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Ivan Simko
Agricultural Research Service, Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Salinas, CA, USA.

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Journal article
Published: 01 July 2021 in Theoretical and Applied Genetics
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Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study, the effects of photoperiod and ambient temperature on bolting and flowering regulation were studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI 251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 h) and long (16 h) days and low (20 °C) and high (35 °C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2), and two candidate genes were identified by fine mapping, homology, and gene expression studies. In short days and high temperature conditions, qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8, and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences and were used to design a genetic marker which may be used to identify the late bolting trait.

ACS Style

Leah Rosental; David W. Still; Youngsook You; Ryan J. Hayes; Ivan Simko. Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce. Theoretical and Applied Genetics 2021, 1 .

AMA Style

Leah Rosental, David W. Still, Youngsook You, Ryan J. Hayes, Ivan Simko. Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce. Theoretical and Applied Genetics. 2021; ():1.

Chicago/Turabian Style

Leah Rosental; David W. Still; Youngsook You; Ryan J. Hayes; Ivan Simko. 2021. "Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce." Theoretical and Applied Genetics , no. : 1.

Journal article
Published: 19 June 2021 in Postharvest Biology and Technology
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Enzymatic browning negatively impacts product quality and shelf-life of packaged fresh-cut lettuce. Metabolite profiles of lettuce are affected by the browning process. The purpose of this study was to identify metabolomic marker compounds to predict lettuce browning, which could be applied to discern accessions suited for commercial production and industrial breeding programs. Romaine lettuce with different browning susceptibilities were evaluated in two independent trials and growing seasons. Metabolites were analyzed using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS). Principal component analysis (PCA) was performed to visualize clusters, trends, and discriminative ion features. Seven metabolites, including quinic acid, caffeoylquinic acid, 3-hydroxytetradecanedioic, cichorioside B, 8-deacetylmatricarin-8-sulfate, dicaffeoylquinic acid and 9S,12S,13S-trihydroxy-10Z-octadecenoic acid, increased with storage time (day 0 vs. day 3) Three metabolites, including lactucopicrin-15-oxalate, tri-4-hydroxyphenylacetyl glucoside and 15-deoxylactucin-8-sulfate, decreased with storage time (day 0 vs. day 3). Two additional phenolic metabolites, dicaffeoyltartaric and caffeoyltartaric acids, were identified as potential marker compounds, whose presence on day 0 samples immediately after cutting was negatively correlated with browning development (represented by ΔHue). The identified metabolites help to elucidate the biochemical metabolism and pathways during enzymatic browning and have the potential to serve as marker compounds for predicting browning resistant accessions.

ACS Style

Zhihao Liu; Jianghao Sun; Zi Teng; Yaguang Luo; Liangli Yu; Ivan Simko; Pei Chen. Identification of marker compounds for predicting browning of fresh-cut lettuce using untargeted UHPLC-HRMS metabolomics. Postharvest Biology and Technology 2021, 180, 111626 .

AMA Style

Zhihao Liu, Jianghao Sun, Zi Teng, Yaguang Luo, Liangli Yu, Ivan Simko, Pei Chen. Identification of marker compounds for predicting browning of fresh-cut lettuce using untargeted UHPLC-HRMS metabolomics. Postharvest Biology and Technology. 2021; 180 ():111626.

Chicago/Turabian Style

Zhihao Liu; Jianghao Sun; Zi Teng; Yaguang Luo; Liangli Yu; Ivan Simko; Pei Chen. 2021. "Identification of marker compounds for predicting browning of fresh-cut lettuce using untargeted UHPLC-HRMS metabolomics." Postharvest Biology and Technology 180, no. : 111626.

Research article
Published: 01 May 2021 in Phytopathology®
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Lettuce (Lactuca sativa) is one of the most economically important vegetables in the United States, with approximately 50% of the domestic production concentrated in the Salinas Valley of California. Verticillium wilt, caused by races 1 and 2 of the fungal pathogen Verticillium dahliae, poses a major threat to lettuce production in this area. Although resistance governed by a single dominant gene against race 1 has previously been identified and is currently being incorporated into commercial cultivars, identification of resistance against race 2 has been challenging and no lines with complete resistance have been identified. In this study, we screened germplasm for resistance and investigated the genetics of partial resistance against race 2 using three mapping populations derived from crosses involving L. sativa × L. sativa and L. serriola × L. sativa. The inheritance of resistance in Lactuca species against race 2 is complex but a common quantitative trait locus (QTL) on linkage group 6, designated qVERT6.1 (quantitative Verticillium dahliae resistance on LG 6, first QTL), was detected in multiple populations. Additional race 2 resistance QTLs located in several linkage groups were detected in individual populations and environments. Because resistance in lettuce against race 2 is polygenic with a large genotype by environment interaction, breeding programs to incorporate these resistance genes should be aware of this complexity as they implement strategies to control race 2.

ACS Style

Germán V. Sandoya; Maria José Truco; Lien D. Bertier; Krishna V. Subbarao; Ivan Simko; Ryan J. Hayes; Richard W. Michelmore. Genetics of Partial Resistance Against Verticillium dahliae Race 2 in Wild and Cultivated Lettuce. Phytopathology® 2021, 111, 842 -849.

AMA Style

Germán V. Sandoya, Maria José Truco, Lien D. Bertier, Krishna V. Subbarao, Ivan Simko, Ryan J. Hayes, Richard W. Michelmore. Genetics of Partial Resistance Against Verticillium dahliae Race 2 in Wild and Cultivated Lettuce. Phytopathology®. 2021; 111 (5):842-849.

Chicago/Turabian Style

Germán V. Sandoya; Maria José Truco; Lien D. Bertier; Krishna V. Subbarao; Ivan Simko; Ryan J. Hayes; Richard W. Michelmore. 2021. "Genetics of Partial Resistance Against Verticillium dahliae Race 2 in Wild and Cultivated Lettuce." Phytopathology® 111, no. 5: 842-849.

Preprint content
Published: 26 April 2021
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Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study the effects of photoperiod and ambient temperature on bolting and flowering regulation was studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 hours) and long (16 hours) days and low (20°C) and high (35°C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2) and two candidate genes were identified by fine mapping, homology and gene expression studies. In short days and high temperature conditions qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8 and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences, and were used to design a genetic marker which may be used to identify the late bolting trait.

ACS Style

Leah Rosental; David W. Still; Youngsook You; Ryan J. Hayes; Ivan Simko. Mapping and Identification of Genetic Loci Affecting Earliness of Bolting and Flowering in Lettuce. 2021, 1 .

AMA Style

Leah Rosental, David W. Still, Youngsook You, Ryan J. Hayes, Ivan Simko. Mapping and Identification of Genetic Loci Affecting Earliness of Bolting and Flowering in Lettuce. . 2021; ():1.

Chicago/Turabian Style

Leah Rosental; David W. Still; Youngsook You; Ryan J. Hayes; Ivan Simko. 2021. "Mapping and Identification of Genetic Loci Affecting Earliness of Bolting and Flowering in Lettuce." , no. : 1.

Research article
Published: 01 March 2021 in Phytopathology®
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Lettuce downy mildew, caused by Bremia lactucae Regel, is the most economically important foliar disease of lettuce (Lactuca sativa L.). The deployment of resistant cultivars carrying dominant resistance genes (Dm genes) plays a crucial role in integrated downy mildew disease management; however, high variability in pathogen populations leads to the defeat of plant resistance conferred by Dm genes. Some lettuce cultivars exhibit field resistance that is only manifested in adult plants. Two populations of recombinant inbred lines (RILs), originating from crosses between the field resistant cultivars Grand Rapids and Iceberg and susceptible cultivars Salinas and PI491224, were evaluated for downy mildew resistance under field conditions. In all, 160 RILs from the Iceberg × PI491224 and 88 RILs from the Grand Rapids × Salinas populations were genotyped using genotyping by sequencing, which generated 906 and 746 high-quality markers, respectively, that were used for quantitative trait locus (QTL) analysis. We found a QTL in chromosome 4 that is present in both Grand Rapids × Salinas and Iceberg × PI491224 populations that has a major effect on field resistance. We also found two additional significant QTLs in chromosomes 2 and 5 in the Iceberg × PI491224 RIL population. Marker-assisted gene pyramiding of multiple Dm genes in combination with QTLs for field resistance provide the opportunity to develop cultivars with more durable resistance to B. lactucae.

ACS Style

Lorena B Parra; Ivan Simko; Richard W. Michelmore. Identification of Major Quantitative Trait Loci Controlling Field Resistance to Downy Mildew in Cultivated Lettuce (Lactuca sativa). Phytopathology® 2021, 111, 541 -547.

AMA Style

Lorena B Parra, Ivan Simko, Richard W. Michelmore. Identification of Major Quantitative Trait Loci Controlling Field Resistance to Downy Mildew in Cultivated Lettuce (Lactuca sativa). Phytopathology®. 2021; 111 (3):541-547.

Chicago/Turabian Style

Lorena B Parra; Ivan Simko; Richard W. Michelmore. 2021. "Identification of Major Quantitative Trait Loci Controlling Field Resistance to Downy Mildew in Cultivated Lettuce (Lactuca sativa)." Phytopathology® 111, no. 3: 541-547.

Research article
Published: 19 February 2021 in PhytoFrontiers™
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The soilborne fungus Sclerotinia minor was not known to produce sclerotia in the stems of infected and uncollapsed Lactuca standing intact until our observation in a greenhouse in 2017. We investigated lettuce–environment–S. minor interactions in two tolerant and four susceptible Lactuca genotypes to determine putative risk factors and targets for disease control. Symptomatological, pathophysiological, developmental, basal stem biophysical, and microclimate responses (27 variables) of the genotypes were determined under field and/or greenhouse conditions. Distinct patterns of infection responses were observed between modern cultivars and their primitive/wild relatives. The modern cultivars were susceptible to rapid basal stem and root degradations by S. minor. The oil-seed lettuce PI 251246 and the wild L. serriola 11-G99 were resilient to degradations and significantly deterred mycelium emergence and symptom development, but sclerotia formed to a significantly higher height in their stems. Photosynthetic efficiency declined rapidly within 1-day postinoculation (dpi) in susceptible plants but remained intact ~5–6 dpi in the tolerant 11-G99. Stomatal conductance spiked rapidly in 11-G99 plants within 1–3 dpi, coinciding with the emergence of fungal mycelia at the crown. A strong negative correlation detected between basal stem degradation severity/collapse and stem mechanical strength indicated that stem strength-mediated genetic factors determine the outcome of Sclerotinia infections of the host. Soft stem is a prominent lettuce drop susceptibility factor that could be targeted in resistance breeding. It also provides the prelude for the analysis of the biological basis of plant architecture-mediated resistance to Sclerotinia spp. in lettuce and other hosts.

ACS Style

Bullo Erena Mamo; Renée L. Eriksen; Neil D. Adhikari; Ryan J Hayes; Beiquan Mou; Ivan Simko. Epidemiological Characterization of Lettuce Drop and Biophysical Features of the Host Identify Soft Stem as a Susceptibility Factor to Sclerotinia minor. PhytoFrontiers™ 2021, 1 .

AMA Style

Bullo Erena Mamo, Renée L. Eriksen, Neil D. Adhikari, Ryan J Hayes, Beiquan Mou, Ivan Simko. Epidemiological Characterization of Lettuce Drop and Biophysical Features of the Host Identify Soft Stem as a Susceptibility Factor to Sclerotinia minor. PhytoFrontiers™. 2021; ():1.

Chicago/Turabian Style

Bullo Erena Mamo; Renée L. Eriksen; Neil D. Adhikari; Ryan J Hayes; Beiquan Mou; Ivan Simko. 2021. "Epidemiological Characterization of Lettuce Drop and Biophysical Features of the Host Identify Soft Stem as a Susceptibility Factor to Sclerotinia minor." PhytoFrontiers™ , no. : 1.

Research article
Published: 18 February 2021 in PhytoFrontiers™
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When disease ratings are obtained over time, area under the disease progress metrics, such as AUDPC (curve) and AUDPS (stairs), which allow integration of these measures into a single value, have found use for both survey or replicated experiment data. ‘IdeTo’, an Excel-based calculator, computes AUDPC, AUDPS, and their standardized and relative values for up to 200 individuals evaluated at 200 timepoints. Besides the areas, descriptive statistics is provided for the group of individuals (e.g. accessions, replicates), and both Pearson and Spearman correlation coefficients between the areas and other traits of interest. Graphs are provided to visualize the progression of disease scores over time, distribution of AUDPC and AUDPS values in the dataset, and also their linear correlation with the traits of interest.

ACS Style

Ivan Simko. IdeTo: Spreadsheets for Calculation and Analysis of Area Under the Disease Progress Over Time Data. PhytoFrontiers™ 2021, 1 .

AMA Style

Ivan Simko. IdeTo: Spreadsheets for Calculation and Analysis of Area Under the Disease Progress Over Time Data. PhytoFrontiers™. 2021; ():1.

Chicago/Turabian Style

Ivan Simko. 2021. "IdeTo: Spreadsheets for Calculation and Analysis of Area Under the Disease Progress Over Time Data." PhytoFrontiers™ , no. : 1.

Preprint content
Published: 05 January 2021
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The concept of competitive balance is considered to be an essential aspect in the field of sport economics. This work describes a novel approach for measuring and evaluating competitive balance through concentration of championships. The concentration of championships was assessed using a sliding window approach with the length of five consecutive competitions (years) and a single competition (year) increment over the whole evaluated period. Because the sliding window was relatively short, the newly developed index, termed ‘We Are the Champions’ (WAC5), is sensitive to rapid changes in competitive balance. The WAC5 index, average WAC5, expected WAC5, and ΔWAC5 were applied to data from 68 competitions of several individual and team sports collected for the 1960 – 2020 period. The significance of indices was tested by resampling (bootstrapping and permutation). The results of the study show a growth in competitive balance of several ice hockey competitions (national and international), but decreasing competitive balance in Formula 1 racing and in several European soccer competitions. In soccer competitions, there was a substantially lower competitive balance in a league than in a domestic cup competition within each country/federation. The difference between the overall competitive balance in the most popular, North American, professional leagues and the top European soccer leagues is growing. A significant grouping of champions was determined for all sports involving individual athletes, but also for several team competitions.

ACS Style

Ivan Simko. We are the Champions. The Index for Evaluating Concentration of Championships Using a Sliding Window Approach. 2021, 1 .

AMA Style

Ivan Simko. We are the Champions. The Index for Evaluating Concentration of Championships Using a Sliding Window Approach. . 2021; ():1.

Chicago/Turabian Style

Ivan Simko. 2021. "We are the Champions. The Index for Evaluating Concentration of Championships Using a Sliding Window Approach." , no. : 1.

Original research
Published: 15 October 2020 in Food and Bioprocess Technology
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Fresh-cut lettuce, stored in modified atmosphere packaging (MAP), is a frequent component of bagged salads. However, even in MAP, fresh-cut lettuce is highly perishable due to non-microbial deterioration manifested by tissue liquefaction. The present study investigated the effects of plant physiology, lettuce processing, storage conditions, and exogenous stimuli on the deterioration of fresh-cut lettuce stored in MAP. Tests were performed on genotypes with a known rate of deterioration after processing. Leaf maturity of slowly deteriorating cultivars was generally negatively correlated with the shelf life, i.e., younger leaves deteriorated more slowly than older leaves. Leaf maturity of rapidly deteriorating cultivars was positively correlated with the shelf life, i.e., younger leaves deteriorated more rapidly than older leaves. The deterioration rate increased with temperature. Larger salad pieces deteriorated slower than smaller pieces and pieces that had additional wounding. Packaged samples of smaller size (less tissue per MAP bag with a constant volume) usually had a slower deterioration rate than larger samples. Reduced humidity in MAP slowed the rate of deterioration, particularly for rapidly deteriorating cultivars. Ethanol and hexanal accelerated the deterioration process of all cultivars in a dose-dependent manner. Sanitization of lettuce with chlorine, or treatments with abscisic acid, methyl jasmonate, salicylic acid, melatonin, or calcium lactate, had no obvious effect on the deterioration rate at the tested concentrations. This work provides insights into factors that need to be optimized to slow the rate of physiological deterioration of fresh-cut salad and identifies the most suitable conditions to reveal genotypic differences among lettuces.

ACS Style

Hui Peng; Jinita Sthapit Kandel; Richard W. Michelmore; Ivan Simko. Identification of Factors Affecting the Deterioration Rate of Fresh-Cut Lettuce in Modified Atmosphere Packaging. Food and Bioprocess Technology 2020, 13, 1997 -2011.

AMA Style

Hui Peng, Jinita Sthapit Kandel, Richard W. Michelmore, Ivan Simko. Identification of Factors Affecting the Deterioration Rate of Fresh-Cut Lettuce in Modified Atmosphere Packaging. Food and Bioprocess Technology. 2020; 13 (11):1997-2011.

Chicago/Turabian Style

Hui Peng; Jinita Sthapit Kandel; Richard W. Michelmore; Ivan Simko. 2020. "Identification of Factors Affecting the Deterioration Rate of Fresh-Cut Lettuce in Modified Atmosphere Packaging." Food and Bioprocess Technology 13, no. 11: 1997-2011.

Original research article
Published: 15 October 2020 in Crop Science
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Robustness is the measure of the ability to perform well across multiple environments. The genetics of robustness in lettuce (Lactuca sativa L.) under changing nitrogen application was studied by two parameters obtained from linear regression analysis. Robustness in changing water application was assessed by two parameters, relative efficiency component (REC) and susceptibility component (SC). The efficiency, sensitivity, and the effect of reduced irrigation on these parameters was assessed for 50 lines of lettuce in 2011. Efficiency, sensitivity, and plant nitrogen uptake and utilization were important traits in robustness under changing nitrogen application. Eight cultivars were re‐evaluated in 2012, 2014, and 2016 under high and low nitrogen treatments in order to estimate the repeatability of efficiency and sensitivity. Repeatability was greater for efficiency than sensitivity. In addition, the genetics of efficiency, sensitivity, REC, SC, nutrient concentration, nutrient content, dry to fresh biomass percentage, bolting, and shoot biomass production were studied by quantitative trait locus (QTL) analysis of a recombinant inbred line population derived from the cultivars Grand Rapids and Iceberg. The population was phenotyped in three experiments and genotyped by sequencing. Major clusters of QTLs for these traits were identified in linkage groups (LGs) 3, 7, and 9. Minor effect QTLs for sensitivity were identified in LGs 3 and 4. Intermediate effect QTLs for SC were identified in LGs 4 and 7. These results provide evidence that the components of robustness under changing nitrogen (efficiency and sensitivity) and water (REC and SC) availability are genetically independent and can be improved through breeding. This article is protected by copyright. All rights reserved

ACS Style

M. Macias‐González; M. J. Truco; R. Smith; M. Cahn; I. Simko; R. Hayes; R. W. Michelmore. Genetics of robustness under nitrogen‐ and water‐deficient conditions in field‐grown lettuce. Crop Science 2020, 61, 1582 -1619.

AMA Style

M. Macias‐González, M. J. Truco, R. Smith, M. Cahn, I. Simko, R. Hayes, R. W. Michelmore. Genetics of robustness under nitrogen‐ and water‐deficient conditions in field‐grown lettuce. Crop Science. 2020; 61 (3):1582-1619.

Chicago/Turabian Style

M. Macias‐González; M. J. Truco; R. Smith; M. Cahn; I. Simko; R. Hayes; R. W. Michelmore. 2020. "Genetics of robustness under nitrogen‐ and water‐deficient conditions in field‐grown lettuce." Crop Science 61, no. 3: 1582-1619.

Journal article
Published: 15 July 2020 in Sensors
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The color of plant leaves is moderated by the content of pigments, which can show considerable dorsiventral distribution. Two typical examples are leafy vegetables and ornamentals, wherein red and green color surfaces can be seen on the same leaf. The proof of concept is provided for predictive modeling of a leaf conceptual mid-point quasi-color (CMQ) from the content of pigments. The CMQ idea is based on the hypothesis that the content of pigments in leaves is associated with the combined color from both surfaces. The CMQ, which is calculated from CIELab color coordinates at adaxial and abaxial antipodes, is thus not an actual color, but a notion that can be used in modeling. The CMQ coordinates, predicted from the content of chlorophylls and anthocyanins by means of an artificial neural network (ANN), matched well with the CMQ coordinates empirically found on photosynthetically active leaves of lettuce (Lactuca sativa L.), but also with other plant species with comparable leaf attributes. Modeled values of lightness (qL*) decreased with the increasing content of both pigments, while the redness or greenness (qa*) and yellowness or blueness (qb*) of the CMQ were affected more by a relative content of chlorophylls and anthocyanins in leaves. The highest vividness of quasi-colors (qC*) was modeled for leaves with a high content of either pigment alone. The model predicted a substantially duller quasi-color for leaves with chlorophylls and anthocyanins present together, particularly when both pigments were present at very high levels.

ACS Style

Ivan Simko. Predictive Modeling of a Leaf Conceptual Midpoint Quasi-Color (CMQ) Using an Artificial Neural Network. Sensors 2020, 20, 3938 .

AMA Style

Ivan Simko. Predictive Modeling of a Leaf Conceptual Midpoint Quasi-Color (CMQ) Using an Artificial Neural Network. Sensors. 2020; 20 (14):3938.

Chicago/Turabian Style

Ivan Simko. 2020. "Predictive Modeling of a Leaf Conceptual Midpoint Quasi-Color (CMQ) Using an Artificial Neural Network." Sensors 20, no. 14: 3938.

Journal article
Published: 03 March 2020 in Horticulturae
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Lettuce harvested at the baby leaf stage is a popular component of mixed salads in ready-to-use packages. Little is known, however, about response of baby leaf lettuce to nitrogen (N), phosphorus (P), and potassium (K) fertilization. Eight lettuce accessions were subjected to five fertilization treatments to investigate genetic differences in reaction to N, P, and K fertilization. The control treatment provided optimal levels of macronutrients for plant growth, while other treatments deprived plants of either N, P, or K. Potassium deprivation had no obvious effect on plant weight or composition, apart from substantially decreased potassium content. Nitrogen and phosphorus deprivations, however, extensively decreased fresh weight and affected plant composition. Phosphorus and nitrogen deprivation considerably increased anthocyanin content in red-colored accessions, but anthocyanin was decreased in dark green-colored accessions, indicating differences in regulation of anthocyanin biosynthesis. Correlations between fresh weight, chlorophyll, anthocyanin, nitrogen, phosphorus, and potassium content were substantially affected by selection of datasets used for analyses; some relationships were revealed when analyzed separately by individual treatments, while others were more likely to be detected when analyzed by individual accessions. Absolute (ΔABS) and relative (2ΔREL) parameters described in this study were suitable for detecting over- and underperforming accessions. The ΔABS identified the absolute Lb-fold (logarithm to the base of 2, binary logarithm) change in performance of an accession in a treatment as compared to its performance in control conditions. The 2ΔREL parameter showed relative Lb-fold change for an accession as compared to the overall mean of ΔABS values of all accessions tested in control and treatment conditions.

ACS Style

Ivan Simko. Genetic Variation in Response to N, P, or K Deprivation in Baby Leaf Lettuce. Horticulturae 2020, 6, 15 .

AMA Style

Ivan Simko. Genetic Variation in Response to N, P, or K Deprivation in Baby Leaf Lettuce. Horticulturae. 2020; 6 (1):15.

Chicago/Turabian Style

Ivan Simko. 2020. "Genetic Variation in Response to N, P, or K Deprivation in Baby Leaf Lettuce." Horticulturae 6, no. 1: 15.

Original article
Published: 02 March 2020 in Theoretical and Applied Genetics
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Two major QTL, one for shelf life that corresponds to qSL4 and one, qDEV7, for developmental rate, were identified. Associated markers will be useful in breeding for improved fresh-cut lettuce. Fresh-cut lettuce in packaged salad can have short shelf life, and visible deterioration may start within a week after processing. Yield and developmental rate are an important aspect of lettuce production. Genetic diversity and genome-wide association studies (GWAS) were performed on 493 accessions with the genotypic data of 4615 high-quality single nucleotide polymorphism markers. Population structure (Q), principal component (PC), and phylogenetic analyses displayed genetic relationships associated with lettuce types and geographic distribution. Data for shelf life, yield, developmental rate, and their stability indices were used for statistical analysis, and GWAS was performed by general and mixed linear models. The genetic relationship among the individuals was incorporated into the models using kinship matrix, PC, and Q. Broad-sense heritability (H2) across environments was 0.43 for shelf life, 0.36 for yield, and 0.60 for developmental rate. There was a negative correlation between yield and developmental rate. Significant marker–trait association (SMTA) was detected for shelf life on chromosome 4. The most significant quantitative trait locus (QTL, qSL4, P = 2.23E−17) explained 24% of the total phenotypic variation (R2). The major QTL for developmental rate was detected on chromosome 7 (qDEV7, P = 2.43E−16, R2 = 17%), while additional QTLs with smaller effect were found in all chromosomes. No SMTA was detected for yield. The study identified lettuce accessions with extended and stable shelf life, stable yield, and desirable developmental rate. Molecular markers closely linked to traits can be applied for selection of preferable genotypes and for identification of genes associated with these traits.

ACS Style

Jinita Sthapit Kandel; Hui Peng; Ryan J. Hayes; Beiquan Mou; Ivan Simko. Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce. Theoretical and Applied Genetics 2020, 133, 1947 -1966.

AMA Style

Jinita Sthapit Kandel, Hui Peng, Ryan J. Hayes, Beiquan Mou, Ivan Simko. Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce. Theoretical and Applied Genetics. 2020; 133 (6):1947-1966.

Chicago/Turabian Style

Jinita Sthapit Kandel; Hui Peng; Ryan J. Hayes; Beiquan Mou; Ivan Simko. 2020. "Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce." Theoretical and Applied Genetics 133, no. 6: 1947-1966.

Article
Published: 16 November 2019 in Molecular Breeding
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Bacterial leaf spot (BLS) is a disease that affects lettuce (Lactuca sativa L.) worldwide. The disease is caused by the bacterium Xanthomonas campestris pathovar vitians (Xcv), which exclusively infects lettuce and is particularly devastating in warm humid climates. Reine des Glaces (RG), an old Batavia-type cultivar, exhibited an uninvestigated partial resistance to Xcv. Quantitative trait loci (QTLs) were analyzed using two recombinant inbred line (RIL) populations derived from RG × Eruption and RG × Delsay using three isolates collected in California and Canada, each representing a different race, and an isolate collected in France. A major QTL was identified in linkage group 2 in both populations; additional, minor QTLs were also detected in other linkage groups. The major QTL collocates with the Xanthomonas resistance 1 (Xar1) and Xanthomonas campestris vitians resistance (Xcvr) genes that had previously been identified using RIL populations derived from Salinas 88 × La Brillante and PI 358001-1 × Tall Guzmaine. RG provides another resistance resource for combating BLS using data provided by this study for marker-assisted selection.

ACS Style

Germán V. Sandoya; Brigitte Maisonneuve; Maria Jose Truco; Carolee Bull; Ivan Simko; Mark Trent; Ryan J. Hayes; Richard W. Michelmore. Genetic analysis of resistance to bacterial leaf spot in the heirloom lettuce cultivar Reine des Glaces. Molecular Breeding 2019, 39, 160 .

AMA Style

Germán V. Sandoya, Brigitte Maisonneuve, Maria Jose Truco, Carolee Bull, Ivan Simko, Mark Trent, Ryan J. Hayes, Richard W. Michelmore. Genetic analysis of resistance to bacterial leaf spot in the heirloom lettuce cultivar Reine des Glaces. Molecular Breeding. 2019; 39 (12):160.

Chicago/Turabian Style

Germán V. Sandoya; Brigitte Maisonneuve; Maria Jose Truco; Carolee Bull; Ivan Simko; Mark Trent; Ryan J. Hayes; Richard W. Michelmore. 2019. "Genetic analysis of resistance to bacterial leaf spot in the heirloom lettuce cultivar Reine des Glaces." Molecular Breeding 39, no. 12: 160.

Journal article
Published: 05 November 2019 in Sensors
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Salinity is a rising concern in many lettuce-growing regions. Lettuce (Lactuca sativa L.) is sensitive to salinity, which reduces plant biomass, and causes leaf burn and early senescence. We sought to identify physiological traits important in salt tolerance that allows lettuce adaptation to high salinity while maintaining its productivity. Based on previous salinity tolerance studies, one sensitive and one tolerant genotype each was selected from crisphead, butterhead, and romaine, as well as leaf types of cultivated lettuce and its wild relative, L. serriola L. Physiological parameters were measured four weeks after transplanting two-day old seedlings into 350 mL volume pots filled with sand, hydrated with Hoagland nutrient solution and grown in a growth chamber. Salinity treatment consisted of gradually increasing concentrations of NaCl and CaCl2 from 0 mM/0 mM at the time of transplanting, to 30 mM/15 mM at the beginning of week three, and maintaining it until harvest. Across the 10 genotypes, leaf area and fresh weight decreased 0–64% and 16–67%, respectively, under salinity compared to the control. Salinity stress increased the chlorophyll index by 4–26% in the cultivated genotypes, while decreasing it by 5–14% in the two wild accessions. Tolerant lines less affected by elevated salinity were characterized by high values of the chlorophyll fluorescence parameters Fv/Fm and instantaneous photosystem II quantum yield (QY), and lower leaf transpiration.

ACS Style

Neil D. Adhikari; Ivan Simko; Beiquan Mou. Phenomic and Physiological Analysis of Salinity Effects on Lettuce. Sensors 2019, 19, 4814 .

AMA Style

Neil D. Adhikari, Ivan Simko, Beiquan Mou. Phenomic and Physiological Analysis of Salinity Effects on Lettuce. Sensors. 2019; 19 (21):4814.

Chicago/Turabian Style

Neil D. Adhikari; Ivan Simko; Beiquan Mou. 2019. "Phenomic and Physiological Analysis of Salinity Effects on Lettuce." Sensors 19, no. 21: 4814.

Original research
Published: 30 August 2019 in Food Science & Nutrition
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Baby leaf lettuce harvested approximately 30 days after planting is the primary component of spring mix salads, a popular type of packaged salads. Very little is known, however, about the content of vitamins, sugars, and pigments in young lettuce plants. Therefore, plants of 42 accessions harvested at baby leaf stage were analyzed for the contents of vitamin C, ß‐carotene, anthocyanins, chlorophylls, glucose, fructose, and sucrose. Significant differences among accessions were found for content of all seven compounds plus sucrose sweetness equivalency (SSE) and average vitamin load (AVLAC). “Floricos” was highest in all sugars, SSE and vitamin C; “Taiwan” was highest in ß‐carotene and AVLAC, and “Annapolis” and “Darkland” were highest for anthocyanins and chlorophyll contents, respectively. The lowest content of glucose and sucrose was found in iceberg “Salinas,” fructose in L. serriola accession UC96US23, vitamin C in PI 257288, and β‐carotene in “Solar.” The lowest relative sweetness (SSE) was calculated for UC96US23, followed by “Salinas,” while the lowest AVLAC was estimated for PI 257288. There were very strong, positive correlations among contents of the three sugars, and between β‐carotene and vitamin C, and β‐carotene and anthocyanins. Composition profiles of accessions presented in this study, together with identified associations between compounds, can be used by breeders, growers, and producers to select lettuces with desirable combinations of sugars, pigments, and vitamins. This information can help in development of new cultivars and breeding lines with desirable combination of traits, pleasing taste, and higher vitamin content.

ACS Style

Ivan Simko. Genetic variation and relationship among content of vitamins, pigments, and sugars in baby leaf lettuce. Food Science & Nutrition 2019, 7, 3317 -3326.

AMA Style

Ivan Simko. Genetic variation and relationship among content of vitamins, pigments, and sugars in baby leaf lettuce. Food Science & Nutrition. 2019; 7 (10):3317-3326.

Chicago/Turabian Style

Ivan Simko. 2019. "Genetic variation and relationship among content of vitamins, pigments, and sugars in baby leaf lettuce." Food Science & Nutrition 7, no. 10: 3317-3326.

Correction
Published: 26 August 2019 in BMC Plant Biology
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Following publication of the original article [1], the author reported a processing error in Figure 5. This has been corrected in the original article.

ACS Style

Patrik Inderbitzin; Marilena Christopoulou; Dean Lavelle; Sebastian Reyes-Chin-Wo; Richard W. Michelmore; Krishna V. Subbarao; Ivan Simko. Correction to: The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. BMC Plant Biology 2019, 19, 1 -2.

AMA Style

Patrik Inderbitzin, Marilena Christopoulou, Dean Lavelle, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, Krishna V. Subbarao, Ivan Simko. Correction to: The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. BMC Plant Biology. 2019; 19 (1):1-2.

Chicago/Turabian Style

Patrik Inderbitzin; Marilena Christopoulou; Dean Lavelle; Sebastian Reyes-Chin-Wo; Richard W. Michelmore; Krishna V. Subbarao; Ivan Simko. 2019. "Correction to: The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce." BMC Plant Biology 19, no. 1: 1-2.

Journal article
Published: 10 July 2019 in BMC Plant Biology
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Verticillium wilt caused by the fungus Verticillium dahliae race 1 is among the top disease concerns for lettuce in the Salinas and Pajaro Valleys of coastal central California. Resistance of lettuce against V. dahliae race 1 was previously mapped to the single dominant Verticillium resistance 1 (Vr1) locus. Lines of tomato resistant to race 1 are known to contain the closely linked Ve1 and Ve2 genes that encode receptor-like proteins with extracellular leucine-rich repeats; the Ve1 and Ve2 proteins act antagonistically to provide resistance against V. dahliae race 1. The Vr1 locus in lettuce contains a cluster of several genes with sequence similarity to the tomato Ve genes. We used genome sequencing and/or PCR screening along with pathogenicity assays of 152 accessions of lettuce to investigate allelic diversity and its relationship to race 1 resistance in lettuce. This approach identified a total of four Ve genes: LsVe1, LsVe2, LsVe3, and LsVe4. The majority of accessions, however, contained a combination of only three of these LsVe genes clustered on chromosomal linkage group 9 (within ~ 25 kb in the resistant cultivar La Brillante and within ~ 127 kb in the susceptible cultivar Salinas). A single allele, LsVe1L, was present in all resistant accessions and absent in all susceptible accessions. This allele can be used as a molecular marker for V. dahliae race 1 resistance in lettuce. A PCR assay for rapid detection of race 1 resistance in lettuce was designed based on nucleotide polymorphisms. Application of this assay allows identification of resistant genotypes in early stages of plant development or at seed-level without time- and labor-intensive testing in the field.

ACS Style

Patrik Inderbitzin; Marilena Christopoulou; Dean Lavelle; Sebastian Reyes-Chin-Wo; Richard W. Michelmore; Krishna V. Subbarao; Ivan Simko. The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. BMC Plant Biology 2019, 19, 1 -14.

AMA Style

Patrik Inderbitzin, Marilena Christopoulou, Dean Lavelle, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, Krishna V. Subbarao, Ivan Simko. The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. BMC Plant Biology. 2019; 19 (1):1-14.

Chicago/Turabian Style

Patrik Inderbitzin; Marilena Christopoulou; Dean Lavelle; Sebastian Reyes-Chin-Wo; Richard W. Michelmore; Krishna V. Subbarao; Ivan Simko. 2019. "The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce." BMC Plant Biology 19, no. 1: 1-14.

Journal article
Published: 17 June 2019 in Postharvest Biology and Technology
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Discoloration (browning) represents a major challenge that limits the quality and shelf life of fresh-cut lettuce. In this study, we aimed to find romaine lettuce (Lactuca sativa var. longifolia) accessions with low browning potential. Midribs of 14 accessions (11 cultivars, two breeding lines, and a single plant introduction) were shredded and packaged in perforated bags for five days. Images of processed samples were captured daily and analyzed with computer vision technology to quantify browning intensity via L*a*b* color values and browning index (BI). Enzymatic activity[phenylalanine lyase (PAL), peroxidase (POD), and polyphenol oxidase (PPO)] and total phenolic content (TPC) were measured daily. After five days in storage, the accessions in the Tall Guzmaine and Parris Island Cos pedigree groups exhibited the greatest and least browning, respectively. In addition, while the PAL, POD, and TPC increased substantially over time, the PPO of twelve accessions fluctuated with only minor increases. For all accessions, the temporal increase of PAL, POD, and TPC showed significant, positive correlation to browning progression. Comparing between accessions, those that had greater amounts of accumulated PAL and smaller amounts of POD tended to have a greater amount of browning after five days of storage, despite relatively low correlation coefficients. However, the accumulation of TPC and PPO was not correlated to browning severity after five days of storage. This systematic study provides lettuce growers and breeders with guidance for selecting accessions with limited browning, and it supplies researchers in plant physiology and genetics with more information on the roles of enzymes in the lettuce browning process.

ACS Style

Zi Teng; Yaguang Luo; Ellen R. Bornhorst; Bin Zhou; Ivan Simko; Frances Trouth. Identification of romaine lettuce (Lactuca sativa var. longifolia) Cultivars with reduced browning discoloration for fresh-cut processing. Postharvest Biology and Technology 2019, 156, 110931 .

AMA Style

Zi Teng, Yaguang Luo, Ellen R. Bornhorst, Bin Zhou, Ivan Simko, Frances Trouth. Identification of romaine lettuce (Lactuca sativa var. longifolia) Cultivars with reduced browning discoloration for fresh-cut processing. Postharvest Biology and Technology. 2019; 156 ():110931.

Chicago/Turabian Style

Zi Teng; Yaguang Luo; Ellen R. Bornhorst; Bin Zhou; Ivan Simko; Frances Trouth. 2019. "Identification of romaine lettuce (Lactuca sativa var. longifolia) Cultivars with reduced browning discoloration for fresh-cut processing." Postharvest Biology and Technology 156, no. : 110931.

Original article
Published: 04 June 2019 in Theoretical and Applied Genetics
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Two QTLs for resistance to lettuce drop, qLDR1.1 and qLDR5.1, were identified. Associated SNPs will be useful in breeding for lettuce drop and provide the foundation for future molecular analysis. Lettuce drop, caused by Sclerotinia minor and S. sclerotiorum, is an economically important disease of lettuce. The association of resistance to lettuce drop with the commercially undesirable trait of fast bolting has hindered the integration of host resistance in control of this disease. Eruption is a slow-bolting cultivar that exhibits a high level of resistance to lettuce drop. Eruption also is completely resistant to Verticillium wilt caused by race 1 of Verticillium dahliae. A recombinant inbred line population from the cross Reine des Glaces × Eruption was genotyped by sequencing and evaluated for lettuce drop and bolting in separate fields infested with either S. minor or V. dahliae. Two quantitative trait loci (QTLs) for lettuce drop resistance were consistently detected in at least two experiments, and two other QTLs were identified in another experiment; the alleles for resistance at all four QTLs originated from Eruption. A QTL for lettuce drop resistance on linkage group (LG) 5, qLDR5.1, was consistently detected in all experiments and explained 11 to 25% of phenotypic variation. On LG1, qLDR1.1 was detected in two experiments explaining 9 to 12% of the phenotypic variation. Three out of four resistance QTLs are distinct from QTLs for bolting; qLDR5.1 is pleiotropic or closely linked with a QTL for early bolting; however, the rate of bolting shows only a small effect on the variance in resistance observed at this locus. The SNP markers linked with these QTLs will be useful in breeding for resistance through marker-assisted selection.

ACS Style

Bullo Erena Mamo; Ryan J. Hayes; Maria José Truco; Krishna D. Puri; Richard W. Michelmore; Krishna V. Subbarao; Ivan Simko. The genetics of resistance to lettuce drop (Sclerotinia spp.) in lettuce in a recombinant inbred line population from Reine des Glaces × Eruption. Theoretical and Applied Genetics 2019, 132, 2439 -2460.

AMA Style

Bullo Erena Mamo, Ryan J. Hayes, Maria José Truco, Krishna D. Puri, Richard W. Michelmore, Krishna V. Subbarao, Ivan Simko. The genetics of resistance to lettuce drop (Sclerotinia spp.) in lettuce in a recombinant inbred line population from Reine des Glaces × Eruption. Theoretical and Applied Genetics. 2019; 132 (8):2439-2460.

Chicago/Turabian Style

Bullo Erena Mamo; Ryan J. Hayes; Maria José Truco; Krishna D. Puri; Richard W. Michelmore; Krishna V. Subbarao; Ivan Simko. 2019. "The genetics of resistance to lettuce drop (Sclerotinia spp.) in lettuce in a recombinant inbred line population from Reine des Glaces × Eruption." Theoretical and Applied Genetics 132, no. 8: 2439-2460.