Nomenclature standards and DNA barcoding of apple varieties originated by VIR Crimean Experimental Breeding Station

Current pace of breeding technologies relies on a tighter control of quality and identity of breeding achievements. Thereby, standardised variety nomenclature becomes of particular relevance to store original genetic information and warrant authenticity of the breeding product. A nomenclature standard regulates the variety’s name and habitus. A herbarium specimen is most appropriate for standardisation, since it defines a set of strongly inherited morphological characters for a variety. Nomenclature standards must be permanently stored in a scientific herbarium collection. The N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in alliance with national plant breeders initiated a first nomenclature standard collection of national-breeding cultivars. Aside to classical herbarising, the collection utilises molecular genetic techniques, particularly genotyping, to enable extended variety verification. The VIR team has developed the nomenclature standards of six apple varieties originated by the Crimean Experimental Breeding Station, a VIR Branch (Beloe Solntse, Zolotoy Potok, Kubanochka, Leto Krasnoe, Luchistoe and Shchedrost). The standards are supplemented with DNA barcodes obtained jointly with the N. I. Vavilov Institute of General Genetics. Fifteen microsatellite markers were used for barcoding. The herbarium nomenclature specimens adhered to the VIR-developed protocol in accordance with the International Code of Nomenclature for Cultivated Plants (ICNCP). The specimens are registered in the VIR Herbarium database and deposited in the World Crop Wild and Weed Relatives (WIR) Herbarium type collection.

Agrobiological estimation of the collection samples of Allium sativum subsp. vulgare (Kuzn.)

Purpose. To study biological features of biological potential realization of softneck garlic productivity. Methods. Field, laboratory, statistical and calculation-analytical. Results. The results of studying local and introduced forms of softneck garlic cultivars (samples No. 1, 14, 16, 19, 24, 27) in comparison with varieties (‘Prometei’ (standard) and ‘Liubasha’) in terms of productivity are presented. In the research, field, laboratory and statistical methods were used. The experimental design was a systemic complete block design without replicates. It was found that all, without exception, softneck garlic cultivars have an erectoid type of leaf placement. Introduced cultivars featured low seedstalk formation, which is a manifestation of adaptation to growing conditions. All studied cultivars were characterized by lower values of the number of air bulbils in the inflorescence compared to the standard cultivar ‘Prometei’. Thus, ‘Liubasha’ formed 16.1% fewer bulbils than the standard; however, its 1000-bulbil weight was 37.2% larger than in ‘Prometei’. The softneck cultivars that formed bulbils on the reduced seedstalk were characterized by a very small number of bulbils − by 89.7–90.8% less than in the standard – however, the formed bulbils had very large 1000-bulbil weight. Thus, sample No. 1 formed bulbils by 542.0% larger in terms of the 1000-bulbil weight than standard; sample No. 16 by 554.3%; sample No. 27 by 752.9%. Samples No. 14, 19 and 24 did not formed seedstalks. In terms of the bulbil yield, the samples that formed bulbils had by 11.7–40.1% lower indicators than the standard. Cultivar ‘Liubasha’ was characterized by a 19.0% higher bulbil yield. The vast majority of collection samples of winter garlic formed smaller bulbs. Sample No. 16 had a large bulb wight compared to the standard. Collection samples had significantly lower yield except for No. 16, which exceeded the standard by 30.2 and 56.8%. Conclusions. Collection samples have a significantly higher dry matter content. The promising samples (No. 14, 16, 19, 24) were selected by a number of characteristics as promising for further breding of softneck table garlic cultivars. In further research, the content of secondary metabolites and the storage of the samples in uncontrolled conditions will be studied in order to create table garlic cultivars suitable for long-term storage.

FeatSet: A Compilation of Visual Features Extracted from Public Image Datasets

In this paper, we present FeatSet, a compilation of visual features extracted from open image datasets reported in the literature. FeatSet has a collection of 11 visual features, consisting of color, texture, and shape representations of the images acquired from 13 datasets. We organized the available features in a standard collection, including the available metadata and labels, when available. We also provide a description of the domain of each dataset included in our collection, with visual analysis using Multidimensional Scaling (MDS) and Principal Components Analysis (PCA) methods. FeatSet is recommended for supervised and non-supervised learning, also widely supporting Content-Based Image Retrieval (CBIR) applications and complex data indexing using Metric Access Methods (MAMs).

EVALUATION OF TRAIT VARIABILITY IN VARIOUS COLLECTION SAMPLES OF ALFALFA

The research was carried out in the field at the Central Experimental Base of the Federal Williams Research Center of Forage Production and Agroecology. The object of research was 41 samples of alfalfa. The samples were sown according to the scheme of a standard collection nursery. All studies and observations were carried out on the herbage of the second and third years of life. Statistical processing of the research results showed a generally high level of variation in the characteristics. We identified the 4 best samples for a set of features. Several significant positive and negative correlations have been identified, which can be used as indirect signs in the evaluation and selection of promising forms. This method allowed us to identify 3 genetically different groups (clusters) of samples that differ in the nature of the formation of traits. The first cluster includes samples 49, 54, 66, ... and 193 belonging to various studied species. But mostly they represent the species Medicago sativa L. The samples differ little in the content of crude fiber and crude protein. The second cluster includes samples 454, 605, 583, ... and 598, which had average values for most indicators. The third group of samples includes 192, 646 and 355 (Medicago lupulina L. and Medicago glutinosa M.B.) with a maximum content of crude protein. The analysis of the distance and kinship between the samples revealed the presence of three clusters that can be used in breeding for combinational ability and consolidation of breeding-valuable traits.

MORPHO-PHYSIOLOGICAL FEATURES OF WILD-GROWING SAMPLES OF MEADOW TIMOTHY GRASS (Phleum pratense L.)

The research was carried out in the field at the Central experimental base of the Federal Williams Re¬search Center. The object of research was 12 samples of wild-growing meadow timothy grass. Samples were sown according to the scheme of a standard collection nursery. All studies and observations were carried out on the herbage of the 2nd and 3rd year of life. Statistical processing of results of researches of meadow timothy indicates a low level of variation in the main morphological and physiological characte¬ristics. Only by the number of vegetative shoots have the coefficient of variation reach 35.8%. Samples 416 and 419 were distinguished by precocity, samples 406 and 419 by the height of plants during flower¬ing, sample 412 by the number of generative shoots, and sample 412 by the yield of air-dry mass. Sam¬ples 409 and 414 were distinguished by the length of the sultan, and the weight of seeds — 414 and 415. Nine reliable correlations were found at the significance level 05 and 01. However, all of them are related to the yield of the number of generative and vegetative shoots. Using the binomial equation, the experi¬mentally obtained variability of dry mass yield from the number of generative and vegetative shoots by 93.1% is described. The optimal productivity of meadow timothy grass stand for generative shoots in the area of 550–600 shoots, and vegetative ones — in the area of 320–350 shoots per square meter. Analysis of remoteness and kinship between samples showed the presence of 2 clusters (genetically different quality groups), which can be used for combinational ability selection and fixing of selection-valuable features and properties.

Greek New Comic Fragments

The expression “Greek New Comedy” traditionally indicates a specific phase of Attic Comedy dated to the late 4th and 3rd centuries bce, although New Comedies continued to be written well into the Imperial period. New Comedies bring onto the stage fictional characters, domestic situations, and love-stories, and their plots tend to repeat common elements. Ancient sources identify over sixty New Comedy poets and consistently name three dramatists as the main representatives of this genre: Menander, Diphilus, and Philemon. Menander was born in 342/1 and died around 290 bce; the biographies of his two rivals are largely obscure but Philemon was reportedly older than Menander while Diphilus was one of Menander’s contemporaries. Unlike Menander, they were both born outside Athens. Two or three more authors were added to the list of the best New Comedy poets: Philippides, Apollodorus of Carystus, and Posidippus. New Comedy poets were generally more prolific than their 5th-century colleagues, but their plays are largely lost. Menander is the only author whose comedies survive thanks to a series of lucky papyrus findings in the 20th century: we have one complete comedy, Dyskolos, and substantial portions of several more. The dramas written by other New Comedy poets survive only in short fragments preserved by a few papyri and, most often, by ancient authors largely interested in linguistic peculiarities or moralizing excerpts. The standard collection of the fragments (F) of Greek Comedy and the testimonia (T) for Greek comic poets is Kassel and Austin 1983–2001 (Poetae Comici Graeci, cited under Editions and Translations), which is generally abbreviated as “K-A.” While surviving fragments are typically not very informative, an important source for our knowledge of Greek New Comedies is Roman Comedy. Roman poets adapted select plays into Latin, often disclosing the titles, the authors, and other details of their Greek models. Roman comedies give us indirect access to their now lost Greek originals.

Should we redefine meiofaunal organisms? The impact of mesh size on collection of meiofauna with special regard to nematodes

Meiofaunal organisms are the predominant metazoans in benthic systems and important members of the benthic food web. They are defined by mesh size and specifically by their retention on a sieve with a 44-µm mesh size. In this study, we examined the accuracy of this standard collection method by counting the number of meiobenthic individuals, life stages and nematode species in a sample. A filter cascade consisting of five different mesh sizes (41 µm, 30 µm, 20 µm, 10 µm and 1 µm) was used to fractionate a natural freshwater meiobenthic collection, and the individuals in each fraction were then counted. In line with the current definition of meiofauna, all tardigrades, microcrustaceans, chironomids and oligochaetes were retained by the largest mesh size, whereas 9% of the rotifers were first retained on the 30-µm meshes. For nematodes, 23% were not retained on the 41-µm meshes and individuals were collected even from the 1-µm fraction. With declining mesh size, the yield of retained nematodes increased, the age structure shifted to juveniles, evenness declined, and the species composition changed. As all of these findings were significant, this study therefore shows that the current definition of meiofauna is not sufficient to encompass the entire spectrum of meiofauna present in a sample and may result in misleading assessments of the diversity and composition of these organisms. We therefore propose that, especially for nematodes, a definition based on a smaller mesh size (at least 20 µm) is more appropriate.

Rapid systematic review of the sensitivity of SARS-CoV-2 molecular testing on saliva compared to nasopharyngeal swabs

ABSTRACT Background: Nasopharyngeal sampling has been the standard collection method for COVID-19 testing. Due to its invasive nature and risk of contamination for health care workers who collect the sample, non-invasive and safe sampling methods like saliva, can be used alternatively. Methods: A rapid systematic search was performed in PubMed and medRxiv, with the last retrieval on June 6th, 2020. Studies were included if they compared saliva with nasopharyngeal sampling for the detection of SARS-CoV-2 RNA using the same RT-qPCR applied on both types of samples. The primary outcome of interest was the relative sensitivity of SARS-CoV-2 testing on saliva versus nasopharyngeal samples (used as the comparator test). A secondary outcome was the proportion of nasopharyngeal-positive patients that tested also positive on a saliva sample. Results: Eight studies were included comprising 1070 saliva-nasopharyngeal sample pairs allowing assessment of the first outcome. The relative sensitivity of SARS-CoV-2 testing on saliva versus nasopharyngeal samples was 0.97 (95% CI=0.92-1.02). The second outcome incorporated patient data (n=257) from four other studies (n=97 patients) pooled with four studies from the first outcome (n=160 patients). This resulted in a pooled proportion of nasopharyngeal positive cases that was also positive on saliva of 86% (95% CI=77-93%). Discussion: Saliva could potentially be considered as an alternative sampling method when compared to nasopharyngeal swabs. However, studies included in this review often were small and involved inclusion of subjects with insufficient information on clinical covariates. Most studies included patients who were symptomatic (78%, 911/1167). Therefore, additional and larger studies should be performed to verify the relative performance of saliva in the context of screening of asymptomatic populations and contact-tracing.

CHEMICAL COMPOSITION OF WILD SAMPLES OFTIMOTHY-GRASS (PHLEUM PRATENSE L.)

The research was carried out in the field at the Central experimental base of the Federal Williams Research Center. The object of research was 13 samples of timothy-grass. Samples were sown according to the scheme of a standard collection nursery. All studies and observations were carried out on the herbage of the 2nd and 3rd year of life. Statistical processing of the research results indicates a low level of variation. The sample № 414 stood out high content of raw protein and raw fat. Two significant correlations were found (between the content of phosphorus and potassium, as well as between crude fiber and crude ash). Analysis of remoteness and kinship between samples showed the presence of 5 clusters (genetically different quality groups), which can be used for breeding for combinational ability and fixing of breeding-valuable features and properties.