Haploid biotechnology as a tool for creating a selection material for sugar beets

Since the discovery of the phenomenon of haploidy, biotechnology has become an integral part in the successful creation of new varieties and hybrids of various plant species. In particular, these technologies are actively used in agriculture, which is concerned with increasing the volume and improving the quality of products. The integration of haploid production techniques together with other available biotechnological tools such as marker selection (MAS), induced mutagenesis and genetic engineering technologies can significantly accelerate crop breeding. This article shows the main stages in the development of biotechnology since 1921. Now they are successfully used to create doubled haploids to accelerate the selection process of various plants and, in particular, sugar beet, which is the most important sugar crop in regions with a temperate climate. There are several methods for obtaining forms with a single set of chromosomes. For sugar beets, the use of gynogenesis turned out to be expedient, since in this case the other methods turned out to be ineffective in the mass production of haploids. The article considers the stages of obtaining the H and DH lines of Beta vulgaris L., as well as the main stages of biotechnological production of homozygous breeding material of this culture. These stages include selecting parental forms – donor explants, sterilizing buds and introducing non-pollinated ovules in vitro, obtaining haploids, doubling their chromosome set, creating doubled haploids, determining ploidy at different stages, relocating the obtained plants to greenhouses and growing stecklings. A number of advantages that the technology of creating doubled haploids in vitro has in comparison with traditional methods of selection are described. It has been shown that the use of these approaches is relevant when obtaining new highly productive hybrids and varieties of agricultural plants; however, the methods for the production of homozygous forms in sugar beet still require additional research aimed at increasing the efficiency and reproducibility of each stage of the process.

Molecular characterization of xerosis cutis: A systematic review

Background Xerosis cutis or dry skin is a highly prevalent dermatological disorder especially in the elderly and in patients with underlying health conditions. In the past decades, numerous molecular markers have been investigated for their association with the occurrence or severity of skin dryness. The aim of this review was to summarize the molecular markers used in xerosis cutis research and to describe possible associations with different dry skin etiologies. Methods We conducted a systematic review of molecular markers of xerosis cutis caused by internal or systemic changes. References published between 1990 and September 2020 were searched using ‘MEDLINE’, ‘EMBASE’ and ‘Biological abstracts’ databases. Study results were summarized and analyzed descriptively. The review protocol was registered in PROSPERO database (CRD42020214173). Results A total of 21 study reports describing 72 molecules were identified including lipids, natural moisturizing factors (NMFs), proteins including cytokines and metabolites or metabolic products. Most frequently reported markers were ceramides, total free fatty acids, triglycerides and selected components of NMFs. Thirty-one markers were reported only once. Although, associations of these molecular markers with skin dryness were described, reports of unclear and/or no association were also frequent for nearly every marker. Conclusion An unexpectedly high number of various molecules to quantify xerosis cutis was found. There is substantial heterogeneity regarding molecular marker selection, tissue sampling and laboratory analyses. Empirical evidence is also heterogeneous regarding possible associations with dry skin. Total free fatty acids, total ceramide, ceramide (NP), ceramide (NS), triglyceride, total free amino acids and serine seem to be relevant, but the association with dry skin is inconsistent. Although the quantification of molecular markers plays an important role in characterizing biological processes, pathogenic processes or pharmacologic responses, it is currently unclear which molecules work best in xerosis cutis.

Creation of new tomato forms with fungal disease resistance genes based on marker selection

Relevance. The presented studies are aimed at obtaining new forms of tomato with a complex of genes for resistance to fungal diseases in combination with a standard type of bush and dark coloring of fruits based on marker-mediated selection.Methodology. The biological objects of the study are varieties and hybrid forms of tomato from the collection of the Michurinsky SAU. Molecular genetic analysis was performed using the following methods. DNA extraction was carried out from young leaves using a kit for isolation of NC Sample NC manufactured by Agrodiagnostika LLC according to the manufacturer's protocol. Fermentas production kits were used for PCR. Identification of the cladosporosis resistance gene was Cf-19 performed using the DNA marker R7. The presence of a fusarious wilting resistance gene was determined by a I-2/5 marker. The amplification results were visualized by agarose gel electrophoresis.Results. During the research, a collection of varieties and hybrid forms of tomato of the Michurinsky GAU was analyzed in order to identify genes for resistance to cladosporiosis Cf-19 and fusarium wilt I-2. A total of 52 genotypes were analyzed. It was found that most samples (41 samples) are characterized by a heterozygous state of the Cf-19 gene. All indeterminant and semi-determinant forms had both alleles. Of the 23 determinant forms presented in the collection, 10 had only one allele corresponding to recessive homozygote. Among all analyzed tomato genotypes, no dominant homozygous forms were noted. The study of the collection revealed several alleles of the I-2 gene. In total, four fragments corresponding to various alleles were amplified. A total of 50 resistant genotypes have been identified in the collection. Two alleys of the I-2 gene (633/693 bp) were identified in 42 tomato samples. Four varieties are homozygous in one allele (633 bp), which determines resistance. Three varieties have a second resistance allele (566 bp). One genotype has only an allele defining susceptibility (693 bp). On the basis of molecular analysis, as well as an assessment of the type of bush and fetal color, initial forms were selected with subsequent hybridization. 67 hybrid tomato plants were obtained. Evaluation of the presence of resistance genes showed that most of the resulting hybrids are resistant to cladosporiosis and fuzariosis. This is due to the presence of dominant alleles of Cf-19 and I-2 genes in a heterozygous state. Among the resulting hybrids, plants with a bark type of bush were identified. A total of 13 such plants were obtained.Conclusion. Thus, the work carried out allowed to obtain hybrid forms of tomato combine the signs of resistance to two pathogens of fungal diseases and the stem type of the bush. These forms are planned to be used in further selection work.

LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement

Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform in silico validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that legumeSSRdb would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.

Development of a 95 SNP Panel To Individually Genotype Mountain Lions (Puma Concolor) For Microfluidic and Other Genotyping Platforms

The mountain lion (Puma concolor) is one of the few remaining large predators in California, USA with density estimation from fecal genotypes becoming an essential component of conservation and management. In highly urbanized southern California, mountain lions are fragmented into small, inbred populations making proper marker selection critical for individual identification. We developed a panel of single nucleotide polymorphism (SNP) markers that can be used for consistent, routine mountain lion monitoring by different laboratories. We used a subset of existing Illumina HiSeq data for 104 individuals from throughout California to design a single, highly heterozygous multiplex of 95 SNPs for the Fluidigm platform. This panel confidently differentiates individual mountain lions, identifies sex, and discriminates mountain lions from bobcats. The panel performed well on fecal DNA extracts and based on design, had sufficient resolution to differentiate individual genotypes in even the population with lowest genetic diversity in southern California.

The Road to Practical Application of Cadmium Phytoremediation Using Rice

Cadmium (Cd) is a toxic heavy metal that causes severe health issues in humans. Cd accumulates in the human body when foods produced in Cd-contaminated fields are eaten. Therefore, soil remediation of contaminated fields is necessary to provide safe foods. Rice is one of the primary candidates for phytoremediation. There is a genotypic variation of Cd concentration in the shoots and grains of rice. Using the world rice core collection, ‘Jarjan’, ‘Anjana Dhan’, and ‘Cho-ko-koku’ were observed with a significantly higher level of Cd accumulation in the shoots and grains. Moreover, OsHMA3, a heavy metal transporter, was identified as a responsive gene of quantitative trait locus (QTL) for high Cd concentration in the shoots of these three varieties likewise. However, it is difficult to apply practical phytoremediation to these varieties because of their unfavorable agricultural traits, such as shatter and easily lodged. New rice varieties and lines were bred for Cd phytoremediation using OsHMA3 as a DNA marker selection. All of them accumulated Cd in the shoots equal to or higher than ‘Cho-ko-koku’ with improved cultivation traits. Therefore, they can be used for practical Cd phytoremediation.

Impact of the Marker Set Configuration on the Accuracy of Gait Event Detection in Healthy and Pathological Subjects

For interpreting outcomes of clinical gait analysis, an accurate estimation of gait events, such as initial contact (IC) and toe-off (TO), is essential. Numerous algorithms to automatically identify timing of gait events have been developed based on various marker set configurations as input. However, a systematic overview of the effect of the marker selection on the accuracy of estimating gait event timing is lacking. Therefore, we aim to evaluate (1) if the marker selection influences the accuracy of kinematic algorithms for estimating gait event timings and (2) what the best marker location is to ensure the highest event timing accuracy across various gait patterns. 104 individuals with cerebral palsy (16.0 ± 8.6 years) and 31 typically developing controls (age 20.6 ± 7.8) performed clinical gait analysis, and were divided into two out of eight groups based on the orientation of their foot, in sagittal and frontal plane at mid-stance. 3D marker trajectories of 11 foot/ankle markers were used to estimate the gait event timings (IC, TO) using five commonly used kinematic algorithms. Heatmaps, for IC and TO timing per group were created showing the median detection error, compared to detection using vertical ground reaction forces, for each marker. Our findings indicate that median detection errors can be kept within 7 ms for IC and 13 ms for TO when optimizing the choice of marker and detection algorithm toward foot orientation in midstance. Our results highlight that the use of markers located on the midfoot is robust for detecting gait events across different gait patterns.

Quality Control of Herbal Medicines: From Traditional Techniques to State-of-the-art Approaches

Herbal medicines are important options for the treatment of several illnesses. Although their therapeutic applicability has been demonstrated throughout history, several concerns about their safety and efficacy are raised regularly. Quality control of articles of botanical origin, including plant materials, plant extracts, and herbal medicines, remains a challenge. Traditionally, qualitative (e.g., identification and chromatographic profile) and quantitative (e.g., content analyses) markers are applied for this purpose. The compound-oriented approach may stand alone in some cases (e.g., atropine in Atropa belladonna). However, for most plant materials, plant extracts, and herbal medicines, it is not possible to assure quality based only on the content or presence/absence of one (sometimes randomly selected) compound. In this sense, pattern-oriented approaches have been extensively studied, introducing the use of multivariate data analysis on chromatographic/spectroscopic fingerprints. The use of genetic methods for plant material/plant extract authentication has also been proposed. In this study, traditional approaches are reviewed, although the focus is on the applicability of fingerprints for quality control, highlighting the most used approaches, as well as demonstrating their usefulness. The literature review shows that a pattern-oriented approach may be successfully applied to the quality assessment of articles of botanical origin, while also providing directions for a compound-oriented approach and a rational marker selection. These observations indicate that it may be worth considering to include fingerprints and their data analysis in the regulatory framework for herbal medicines concerning quality control since this is the foundation of the holistic view that these complex products demand.