

Utility of Climatic Information via Combining Ability Models to Improve Genomic Prediction for Yield Within the Genomes to Fields Maize Project

Genomic prediction provides an efficient alternative to conventional phenotypic selection for developing improved cultivars with desirable characteristics. New and improved methods to genomic prediction are continually being developed that attempt to deal with the integration of data types beyond genomic information. Modern automated weather systems offer the opportunity to capture continuous data on a range of environmental parameters at specific field locations. In principle, this information could characterize training and target environments and enhance predictive ability by incorporating weather characteristics as part of the genotype-by-environment (G×E) interaction component in prediction models. We assessed the usefulness of including weather data variables in genomic prediction models using a naïve environmental kinship model across 30 environments comprising the Genomes to Fields (G2F) initiative in 2014 and 2015. Specifically four different prediction scenarios were evaluated (i) tested genotypes in observed environments; (ii) untested genotypes in observed environments; (iii) tested genotypes in unobserved environments; and (iv) untested genotypes in unobserved environments. A set of 1,481 unique hybrids were evaluated for grain yield. Evaluations were conducted using five different models including main effect of environments; general combining ability (GCA) effects of the maternal and paternal parents modeled using the genomic relationship matrix; specific combining ability (SCA) effects between maternal and paternal parents; interactions between genetic (GCA and SCA) effects and environmental effects; and finally interactions between the genetics effects and environmental covariates. Incorporation of the genotype-by-environment interaction term improved predictive ability across all scenarios. However, predictive ability was not improved through inclusion of naive environmental covariates in G×E models. More research should be conducted to link the observed weather conditions with important physiological aspects in plant development to improve predictive ability through the inclusion of weather data.

Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

OBJECTIVES

Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017.

DATA DESCRIPTION

Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.

Stability Analysis of Kernel Quality Traits in Exotic-Derived Doubled Haploid Maize Lines

Variation in kernel composition across maize ( L.) germplasm is affected by a combination of the plant's genotype, the environment in which it is grown, and the interaction between these two elements. Adapting exotic germplasm to the US Corn Belt is highly dependent on the plant's genotype, the environment where it is grown, and the interaction between these components. Phenotypic plasticity is ill-defined when specific exotic germplasm is moved over large latitudinal distances and for the adapted variants being created. Reduced plasticity (or stability) is desired for the adapted variants, as it allows for a more rapid implementation into breeding programs throughout the Corn Belt. Here, doubled haploid lines derived from exotic maize and adapted through backcrossing exotic germplasm to elite adapted lines were used in conjunction with genome-wide association studies to explore stability in four kernel composition traits. Genotypes demonstrated a response to environments that paralleled the mean response of all genotypes used across all traits, with protein content and kernel density exhibiting the highest levels of Type II stability. Genes such as , , and were identified as potential candidates within quantitative trait locus regions. The findings within this study aid in validating previously identified genomic regions and identified novel genomic regions affecting kernel quality traits.

An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels

The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach now makes it practical to use the LMM to search for markers associated with such binary traits on a genome-wide scale. Therefore, the purpose of this work was to assess the applicability of the LMM for GWAS in crop diversity panels. We dichotomized three publicly available quantitative traits in a maize diversity panel and two quantitative traits in a sorghum diversity panel, and them performed a GWAS using both the LMM and the unified mixed linear model (MLM) on these dichotomized traits. Our results suggest that the LMM is capable of identifying statistically significant marker-trait associations in the same genomic regions highlighted in previous studies, and this ability is consistent across both diversity panels. We also show how subpopulation structure in the maize diversity panel can underscore the LMM’s superior control for spurious associations compared to the unified MLM. These results suggest that the LMM is a viable model to use for the GWAS of binary traits in crop diversity panels and we therefore encourage its broader implementation in the agronomic research community.

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

OBJECTIVES

Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available.

DATA DESCRIPTION

Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are released as comma separated value spreadsheets accompanied by extensive README text descriptions. For genotypic and phenotypic data, both raw data and a version with outliers removed are reported. For weather data, two versions are reported: a full dataset calibrated against nearby National Weather Service sites and a second calibrated set with outliers and apparent artifacts removed.

Association Mapping of Flowering and Height Traits in Germplasm Enhancement of Maize Doubled Haploid (GEM-DH) Lines

Flowering and height related traits are extensively studied in maize for three main reasons: 1) easily obtained phenotypic measurements, 2) highly heritable, and 3) importance of these traits to adaptation and grain yield. However, variation in flowering and height traits is extensive and findings from previous studies are genotype specific. Herein, a diverse panel of exotic derived doubled haploid lines, in conjunction with genome-wide association analysis, is used to further explore adaptation related trait variation of exotic germplasm for potential use in adapting exotic germplasm to the U.S. Corn-Belt. Phenotypes for the association panel were obtained from six locations across the central-U.S. and genotyping was performed using the genotyping-by-sequencing method. Nineteen flowering time candidate genes were found for three flowering traits. Eighteen candidate genes were found for four height related traits, with the majority of the candidate genes relating to plant hormones auxin and gibberellin. A single gene was discovered for ear height that also had effects on -like flowering gene expression levels. Findings will be used to inform future research efforts of the USDA Germplasm Enhancement of Maize project and eventually aid in the rapid adaptation of exotic germplasm to temperate U.S. environments.

Response of Maize Hybrids With and Without Rootworm- and Drought-Tolerance to Rootworm Infestation Under Well-Watered and Drought Conditions

Anecdotal data in the past have suggested that the effect of the western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), on maize yield is greater under drought and the effect of drought is greater under rootworm infestations, but no field experiments have controlled both moisture and rootworm levels. Field studies were conducted in 2012, 2013, and 2014 with treatments in a factorial arrangement of western corn rootworm infestation levels, and maize hybrids (with and without tolerance to drought and rootworm feeding). The experiment was repeated under well-watered and drought conditions in adjacent plots. Leaf water potential and stomatal conductance data suggested significant plant stress was achieved in the drought plots toward the end of the season each year and maize hybrids only played a minor role. In particular, in 2012 and 2013 yield was dramatically lower for the drought experiment than for the well-watered experiment. However, the impacts of rootworm infestation level and maize hybrids on water potential, stomatal conductance, and yield were variable across years and between experiments. In fact, the only year that the main effect of rootworm infestation levels significantly impacted yield was in 2014, when an extremely high infestation level was added and this was only for the well-watered portion of the experiment. Overall, rootworm infestation level played a relatively minor role in maize productivity and it did not appear that soil moisture level influenced that to a large degree.

The effect of artificial selection on phenotypic plasticity in maize

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.

Breeding has increased crop productivity, but whether it has also changed phenotypic plasticity is unclear. Here, the authors find maize genomic regions selected for high productivity show reduced contribution to genotype by environment variation and provide evidence for regulatory control of phenotypic stability.

Overcompensation in response to herbivory in Arabidopsis thaliana: the role of glucose-6-phosphate dehydrogenase and the oxidative pentose-phosphate pathway

That some plants benefit from being eaten is counterintuitive, yet there is now considerable evidence demonstrating enhanced fitness following herbivory (i.e., plants can overcompensate). Although there is evidence that genetic variation for compensation exists, little is known about the genetic mechanisms leading to enhanced growth and reproduction following herbivory. We took advantage of the compensatory variation in recombinant inbred lines of Arabidopsis thaliana, combined with microarray and QTL analyses to assess the molecular basis of overcompensation. We found three QTL explaining 11.4, 10.1, and 26.7% of the variation in fitness compensation, respectively, and 109 differentially expressed genes between clipped and unclipped plants of the overcompensating ecotype Columbia. From the QTL/microarray screen we uncovered one gene that plays a significant role in overcompensation: glucose-6-phosphate-1-dehydrogenase (G6PDH1). Knockout studies of Transfer-DNA (T-DNA) insertion lines and complementation studies of G6PDH1 verify its role in compensation. G6PDH1 is a key enzyme in the oxidative pentose-phosphate pathway that plays a central role in plant metabolism. We propose that plants capable of overcompensating reprogram their transcriptional activity by up-regulating defensive genes and genes involved in energy metabolism and by increasing DNA content (via endoreduplication) with the increase in DNA content feeding back on pathways involved in defense and metabolism through increased gene expression.

Improvement of cognitive functions in chronic schizophrenic patients by recombinant human erythropoietin

Schizophrenia is increasingly recognized as a neurodevelopmental disease with an additional degenerative component, comprising cognitive decline and loss of cortical gray matter. We hypothesized that a neuroprotective/neurotrophic add-on strategy, recombinant human erythropoietin (rhEPO) in addition to stable antipsychotic medication, may be able to improve cognitive function even in chronic schizophrenic patients. Therefore, we designed a double-blind, placebo-controlled, randomized, multicenter, proof-of-principle (phase II) study. This study had a total duration of 2 years and an individual duration of 12 weeks with an additional safety visit at 16 weeks. Chronic schizophrenic men (N=39) with defined cognitive deficit (>or=1 s.d. below normal in the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS)), stable medication and disease state, were treated for 3 months with a weekly short (15 min) intravenous infusion of 40,000 IU rhEPO (N=20) or placebo (N=19). Main outcome measure was schizophrenia-relevant cognitive function at week 12. The neuropsychological test set (RBANS subtests delayed memory, language-semantic fluency, attention and Wisconsin Card Sorting Test (WCST-64) - perseverative errors) was applied over 2 days at baseline, 2 weeks, 4 weeks and 12 weeks of study participation. Both placebo and rhEPO patients improved in all evaluated categories. Patients receiving rhEPO showed a significant improvement over placebo patients in schizophrenia-related cognitive performance (RBANS subtests, WCST-64), but no effects on psychopathology or social functioning. Also, a significant decline in serum levels of S100B, a glial damage marker, occurred upon rhEPO. The fact that rhEPO is the first compound to exert a selective and lasting beneficial effect on cognition should encourage new treatment strategies for schizophrenia.

Grouping of accessions of Mexican races of maize revisited with SSR markers

Mexican races of maize (Zea mays L.) represent a valuable genetic resource for breeding and genetic surveys. We applied simple sequence repeat (SSR) markers to characterize 25 accessions of races of maize from Mexico. Our objectives were to (1) study the molecular genetic diversity within and among these accessions and (2) examine their relationships as assumed previously on the basis of morphological data. A total of 497 individuals were fingerprinted with 25 SSR markers. We observed a high total number of alleles (7.84 alleles per locus) and total gene diversity (0.61), confirming the broad genetic base of the maize races from Mexico. In addition, the accessions were grouped into distinct racial complexes on the basis of a model-based clustering approach. The principal coordinate analyses of the four Modern Incipient hybrids corroborated the proposed parental races of Chalqueño, Cónico Norteño, Celaya, and Bolita on the basis of the morphological data. Consequently, for some of the accessions, hybridizations provide a clue that can further be used to explain the associations among the Mexican races of maize.

Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years

It has been claimed that the system that delivers the products of plant breeding reduces the diversity of cultivated varieties leading to an increased genetic vulnerability. The main goal of our study was to monitor the temporal trends in genetic diversity over the past five decades among maize cultivars with the largest acreage in Central Europe. Our objectives were to (1) investigate how much of the genetic diversity present in important adapted open-pollinated varieties (OPVs) has been captured in the elite flint germ plasm pool, (2) examine changes in the genetic diversity among the most important commercial hybrids as well as in their dent and flint parents, (3) analyze temporal changes in allele frequencies between the dent and flint parental inbreds, and (4) investigate linkage disequilibrium (LD) trends between pairs of loci within the set of parental dent and flint lines. We examined 30 individuals of five prominent OPVs from Central Europe, 85 maize hybrids of economic importance, and their dent and flint parental components with 55 SSRs. LD was significant at probability level P=0.01 for 20.2% of the SSR marker pairs in the 82 dent lines and for 17.2% in the 66 flint lines. The dent and flint heterotic groups were clearly separated already at the beginning of hybrid breeding in Central Europe. Furthermore, the genetic variation within and among varieties decreased significantly during the five decades. The five OPVs contain numerous unique alleles that were absent in the elite flint pool. Consequently, OPVs could present useful sources for broadening the genetic base of elite maize breeding germ plasm.

Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks

Landraces of maize represent a valuable genetic resource for breeding and genetic studies. Using simple sequence repeat (SSR) markers, we analysed five flint maize populations from Central Europe that had played an important role in the pre-hybrid era in Germany. Our objectives were to (1) investigate the molecular genetic diversity within and among the populations based on the SSR analysis of individuals, (2) compare these results of the SSR analysis based on individuals with those based on bulks, (3) examine genotype frequencies for deviations from Hardy-Weinberg equilibrium (HWE) at individual loci, and (4) test for linkage disequilibrium (LD) between pairs of loci within populations. Thirty individuals and their bulked DNA per population were fingerprinted with 55 SSR markers. Across all populations, 46.7% of the SSR markers deviated significantly from HWE, with an excess of homozygosity in 97% of the cases. This excess of homozygosity can largely be explained by experimental errors during the amplification of SSRs apart from genuine genetic causes. Allele frequencies of the SSR analyses of individuals and bulks were significantly correlated (r=0.85, P< 0.01), suggesting that SSR analysis of bulks is very cost-effective for large-scale molecular characterisation of germ plasm collections. No evidence for genome-wide LD among pairs of loci was observed, indicating that the populations are well suited for high resolution association mapping studies.

Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations

Genetic similarities (GS) based on molecular markers have been proposed as a tool for identification of essentially derived varieties (EDVs). Nevertheless, scientifically reliable criteria for discrimination of EDVs and independently derived varieties with GS estimates are scanty, and implementation into practical breeding has not yet taken place. Our objectives were to (1) assess the influence of chromosome number and length, marker density, and distribution, as well as the degree of polymorphism between the parental inbreds on the distribution of GS between parental inbreds and their progenies [GS(P1,O)] derived from F2 and different backcross populations and (2) evaluate these factors with regard to the power for distinguishing F2- versus BC1- and BC1- versus BC2-derived lines with molecular markers. We developed an approach based on statistical test theory for the identification of EDVs with molecular markers. Standard deviations and overlaps of distributions of GS(P1,O) of F2-, BC1-, and BC2-derived lines were smaller with (1) increasing chromosome number and length, (2) increasing marker density, and (3) uniformly instead of randomly distributed markers, approaching a lower boundary determined by the genetic parameters. The degree of polymorphism between the parental inbreds influenced the power only if the remaining number of polymorphic markers was low. Furthermore, suggestions are made for (1) determining the number of markers required to ascertain a given power and (2) EDV identification procedures.

Wheat genetic diversity trends during domestication and breeding

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheat's genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.

QTL mapping for European corn borer resistance ( Ostrinia nubilalis Hb.), agronomic and forage quality traits of testcross progenies in early-maturing European maize ( Zea mays L.) germplasm

In hybrid breeding the performance of lines in hybrid combinations is more important than their performance per se. Little information is available on the correlation between individual line and testcross (TC) performances for the resistance to European corn borer (ECB, Ostrinia nubilalis Hb.) in maize ( Zea mays L.). Marker assisted selection (MAS) will be successful only if quantitative trait loci (QTL) found in F(2) derived lines for ECB resistance are still expressed in hybrid combinations. The objectives of our study were: (1) to identify and characterize QTL for ECB resistance as well as agronomic and forage quality traits in a population of testcrossed F(2:3) families; (2) to evaluate the consistency of QTL for per se and TC performances; and (3) to determine the association between per se and TC performances of F(2:3) lines for these traits. Two hundred and four F(2:3) lines were derived from the cross between maize lines D06 (resistant) and D408 (susceptible). These lines were crossed to D171 and the TC progenies were evaluated for ECB resistance and agronomic performance in two locations in 2000 and 2001. Using these TC progenies, six QTL for stalk damage rating (SDR) were found. These QTL explained 27.4% of the genotypic variance in a simultaneous fit. Three QTL for SDR were detected consistently for per se and TC performance. Phenotypic and genotypic correlations were low for per se and TC performance for SDR. Correlations between SDR and quality traits were not significant. Based on these results, we conclude that MAS will not be an efficient method for improving SDR. However, new molecular tools might provide the opportunity to use QTL data as a first step to identify genes involved in ECB resistance. Efficient MAS procedures might then be based on markers designed to trace and to combine specific genes and their alleles in elite maize breeding germplasm.

Use of SSRs for establishing heterotic groups in subtropical maize

Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objectives of our research were to: (1) investigate the relationship of simple sequence repeats (SSR) based genetic distances between populations and panmictic midparent heterosis (PMPH) in a broad range of CIMMYT maize germplasm, (2) evaluate the usefulness of SSR markers for defining heterotic groups and patterns in subtropical germplasm, and (3) examine applications of SSR markers for broadening heterotic groups by systematic introgression of other germplasm. Published data of two diallels and one factorial evaluated for grain yield were re-analyzed to calculate the PMPH in population hybrids. Additionally, 20 pools and populations widely used in CIMMYT's breeding program were assayed with 83 SSR markers covering the entire maize genome. Correlations of squared modified Roger's distance (MRD(2)) and PMPH were mostly positive and significant, but adaption problems caused deviations in some cases. For intermediate- and early-maturity subtropical germplasm, two heterotic groups could be suggested consisting of a flint and dent composite. We concluded that the relationships between the populations obtained by SSR analyses are in excellent agreement with pedigree information. SSR markers are a valuable complementation to field trials for identifying heterotic groups and can be used to introgress exotic germplasm systematically.

Plasma total homocysteine levels and prognosis in patients with previous premature myocardial infarction: a 10-year follow-up study

OBJECTIVES

To explore plasma total homocysteine (tHcy) as a predictor of long-term prognosis after premature myocardial infarction (MI).

DESIGN

Prospective cohort study.

SETTINGS

Akershus University Hospital.

SUBJECTS

A total of 247 patients (193 men and 54 women) in stable clinical phase after premature MI (males: first MI at age < or =55; females < or =60).

MAIN OUTCOME MEASURES

The primary end-point was total mortality and the secondary end-point was cardiac death. The third end-point was major cardiac events: a combination of cardiac death, MI and cardiac arrest.

RESULTS

After 10 years, 44 patients had died, 36 from cardiac causes. Major cardiac event occurred in 70 patients. The relative risk for death of all causes increased 1.43 (95% CI, 1.08-1.88) per tHcy quartile (P for trend = 0.01), and was only modestly reduced after adjustment for age, ejection fraction, total cholesterol, C-reactive protein, fibrinogen, smoking and hypertension to 1.37 (95% CI, 1.04-1.80) (P for trend = 0.03). Similar results were observed when cardiac death was used as the end-point, but we observed no association between tHcy and the end-point major cardiac event.

CONCLUSIONS

Total homocysteine was an independent predictor of total and cardiac mortality in stable patients following premature MI. tHcy had no effect on major cardiac event in contrast to most other risk factors in this study. Thus, the mechanism(s) underlying the effects of homocysteine on coronary heart disease may differ from other risk factors.

Plasma N-terminal pro-atrial natriuretic peptide predicts death after premature myocardial infarction, but not as well as radionuclide ejection fraction. A ten-year follow-up study

OBJECTIVE

To assess N-terminal pro-atrial peptide (N-ANP) as a predictor of total and cardiac death in patients with previous premature myocardial infarction (MI).

DESIGN

In this prospective cohort study, we measured plasma N-ANP by ELIZA assays and ejection fraction (EF) by radionuclide ventriculography in a cohort of 247 patients (193 men and 54 women) who had had MI at a relatively young age (males: first MI at age < or =55; females <60).

RESULTS

After 10 years 44 patients had died, 36 from cardiac causes. After using a stepwise procedure to adjust for other prognostic factors (i.e. plasma total homocysteine (tHcy), C-reactive protein and age), the relative risk (RR) was 2.00 (95% confidence interval (CI) 1.05-3.80) (p = 0.03) for death of all causes and 2.32 (95% CI 1.19-4.55) (p=0.01) for cardiac death when the top quartile was compared to the three lower quartiles of N-ANP. When radionuclide EF entered the Cox model, N-ANP became insignificant as a predictor of mortality.

CONCLUSION

N-ANP was a significant predictor of total death and cardiac death in young survivors of MI, but radionuclide EF was a more independent prognostic variable.

Plasma fibrinogen level and long-term prognosis in Norwegian middle-aged patients with previous myocardial infarction. A 10 year follow-up study

OBJECTIVES

To investigate the prognostic value of plasma fibrinogen level amongst middle-aged survivors of myocardial infarction (MI).

DESIGN

Prospective cohort study.

SETTINGS

Determination of fibrinogen and other prognostic variables in MI patients recruited in a presumably stable phase of coronary heart disease (CHD).

SUBJECTS

A total of 247 middle-aged CHD patients (54 women and 193 men) who had their first MI at age < or = 60 (women) or < or = 55 (men) were recruited at least 3 months after (mean 2.1 years) the most recent MI.

MAIN OUTCOME MEASURES

The primary endpoint was total mortality, and the secondary endpoint was cardiac deaths. The tertiary endpoint was major cardiac events (cardiac death, MI and cardiac arrest).

RESULTS

During a follow-up period of 10 years a total of 44 patients had died, 36 from cardiac causes. Major cardiac event occurred in 70 patients. After adjusting for age, ejection fraction (EF), total serum cholesterol (TC), smoking and hypertension, patients in the top quartile of fibrinogen (> or = 4.0 g L-1) had a relative risk (RR) of 1.8 (95% CI 1.0-3.6) (P = 0.07) for death of all causes. The top quartile of fibrinogen was a stronger predictor of cardiac death; RR = 2.2 (95% CI 1.1-4.4) (P = 0.03), whilst the effect on the endpoint major cardiac event was not significant; RR=1.1 (95% CI 0.6-1.9) (P = 0.69).

CONCLUSIONS

A plasma fibrinogen level in the top quartile predicted cardiac death in middle-aged patients who had suffered MI.

Lipid Composition and Fluidity of Plasma Membranes Isolated from Corn (Zea mays L.) Roots

Although the results of lipid analyses from several plant species have been available for many years a complete characterization of the corn root plasma membrane is still lacking. The present study provides a detailed analysis of individual lipids and a characterization of the membrane fluidity of corn (Zea mays L.) root plasma membranes isolated by phase-partitioning. Phospholipids (43.9 mol%), sterols (40.8 mol%), and sphingolipids in the form of glucocerebroside (6.8 mol%) constitute the major lipid classes. Stigmasterol (19.8 mol%), campesterol (13.0 mol%), phosphatidylcholine 15.8 mol%), and phosphatidylethanolamine (14.2 mol%) represent the most ubiquitous individual lipids. Hydroxy fatty acids make up 80.9 mol% and very long chain fatty acids are almost 78% of fatty acids in glucocerebroside. Hydroxy arachidic acid (20:0 h) and hydroxy lignoceric acid (24:0 h) are most prominent and glucocerebroside from corn root plasma membranes contains virtually no unsaturated fatty acids. Among the phospholipids only phosphatidylserine displayed a high proportion of very long chain fatty acids (e.g., behenic and lignoceric acid). Membrane fluidity was estimated by fluorescence anisotropy. Due to the high sterol content the plasma membrane of corn roots is relatively rigid.

The dermatopharmacologic profile of ciclopirox 8% nail lacquer

Ciclopirox 8% nail lacquer is a recently introduced topical formulation of the hydroxypyridone antimycotic ciclopirox. In vitro data indicate that ciclopirox has activity against the important pathogenic dermatophytes responsible for onychomycosis. The lacquer delivery system provides a high concentration gradient for the transfer of the antifungal agent through the nail plate. Daily application to the toenail surface of healthy subjects resulted in good penetration and distribution within all nail layers. Systemic absorption of ciclopirox in five patients with onychomycosis was minimal.

Dermatopharmacology of ciclopirox nail lacquer topical solution 8% in the treatment of onychomycosis

Ciclopirox is a synthetic hydroxypyridone antifungal agent. In contrast to the azoles, glucuronidation is the main metabolic pathway of ciclopirox; therefore interactions with drugs metabolized via the cytochrome P450 system are unlikely Ciclopirox is also distinct from the common systemic agents, which interfere with sterol biosynthesis. In fact, ciclopirox chelates trivalent cations (such as Fe3+), inhibits metal-dependent enzymes that are responsible for degradation of toxic metabolites in the fungal cells, and targets diverse metabolic (eg, respiratory) and energy producing processes in microbial cells. Ciclopirox is a broad spectrum antimicrobial with activity against all the usual dermatophytes as well as yeast and nondermatophyte molds. It has demonstrated activity against gram positive and negative bacteria, including resistant strains of Staphlococcus aureus. Ciclopirox exhibits fungal inhibitory activity (minimum inhibitory concentration < 4 microg/mL for dermatophytes) as well as fungicidal activity; to date resistance to the drug has not been identified. Ciclopirox has been formulated in a nail lacquer delivery system. After evaporation of volatile solvents in the lacquer, the concentration of ciclopirox in the remaining lacquer film reaches approximately 35%, providing a high concentration gradient for penetration into the nail. Radiolabel data demonstrate penetration into infected nails after only 1 application of the lacquer. Ciclopirox nail lacquer is a topical product that provides an active fungicidal agent in a delivery system capable of promoting nail penetration. With repeated applications, the antifungal agent is homogeneously distributed through all layers of the toenail achieving concentrations of ciclopirox in excess of inhibitory and fungicidal concentrations for most pathogens. Although ciclopirox readily penetrates nails, very low levels of ciclopirox are recoverable systemically, even after chronic use. Ciclopirox nail lacquer 8% is a topical product that provides an active fungicidal agent in a delivery system capable of penetrating nails.

Experimental evidences for a role of subinhibitory concentrations of rilopirox, nystatin and fluconazole on adherence of Candida spp. to vaginal epithelial cells

Candidiasis is frequently localized in the mucosal epithelium which covers the vaginal and oral cavity. The pathogenicity of Candida is correlated with its ability to adhere to epithelial cells and this is the resultant of both fungal and host cell properties and their physicochemical interactions. This study was performed to investigate the ability of subinhibitory concentrations (sub-MICs) of rilopirox, a new antimycotic drug, to interfere with the adhesion of Candida albicans, Candida tropicalis and Candida glabrata to human vaginal cells, in comparison with sub-MICs of nystatin and fluconazole. The three drugs are more active on C. albicans, followed by C. tropicalis and, last, C. glabrata, on which fluconazole was inactive (MIC > 24 micrograms/ml). Rilopirox, nystatin and fluconazole have different mechanisms of action, and different molecular weights, so a comparative analysis of data was performed by means of their sub-MICs. On this basis the order of activity was nystatin [symbol: see text] rilopirox > fluconazole. These findings can be of use for optimizing also the posologic design by regarding sub-MICs which are still active in reducing the adhesiveness of Candida to cells of the vaginal mucosa.

QTL for insect resistance and drought tolerance in tropical maize: prospects for marker assisted selection

Insects and drought cause severe losses in the production of maize in many developing countries. Conventional breeding efforts to enhance the level of resistance to a number of insect pests and tolerance to drought have been successful, although only through large efforts of many breeders and over a large period of time. Continued improvements will only be possible through substantial investment of resources. Recently, success in identifying quantitative trait loci (QTL) in several plant species using various molecular marker systems offers alternative methods for accelerating conventional breeding programs. As the first step towards using molecular markers in CIMMYT's maize breeding program, restriction fragment length polymorphisms (RFLPs) have been used to understand the genetic basis of resistance to two corn borer species, southwestern corn borer and sugarcane borer, and to one major component of drought tolerance, anthesis-silking interval. A number of QTL with effects large enough to be regarded as significant in breeding were detected for each of these traits and many of them presented stable effects over environments. While variability in the number and location of QTL has been found when compared across populations, several loci were found to be quite consistent. Simple calculations can be made which estimate that the total genetic potential in maize for these traits is high. It is argued that to ultimately access and manipulate this potential, the use of linked molecular markers as indirect selectable markers is both feasible and necessary.

Alterations in surface morphology of Candida albicans produced by rilopirox: a scanning electron microscopy study

The topological changes produced in Candida albicans cells by incubation in vitro with rilopirox have been investigated by scanning electron microscopy. Rilopirox is a new hydroxypyridone compound with fungicidal activity and the effects of 1x MIC (2.9 micrograms/ml) and 4 x MIC (11.6 micrograms/ml) after 1, 12, 24 hours of incubation were evaluated. The morphological alterations produced by rilopirox are round shapes, collapsed cells, surface folds, clusters, holes and thorn-like extrusion. The effects of rilopirox are already evident at 1 x MIC and after 1 h but their frequency and severity are correlated with the time of incubation and the MIC.

Inhibition of Candida albicans adhesiveness to human buccal and vaginal cells by sub-inhibitory concentrations of rilopirox

Candida albicans is an opportunistic dimorphic pathogenic yeast which is present on the human mucosal epithelial cell surface. Its adhesion is considered to be an important first step in colonization and in the subsequent symptomatic or asymptomatic infection of buccal or vaginal mucosa. Because the ability to adhere is an important element of the pathogenicity of Candida we investigated in this study the compared effects of sub-inhibitory concentrations (sub-MICs) of rilopirox (CAS 104153-37-9) with those of ciclopirox olamine (CAS 41621-49-2) in inhibiting Candida adhesion to human buccal (BEC) and vaginal cells (VEC). Rilopirox is a new hydroxypyridone antimycotic agent with strong activity, especially against Candida albicans. There was a significant reduction in the mean number of Candida adhering to both buccal and vaginal cells with up to 1/8 MIC rilopirox for buccal and 1/16 MIC for vaginal cells, while for ciclopirox olamine reduction was significant up to 1/16 MIC for buccal and 1/8 MIC for vaginal cells. There were no significant differences in the dose-effect curves for BEC and VEC with either rilopirox and ciclopirox olamine, but on a molar basis, rilopirox was more active than ciclopirox olamine. The present in-vitro results support the developmental concept of an oropharyngeal and vaginal preparation of rilopirox. It can be expected that even sub-inhibitory concentrations of rilopirox exert an important additional effect in the treatment of oral and vaginal candidosis by impairing the pathogenic adhesion process of the fungus.

XbaI polymorphism in DNA at the apolipoprotein B locus is associated with myocardial infarction (MI)

High levels of low density lipoprotein (LDL) and its apolipoprotein B (apoB) are risk factors for atherosclerosis and myocardial infarction (MI). There is rich genetic polymorphism in apoB, first detected as the Ag allotypes of LDL, but today mostly examined at the DNA level. Genes contribute to the population variation in LDL and apoB levels and alleles in polymorphisms at the apoB locus are candidate genes with respect to control of lipid levels and susceptibility to atherosclerosis and MI. The XbaI polymorphism at the apoB locus, which involves the third base of threonin codon 2488 (ACC-->ACT) without changing the amino acid sequence was examined in a case-control study comprising 238 survivors of myocardial infarction (MI) and 621 controls. In univariate analysis, frequencies of genotypes in this polymorphism were not statistically different between patients and controls of either sex. However, in multivariate logistic regression analysis, the odds ratio X-X- homozygotes (homozygotes for absence of restriction site) for having MI compared to the pooled group of heterozygotes and X+X+homozygotes (homozygotes for presence of restriction site) was 2.16 (p = 0.007), after adjustments for age, sex, and levels of apoB, high density lipoprotein (HDL) cholesterol (HDLC) and Lp(a) lipoprotein. It appeared that heterozygotes do not have increased risk, compared to the X+X+ homozygotes. Stratification according to low or high levels of apoB, HDLC and Lp(a) lipoprotein, showed that the X-X- genotype was more common in patients than controls, in all subgroups.(ABSTRACT TRUNCATED AT 250 WORDS)

The Effect of Practical Dietary Counseling on Food Variety and Regurgitation Frequency after Gastroplasty for Obesity

After obesity surgery, the primary measurement of success is the amount of weight lost. There has, however, been little assessment of how patients cope with the dietary constraints imposed by gastroplasty. Similarly, dietary patterns adopted to cope with these constraints have not been studied fully. These factors are of great importance in terms of nutritional adequacy, patient acceptability and long-term success. A study involving 32 patients was conducted to ascertain whether practical nutritional intervention and extensive follow-up would improve the overall outcome of the gastroplasty operation with respect to the type of foods tolerated and the incidence of regurgitation or vomiting experienced. To quantify success in terms of frequency of regurgitation and variety of food intake a vomiting/eating (V/E) score was devised. The results showed that the group of patients with more intensive practical education and counseling had a more varied intake of food and coped better with a wider variety of solid foods in the long term. Despite a more solid diet they did not regurgitate food as frequently as patients with less education, and over half the study group of patients reported no regurgitation at all. From this study, it is proposed that patients can be assessed and categorized postoperatively using a V/E scale. This scale numerically scores success with diet after gastroplasty, which, when recorded in conjunction with subsequent weight loss, can give a better quantification of success after obesity surgery.

Synthesis markers in illegally manufactured 3,4-methylenedioxyamphetamine and 3,4-methylenedioxymethamphetamine

In this paper the isolation and identification of 12 compounds as impurities in illicit 3,4-methylenedioxyamphetamine (MDA) and 3,4-methylenedioxymethamphetamine (MDMA) is reported. Isolation of these substances is performed by preparative TLC, while identification is performed by using mass spectrometry and 1H-NMR spectroscopy. A simple and rapid method for detection of these impurities in seized MDA and MDMA samples is described. The identification of the impurities can provide numerous points on which to base comparative analysis of different exhibits.

[Biofeedback without a technical team--simple and cost effective]

An important psychotherapeutic process is that of autogenous training, whose effectiveness can be improved by the use of biofeedback. Biofeedback procedures have hitherto called for considerable expenditure on apparatus and frequent therapy sessions. Despite this, it has not been possible to extend the relaxation effect to more general situations. This paper describes an inexpensive and practical method of utilising all the advantages afforded by the underlying therapeutic concept, on the basis of experience gained with cutaneous thermography. Further information, notably on the preparation of the laminae, can be had on request from the authors.

Different actions of 2 antidiarrheal agents, lidamidine and loperamide, on motility of the isolated cat colon muscle

Besides their action on intestinal absorption and secretion antidiarrheal agents may affect gastrointestinal motility. Little is known about motor actions in the large intestine. Therefore, the effects of loperamide and lidamidine on contractile and myoelectrical activity were studied in strips of the circular muscle of the cat colon in vitro. Both drugs caused a concentration dependent increase in spontaneous contractions, but the potency of loperamide was greater than that of lidamidine and the efficacy of lidamidine greater than that of loperamide. The corresponding EC50 were 2.9 X 10(-9) M and 1.4 X 10(-5) M, respectively, and the EC100 2.7 X 10(-7) M and 10(-4) M, respectively. In the myoelectrical tracings loperamide stimulated predominantly spike activity, lidamidine oscillatory potentials. The effect of loperamide was antagonized by naloxone, thus indicating an action on opiate receptors. The effect of lidamidine was not inhibited by a variety of drugs. Tetrodotoxin and alpha-adrenergic inhibitors even exaggerated the lidamidine effect, probably by a suppression of tonic nervous inhibition. The receptor for the lidamidine action has yet to be determined. In conclusion, the motor effects may play an important role in the antidiarrheal action of loperamide, but probably not in that of lidamidine, at least not within the range of clinically used doses.

A stretch of "late" SV40 viral DNA about 400 bp long which includes the origin of replication is specifically exposed in SV40 minichromosomes

Examination of DNA fragments produced from either formaldehyde-fixed or unfixed SV40 minichromosomes by multiple-cut restriction endonucleases has led to the following major results: Exhaustive digestion of unfixed minichromosomes with Hae III generated all ten major limit-digest DNA fragments as well as partial cleavage products. In striking contrast to this result, Hae III acted on formaldehyde-fixed minichromosomes to yield only one of the limit-digest fragments, F, which is located in the immediate vicinity of the origin of replication, spanning nucleotides 5169 and 250 on the DNA sequence map of Reddy et al. (1978). This 300 base pair (bp) fragment was released as naked DNA from formaldehyde-fixed, Hae III-digested minichromosomes following treatment either by pronase-SDS or by SDS alone. In the latter case, the remainder of the minichromosome retained its compact configuration as assayed by both sedimentational and electrophoretic methods. In minichromosomes, the F fragment is therefore not only accessible to Hae III at its ends, but is also neither formaldehyde cross-linked into any SDS-resistant nucleoprotein structure nor topologically "locked" within the compact minichromosomal particle. This same fragment was preferentially produced during the early stages of digestion of unfixed minichromosomes with Hae III, and its final yield in the exhaustive Hae III digest was significantly higher than that of other limit-digest fragments. Similar results were obtained upon digestion of either unfixed or formaldehyde-fixed minichromosomes with Alu I. In particular, of approximately twenty major limit-digest DNA fragments, only two fragments (F and P, encompassing nucleotides 5146 to 190, and 190 to 325, respectively) were produced by Alu I from the formaldehyde-fixed minichromosomes. All other restriction endonucleases tested (Mbo I, Mbo II, Hind III, Hin II+III and Hinf I), for which there are no closely spaced recognition sequences in the above mentioned regions of the SV40 genome, did not produce any significant amount of limit-digest DNA fragments from formaldehyde-fixed minichromosomes. These findings, taken together with our earlier data on the preferential exposure of the origin of replication in SV40 minichromosomes (Varshavsky, Sundin and Bohn, 1978), strongly suggest that a specific region of the "late" SV40 DNA approximately 400 bp long is uniquely exposed in the compact minichromosome. It is of interest that, in addition to the origin of replication, this region contains binding sites for T antigen (Tjian, 1977), specific tandem repeated sequences and apparently also the promoters for synthesis of late SV40 mRNAs (Fiers et al., 1978; Reddy et al., 1978).