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GAMMA irradiation might be an alternative strategy for increasing crop yield and/or introducing new varieties. Reddish-brown Phaseolus vulgaris L. cv Abo Yousuf was exposed to 50Gy of γ-radiation produced M2 seeds, while 100 and 300Gy were lethal. M2 seeds were cultivated to investigate the segregated traits in M3 and M4 plants. Segregation of purple and green: hypocotyls, lower venation, and pods, besides purple flowers and emarginated leaf apex, were observed in M3 plants. M3 seeds showed five seed coat colors: reddish-brown, brown, dark brown, grayish brown, and gray. The reddish-brown seeds had the highest weight, 30.74%, whereas the gray seeds had a much lighter weight, 23.14%. The flower color was light purple in three lines viz; control, M2 50Gy, and M3 reddish brown and white in M3 dark brown line. While M3 brown and gray seeds produced four flower colors: dark purple, purple, light purple, and white. Whereas, M3 grayish brown seeds produced three flower colors: dark purple, purple, and white. Furthermore, γ-radiation induced 15 new seed coat colors in M4 progeny. Molecular characterization showed different fingerprints correlated with the segregated morphological traits and seed coat colors. Both the PCR fingerprints and the dendrograms produced by cluster analysis of the selected four RAPD differentiated clearly between the different M3 segregating genotypes of cv Abo Yousuf from M2 and control plants more than the two ISSR primers. Such findings indicated the pleiotropic effects of seed coat color genes and provided helpful information on gene(s) that govern these traits. [ABSTRACT FROM AUTHOR]

The adulteration of plants and their materials used in herbal formulations poses a severe health concern. Hence, there is a need to establish a reliable, cost-effective, and robust molecular biomarker to distinguish among species and identify herbal plants and raw drugs from adulterants. The present study used suppressive subtractive hybridization and next-generation sequencing technology to identify novel DNA markers for Boerhavia diffusa L. and Tinospora cordifolia (Willd.) Miers. We identified two primer sets for B. diffusa and one for T. cordifolia. The DNA markers were validated in different accessions of B. diffusa and T. cordifolia and their common adulterants to determine the sensitivity and specificity of developed DNA markers. The designed DNA markers showed 100% sensitivity and specificity in detecting B. diffusa and T. cordifolia from their adulterants. The strategy described here can be extrapolated for developing DNA markers to authenticate other plant species. [ABSTRACT FROM AUTHOR]

There has always been a tendency of medicine to take an individualised approach to treating patients, but the most significant advances were achieved through the methods of molecular biology, where the nucleic acids are in the limelight. Decades of research of molecular biology resulted in setting medicine on a completely new platform. The most significant current research is related to the possibilities that DNA and RNA analyses can offer in terms of more precise diagnostics and more subtle stratification of patients in order to identify patients for specific therapy treatments. Additionally, principles of structure and functioning of nucleic acids have become a motive for creating entirely new therapy strategies and an innovative generation of drugs. All this also applies to cardiovascular diseases (CVDs) which are the leading cause of mortality in developed countries. This review considers the most up-to-date achievements related to the use of translatory potential of DNA and RNA in treatment of cardiovascular diseases, and considers the challenges and prospects in this field. The foundations which allow the use of translatory potential are also presented. The first part of this review focuses on the potential of the DNA variants which impact conventional therapies and on the DNA variants which are starting points for designing new pharmacotherapeutics. The second part of this review considers the translatory potential of non-coding RNA molecules which can be used to formulate new generations of therapeutics for CVDs. [ABSTRACT FROM AUTHOR]

Efficiently distinguishing various Syzygium cumini L. Skeels (jamun) accessions holds practical significance for selection purposes. This study concentrated on 15 superior genotypes of jamun from the North Western Indian Himalayas, selected for their pivotal horticultural traits. Drawn from a pool of 82 collected genotypes and assessed across two consecutive years (2019 and 2020), these genotypes underwent morphological evaluations utilizing a randomized block design replicated thrice. Concurrently, random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers were employed for molecular analysis. Substantial variations surfaced among genotypes, both in morphological traits and fruit biochemistry. Notably, tree 43 exhibited promise across multiple horticultural facets, encompassing fruit weight, length, pulp weight, pulp-to-seed ratio and pulp percentage. Conversely, tree 49 excelled in elevated levels of total soluble solids, total sugar and reducing sugar. While principal component analysis and cluster analysis unveiled modest genetic variability, RAPD and ISSR markers unveiled pronounced molecular-level polymorphism. Agglomerative hierarchical clustering delineated the genotypes into five distinct clusters. Cluster I encompassed two genotypes, cluster II embraced five while the largest group, cluster III, included six genotypes. Clusters IV and V highlighted individual genotypes, trees 43 and 54 respectively. In the molecular analysis, UPGMA clustering yielded two primary clusters, spotlighting the noteworthy similarity between genotypes trees 49 and 52 whereas, trees 40, 43, 44 and 48 stood distinct. The observed genetic diversity stands as a valuable resource with substantial potential to enrich diverse breeding initiatives. These salient genetic variations underscore the richness within the studied population, offering a valuable asset for focused future pursuits. [ABSTRACT FROM AUTHOR]

The work was performed in order to study the morphological and agriculturally important traits and molecular genetic allelic polymorphism of the cultivated varieties and wild forms of soybean using microsatellite DNA with the aim of identification and certification of their genotypes. Unique DNA profiles of the studied soybean cultivars and wild forms were obtained by PCR analysis using six microsatellite loci (Satt1, Satt2, Satt5, Satt9, Sourgr1, and Soyhsp176). Twenty-four alleles have been identified, with the number of alleles per locus ranging from two to ten. For each locus, Polymorphism Information Content (PIC) varied from 0.28 to 0.86 and the average was 0.62; the effective number of alleles varied from 1.38 to 6.92 and the average was 3.30. Cultivated soybean varieties differed by from 1 to 4 loci. The dendrogram constructed for the studied soybean genotypes by the unweighted pair group method with arithmetic mean (UPGMA) with the aid of the POPGENE v. 1.32 software revealed two large clusters. Cluster I included the cultivated soybean varieties, while cluster II included wild soybean forms, which overall pointed to the significant genetic differences between these two groups. The highest morphological differences were revealed between the Topaz and Dauriya varieties, both in the phenotype (pubescence coloration and density and seed and eye color and shape) and in all agriculturally important traits (vegetation period—95 and 112 days; yield—26.8 and 30.9 hundred kg/ha; plant height—64 and 81 cm; lower bean attachment height—13 and 16 cm; weight of 1000 seeds—174.7 and 185.4 g; protein content—40.3 and 38.2%; oil content—19.2 and 19.8%, respectively). For the first time, molecular genetic passports of nine soybean cultivars bred in the All-Russia Soybean Research Institute for their genotype identification have been obtained based on the findings of this study. [ABSTRACT FROM AUTHOR]

The Rpi-chc1 gene confers resistance to late blight (LB) in the wild South American species Solanum chacoense. The goal of this study was to enhance our insight into polymorphism of this gene in the genus Solanum, which is the source of valuable donors of resistance to LB. To this end, we analyzed 122 accessions of the working collection, consisting of potato cultivars, complex interspecific hybrids, and representatives of 11 wild Solanum species. We studied the polymorphism of the region of this gene that encodes the most polymorphic LRR domain. As a result, in the species S. chacoense, S. berthaultii, S. tuberosum, S. microdontum, and S. maglia we found previously unknown variants of the Rpichc1 gene, which differ in their amino acid sequence from both the functional and non-functional variant of the Rpi-chc1 gene. Therefore, the function of these homologues cannot be unambiguously predicted, but must be further studied. [ABSTRACT FROM AUTHOR]

Background: Astragali Radix is regarded as an important traditional medicinal plant and has been widely used as a Qi-Invigoratin medicine for more than 2000 years. However, the mechanism of its medicinal and nutritional components in different accessions is unexplored. Moreover, the lack of SSR markers for Astragali Radix has stalled genetic breeding and variety identification. To develop EST-SSRs, transcriptome sequencing was performed based on the Illumina platform. Results: Approximately 99.6 million raw data points were collected, and 296,618 unigenes with an average length of 1,459 bp were obtained. A total of 71,207 SSR loci within 56,097 SSR-containing unigenes were identified. Of these SSR-containing unigenes, 26,188 (46.7%), 16,736 (29.8%), and 8,858 (15.8%) were related to items in the GO database, KEGG database, and COG database, respectively. The motifs A/T, AG/CT, AT/AT, and AAT/ATT were the most common types, accounting for 39.78%, 19.14%, 10.12%, and 4.60%, respectively, and the average length of the EST-SSRs was 17.16 bp. We acquired 8 functional markers linked to key genes correlated with the biosynthesis of flavonoids. The genetic similarity among the 60 AR varietal resources ranged from 0.2692 to 0.8077, with an average of 0.5742. The dendrogram results indicated that the 60 AR samples tested had high levels of genetic similarity. Conclusions: The 71,207 EST-SSR loci identified here offer valuable source of DNA markers for the genetic diversity identification of 60 Astragali Radix varieties. These results will facilitate genetic map construction, functional gene identification, variety identification, molecular marker-assisted breeding, and genetic diversity analysis in Astragali Radix.How to cite: Jiang M, Yan S, Ren W, et al. Genetic diversity of the Chinese medicinal plant Astragali Radix based on transcriptome-derived SSR markers. Electron J Biotechnol 2023;62. https://doi.org/10.1016/j.ejbt.2022.12.001.

Sheath blight disease caused by the necrotrophic, soil-borne pathogen Rhizoctonia solani Kuhn, is the global threat to rice production. Lack of reliable stable resistance sources in rice germplasm pool for sheath blight has made resistance breeding a very difficult task. In the current study, 101 rice landraces were screened against R. solani under artificial epiphytotics and identified six moderately resistant landraces, Jigguvaratiga, Honasu, Jeer Sali, Jeeraga-2, BiliKagga, and Medini Sannabatta with relative lesion height (RLH) range of 21–30%. Landrace Jigguvaratiga with consistent and better level of resistance (21% RLH) than resistant check Tetep (RLH 28%) was used to develop mapping population. DNA markers associated with ShB resistance were identified in F2 mapping population developed from Jigguvaratiga × BPT5204 (susceptible variety) using bulk segregant analysis. Among 56 parental polymorphic markers, RM5556, RM6208, and RM7 were polymorphic between the bulks. Single marker analysis indicated the significant association of ShB with RM5556 and RM6208 with phenotypic variance (R2) of 28.29 and 20.06%, respectively. Co-segregation analysis confirmed the strong association of RM5556 and RM6208 located on chromosome 8 for ShB trait. This is the first report on association of RM6208 marker for ShB resistance. In silico analysis revealed that RM6208 loci resides the stearoyl ACP desaturases protein, which is involved in defense mechanism against plant pathogens. RM5556 loci resides a protein, with unknown function. The putative candidate genes or quantitative trait locus harbouring at the marker interval of RM5556 and RM6208 can be further used to develop ShB resistant varieties using molecular breeding approaches.

Blueberries (Vaccinium L. spp.) are an economically and medicinally important plant. Their antioxidant properties are well-known for their medicinal value in negating the harmful effects of free radicals. It is very important to develop genotypes that are high in health-promoting factors and economic value to meet present world needs. Estimation of genetic diversity using molecular markers, antioxidant properties, and their association can reveal genotypes with important characteristics and help in berry improvement programs. Wild blueberries are a better source of antioxidant metabolites compared to cultivated ones. Extensive variations are present in molecular and biochemical contents among wild clones and cultivars. The current review provides detailed and updated information on the economic and medicinal importance of blueberries, the application of molecular markers, and biochemical estimation in berry improvement and conservation, filling the gap in the literature. [ABSTRACT FROM AUTHOR]

Simple Summary: Autochthonous pig breeds are important genetic resources, well adapted to local climatic conditions, environments, and traditional production systems, where they are associated with local and niche markets. The Greek Black Pig breed is the only local pig breed recognized in Greece. In this study, we started a population genetic characterization of this breed by analyzing a few gene markers associated with morphological and production traits and that usually differentiate wild boars from domestic breeds. The obtained results showed that, in the past, this breed experienced genetic admixture from two sources, wild boars and cosmopolitan breeds. On the one hand, this situation might raise some concerns for the genetic integrity of this animal genetic resource. On the other hand, this might contribute to within-population genetic variability reducing the problem of inbreeding of the small breed population. In this breed, we also identified a novel allele in the melanocortin 1 receptor (MC1R) gene, resulting in a new hypothesis on the function of the encoded protein in regulating the cascade signals and leading to the production of different pigmentation. This result showed that local untapped breeds can be the reservoir of interesting genetic variants useful to better understanding underlying basic biological functions in mammals. The Greek Black Pig (or Greek Pig) is the only recognized autochthonous pig breed raised in Greece, usually in extensive or semi-extensive production systems. According to its name, the characteristic breed coat color is solid black. In this study, with the aim to start a systematic genetic characterization of the Greek Black Pig breed, we investigated polymorphisms in major genes well known to affect exterior and production traits (MC1R, KIT, NR6A1, VRTN and IGF2) and compared these data with population genetic information available in other Mediterranean and Western Balkan pig breeds and wild boars. None of the investigated gene markers were fixed for one allele, suggesting that, in the past, this breed experienced introgression from wild boars and admixture from cosmopolitan pig breeds, enriching the breed genetic pool that should be further investigated to design appropriate conservation genetic strategies. We identified a new MC1R allele, containing two missense mutations already reported in two other independent alleles, but here present in the same haplotype. This allele might be useful to disclose biological information that can lead to better understanding the cascade transmission of signals to produce melanin pigments. This study demonstrated that autochthonous genetic resources can be an interesting reservoir of unexpected genetic variants. [ABSTRACT FROM AUTHOR]

Bibrik sheep is found vastly in Baluchistan province in Pakistan. Randomly sampled animals of this breed were subjected to genetic analysis using ovine molecular markers where fifteen sheep SSR genetic markers were employed for describing multiple-allelomorphism. The average observed number of alleles (Na), effective number of alleles (Ne) and Shannon's Information Index were 2.07 ± 0.79, 1.86 ± 0.69 and 0.54 ± 0.29, respectively. Heterozygosity was described by the average, observed and expected heterozygosities whose values were found to be 0.56 ± 0.27, 0.44 ± 0.27 and 0.43 ± 0.26, respectively. Slightly higher magnitude of observed heterozygosity indicated that forces affecting Hardy-Weinburg Equilibrium were not much effective in these flocks and outbreeding was common phenomenon that reduced the inbreeding in the flocks as inbreeding tends to promote homozygosity. The range in observed heterozygosity was very wide for different molecular markers. These measurements underlined the absence of inbreeding in the flocks that commonly causes inbreeding depression. The presence of genetic diversity was apparent and these markers would be employed for identification of Bibrik sheep through DNA fingerprinting. It was concluded that present assessment of genetic diversity could be used as tool for making future breeding plans but large scale enumeration is required for the Bibrik sheep. [ABSTRACT FROM AUTHOR]

Evaluation of genetic uniformity is important in a perennial plant like coffee propagated through somatic embryogenesis. In this study, we compared the genetic homogeneity of somatic embryo-derived plants and the seed-derived plants obtained from a single mother plant of robusta coffee cultivar by employing Sequence Related Amplified Polymorphism (SRAP) and Start Codon Targeted (SCoT) molecular markers and sequencing four functional genes. The SRAP and SCoT molecular markers revealed 96% genetic similarity between somatic embryo-derived and seed-derived plants with the mother plant. The sequencing analysis has shown the minimum sequence variability in the chloroplast maturase K gene and the highest sequence variability in the zinc finger protein gene compared to NAC25 and UDP-glycosyltransferase genes. The presence of SNP and indels created polymorphism in gene sequences. The percent frequency of SNP varied from 0.0 to 0.45 in matK, 0.36 to 1.40 in NAC25, 0.81 to 2.63 in the UDP-glycosyltransferase gene and 3.30 to 8.70 in the zinc finger protein gene. In the case of NAC25 and UDP-glycosyltransferase genes, the seed-derived plants have shown a higher frequency of SNP compared to somatic embryo-derived plants. However, in the case of zinc finger protein gene, tissue culture-derived plants accumulated a two-fold higher frequency of SNP compared to the seed-derived plants. The sequence characterization of the four genes has revealed the presence of a higher frequency of non-synonymous SNPs compared to synonymous SNPs. This is the first report on the comparative genetic uniformity analysis of somatic embryo-derived and seed-derived plants in robusta coffee cultivar with significant practical implications. Key message: Molecular marker based genetic homogeneity assessment of somatic embryo and seed-derived plants of Coffea canephora revealed 96% similarity with the mother plant. The SE derived plants exhibited higher sequence variability in zinc finger protein gene. [ABSTRACT FROM AUTHOR]

Potato is the third most important crop. Its production and quality is greatly affected by various biotic stresses. In this study, 216 Solanum tuberosum subsp. tuberosum accessions were screened for late blight, viruses (PVY and PVX) and potato cyst nematodes (PCNs) resistance using robust molecular markers. Solitary or combined late blight resistant genes (R1, Rpi-abpt, R3a, R3b) presence was observed in 51 accessions. For PVY resistance, markers STM0003, RYSC3, and YES3-3 A were found in 38, 3, and 1 accession, respectively, and PVX resistance gene markers 1Rx1 and 106Rx2 were found in 19 and 10 accessions, respectively. The STM0003 marker was present in 38 accessions, of which 12 were resistant to PVY and 10 were susceptible. The genotype data on six markers for both the species of PCN showed 45 resistant accessions. A combined analysis of all markers for late blight identified six accessions with all the three resistance genes. Similarly, four accessions, i.e., CP 4226, CP 2049, CP 3696, and CP 3651 had both Rx1 and Rx2 genes for PVX resistance, while only one accession, viz., CP 2049 showed the presence of both H1 and HC genes along with the Gpa2 marker for PCN resistance. There were also seven resistance genes found in CP 2049 for late blight (2), PCN (4), and PVX (2), but none of the accession had genes for all four traits. The results revealed that developing potato varieties with combined resistance to late blight, viruses, and PCN requires concerted hybridization between different parental lines. [ABSTRACT FROM AUTHOR]

Avena sativa L. is a very common specie for human consumption that provide different health benefits. As a dual purpose crop, oat provide a source of protein, fiber and minerals. Here, homologs of Bet v 1 allergen genes were used as DNA markers to analyse their utilization for genomic variability of oat varieties. The presence of Bet v 1 homologues in seven oat varieties were examined and their length polymorphism was analysed. Bet v 1 based amplified profile - BBAP-was used to obtain the polymorphic profiles for the used oat varieties by a combination of specific and degenerated primer pair. This method was reported to be universal in plants for screening of variability of coding regions. Using the primer pair Bet v 1 forward and degenerated Bet v 1 reverse 49 amplicons were amplified in a total. The length of the amplicons varied from 265 base pairs to 1929 base pairs. All analysed oat varieties generated unique amplicons, but there was not a size of amplicon that all cultivars shared. Constructed dendrogram based on hierarchical cluster analysis using UPGMA algorithm grouped the analysed varieties genotypes into three main clusters - Black Beauty and Zvolen varieties, Valentín and Earl and Vendelín varieties and Floron and Dagles varieties. BBAP technique provide a high polymorphism in the Bet v 1 isoforms present in oat and all of the analysed varieties were distinguished what showed the utility of this marker technique for analysis of genetic diversity and genotype identification of oat varieties. [ABSTRACT FROM AUTHOR]

American mink is involved in the economic activity of the Republic of Belarus since it belongs to resource hunting species as well as breeds for fur production. We propose an identification test system consisting of 11 microsatellite DNA loci designed for forensic investigation of cases of illegal hunting and animals stealing for their precious furs. Informative relevance of the test system studied using two samples of farm minks and a sample from a wild population of M. vision geographically isolated from fur farms. It is shown that there are The significant genetic differences between wild and farmed minks (Fst = 0.04397, P < 0.005) showed with a random match probability of the 11-locus genotypes calculated with and without taking into account the Fst value differing by two orders of magnitude (1.84 × 10–8 and 1.39 × 10–10 respectively). As concerns forensic DNA analysis, reference databases should be formed for wild and farm animals separately. [ABSTRACT FROM AUTHOR]

Sambucus is a cosmopolitan plant genus that has been used for centuries for its medicinal properties and nutritional value. Sambucus nigra, the most studied species, contains a wide range of bioactive compounds that have been linked to various health benefits. Moreover, the fruit of the elderberry is a rich source of phytochemicals and is used to make a variety of food products. In this review, after an introduction of the species, we outline the main points for its cultivation and production. We then illustrate the major phytochemical components and related beneficial properties, such as antioxidant, antimicrobial, and pharmaceutical activities. We also provide insights into genetic variability, functional diversity, and some evolutionary relationships that were evaluated with DNA-based techniques. We discuss that despite its long history of use and potential benefits, Sambucus nigra has received relatively little attention in terms of horticulture, breeding, and molecular genetics, while studies on its biochemical composition and health benefits are well developed. Further research is also needed to better understand the pre-harvest and post-harvest factors that influence plant growth and production, as well as to explore new applications and industrial uses of this underutilized species. [ABSTRACT FROM AUTHOR]

DNA markers help detect the intraspecific genetic diversity of yeast strains. Eight ISSR (Inter Simple Sequence Repeats) primers were used to assess the intraspecific diversity of Saccharomyces cerevisiae (n = 96) from different populations (n = 3), evaluate the technological characteristics, and investigate trait-loci associations. The primers amplified 154 reproducible and scorable bands, of which 79.87% were polymorphic. The UPGMA (unweighted pair group method with arithmetic mean) dendrogram clustered 96 isolates into two main clusters, supported by STRUCTURE HARVESTER results (ΔK = 2). Analysis of molecular variance (AMOVA) indicated significant genetic differences between (15%) and within the populations (85%) (p < 0.001). Twenty-nine genetically distinct strains were selected for the technological characterization. Principal component analysis (PCA) revealed that five strains with high fermentation capacity, leavening activity, high growth index at 37 °C, and harsh growth conditions were technologically relevant. Trait-loci association analyses indicated that the highest correlation (r = 0.60) was recorded for the fermentation capacity on the 8th and 113th loci, amplified by ISSR-1 and ISSR-6 primers, respectively (p < 0.05). The strains yielding high performances and the associated loci amplified by ISSR markers possess a high potential to generate locus-specific primers to target the strains with high fermentation capacity. [ABSTRACT FROM AUTHOR]

The culture conditions influence the magnitude of genetic expression in fish. This study was undertaken to assess the impact of Genotype (G) × Environment (E) interaction on the growth performance of hatchery produced Catla catla. The different hatchery stocks including Farooqabad (FQB), Lahore (LHR), Faisalabad (FSD), Bhalwal (BHL) and Qadirabad (QBD) assumed as five distinct genotypes were compared for genetic variability in relation to growth performance. Appraisal fish fingerlings were reared in glass aquaria (twenty fish per population) for 60 days under similar environmental conditions. Condition factor (K) and growth parameters (wet weight, fork and total length) were measured fortnightly. The morphometric data were analyzed using SPSS. Genetics characterization was performed by employing five species specific polymorphic microsatellite markers. Overall, the results of growth trial confirmed that FQB genotype performed maximum while QBD evinced lowest performance among all the genotypes based on wet weight (g) and total length (mm). Genetic analysis revealed significant differences based on allelic frequencies, heterozygosity, inbreeding and genetic distance among hatchery genotypes. Impact of G×E interaction is illustrated by results where genetically diverse FQB genotype performed maximum under similar cultural environment among all genotypes. [ABSTRACT FROM AUTHOR]

The instability of in vitro cultures may cause genetic and epigenetic changes in crops called somaclonal variations. Sometimes, these changes produce beneficial effects; for example, they can be used in breeding programs to generate new cultivars with desirable characteristics. In this article, we present a systematic review designed to answer the following question: How does somaclonal variation contribute to plant genetic improvement? Five electronic databases were searched for articles based on pre-established inclusion and exclusion criteria and with a standardized search string. The somaclonal variation technique has been most frequently applied to ornamental plants, with 49 species cited in 48 articles, and to the main agricultural crops, including sugarcane, rice, banana, potato and wheat, in different countries worldwide. In 69 studies, a technique was applied to evaluate the genetic diversity generated between clones, and, in 63 studies, agronomic performance characteristics were evaluated. Other studies are related to resistance to pathogens, ornamental characteristics and resistance to abiotic stresses. The application of the plant growth regulators (PGRs) benzylaminopurine (BAP) and dichlorophenoxyacetic acid (2,4-D) was the most common method for generating somaclones, and randomly amplified polymorphic DNA (RAPD) molecular markers were the most commonly used markers for identification and characterization. Somaclonal variation has been used in genetic improvement programs for the most economically important crops in the world, generating genetic diversity and supporting the launch of new genotypes resistant to diseases, pests and abiotic stresses. However, much remains to be explored, such as the genetic and epigenetic mechanisms from which somaclonal variation is derived. [ABSTRACT FROM AUTHOR]

Lingxiaohua (Campsis Flos, Campsis grandiflora (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood circulation. It also possesses anti-inflammatory and antioxidative properties. This non-poisonous plant is frequently confused with poisonous Yangjinhua (Daturae Metelis Flos, Datura metel Linnaeus) in the market, resulting in serious anticholinergic poisoning. The confusion of these two herbs is due to the similarity in their appearances. In our study, we compared the complete chloroplast genomes of the two plants and found that they are very different in terms of their gene content and gene arrangement. There were also significant differences in the number and repeating motifs of microsatellites and complex repeats. We used universal primers for the amplification of rbcL, matK, psbA-trnH, and ITS2 regions and successfully differentiated the two plants. Furthermore, we designed two pairs of primers based on the nucleotide differences in chloroplast genomes at the rps14 and rpoC1 regions to provide additional authentication markers. The universal primers and specific primers when used together can accurately discriminate Lingxiaohua and Yangjinhua. [ABSTRACT FROM AUTHOR]

In this paper, the genetic diversities of 12 rice genotypes (Oryza sativa L.), representing Indica, Japonica, and Indica–Japonica varieties, were assessed using twelve ISSR and five SSR markers. In addition, the rice genotypes were evaluated for 11 agro-morphological traits in a two-year trial. Association mapping was performed to detect any association between the DNA markers and the agro-morphological traits. An association analysis was conducted considering the relative kinship among the genotypes and accounting for the population structure using the unified mixed-model approach to avoid possible false-positive associations. Seventy-three alleles were collectively produced by ISSRs and SSRs, with an average of 6.3 and 2.8 alleles per locus, respectively. Both marker systems were informative, and the average polymorphism information content (PIC) was 0.222 and 0.352 for ISSRs and SSRs, respectively. The average expected heterozygosity (Hexp) was 0.264 for ISSRs compared to 0.457 for SSRs. After using the false discovery rate (FDR) method, the association analysis revealed a total of 12 significant marker–trait associations with six agro-morphological traits, including the no. of unfiled grains panicle−1, panicle length, panicle weight, the no. of panicles plant−1, the no. of tillers plant−1, and 1000-grain weight. ISSRs showed seven significant associations with five markers, while SSRs showed three significant associations with three markers. The phenotypic variance (R2) explained by each marker ranged between 29.2% for the ISSR marker HB11 (associated with 1000-grain weight) and 49.3% for the ISSR marker HB8 (associated with the no. of tillers plant−1). The identified marker–trait associations reported herein may improve the expected gain of future molecular-based rice-breeding programs, particularly those designed for improving grain-related or harvest-related traits. [ABSTRACT FROM AUTHOR]

In order to study a regulation mechanism for one of the most ancient processes of anthocyanin biosynthesis in plants based on comparison of R2R3-MYB genes in Solanaceae (S. lycopersicum: Ant1, An2; S. melongena: Myb1; C. annuum: Myb113-like1 and Myb113-like2) and Brassicaeae crops, a search for orthologous sequences in Brassica oleracea was performed. A sequence encoding MYB114 TF was found to be the closest in a nucleotide structure to the previously investigated genes in Solanaceae. Primers were selected and a comparative analysis of the Myb114 gene sequences was performed in B. oleracea varieties (white cabbage, red cabbage, kale, cauliflower, broccoli, and kohlrabi) with a wide intraspecies diversity by the anthocyanin accumulation in leaves and various food organs: heads, curds, and stems. Alignment of Myb114 sequences revealed a number of gene polymorphisms that closely correlate with high anthocyanin accumulation in B. oleracea leaves, including three SNPs in exon regions and a 271 bp deletion in the first intron. The identified SNPs lead to the replacement of two amino acids located in the region of DNA-binding domains, which leads to a change in the binding efficiency of this transcription factor with the promoters of structural biosynthesis genes and a decrease in their expression level in the forms without anthocyanin accumulation in leaves compared with the forms with their accumulation in vegetative plant parts. A molecular marker MYB114.2 has been proposed that may be used for the identification of cabbages and kales with high/low anthocyanin accumulation. By the amino acid structure and phenotypic manifestation (regulation of anthocyanin accumulation in leaves), Myb114 of B. oleracea is the closest to An2 tomato, Myb2 eggplant, and Myb113-like2 pepper alleles. A high degree of conservatism of the SANT DNA-binding domains of MYB114 TF of B. oleracea and R2R3-MYB TF of nightshades was established. [ABSTRACT FROM AUTHOR]

Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks. [ABSTRACT FROM AUTHOR]

Apricot (Prunus armeniaca L.) is a cosmopolitan, major stone fruit species cultivated for its delicious drupes. Strong concerns about loss of diversity in apricot have been recently put forward mainly because of the enduring transition from local to globalized varieties more suitable for intensive agriculture. Italy, one of the top producing countries in the world, has arguably one of the richest apricot germplasms, with the Campania region being a traditional and leading area of cultivation since Roman times. This work aimed to study the molecular diversity of an ex-situ collection of local apricot varieties. They once flourished in conventional cropping systems, but are nowadays neglected, surviving in family farms, and sold only in local markets. We investigated the level of genetic and genotypic diversity, assessed clonality in the population, and verified the presence of genetic structure and differentiation in 73 apricot varieties by using fluorescent SSR markers resolved in capillary electrophoresis (SSR-CE). The analysis indicated a high level of genetic diversity (with little locus-specific differences) and of genotypic assortment, with few possible synonyms. Moreover, the investigation of relatedness among apricot landraces and the negligible within-landraces differentiation are consistent with a common origin of the germplasm, a likely result of an adaptive diversification that is mainly due to similar environmental and agricultural factors. This work highlights the value of the traditional germplasm where crops thrived. Moreover, it provides support for studying the possible mechanisms of evolution and adaptation and for implementing measures for the exploitation, regeneration, and on-farm promotion of the apricot landraces. [ABSTRACT FROM AUTHOR]

Background. The harmful organisms affecting potato cause great economic damage in all areas where the crop is grown. One of the most economically important pathogens is the potato late blight (agent Phytophthora infestans Mont. (de Bary)). Also, Potato Virus Y (PVY) and potato cyst nematode (PCN) of the Ro1 pathotype, the only one that occurs in the Russian Federation, cause significant yield losses. Materials and methods. Phytopathological and molecular screening was carried out on original interspecific potato hybrids obtained in 11 crossing combinations, seven of which were studied for the first time. Hybrids resulted from crosses that involved Mexican and South American potato species as sources of late blight and PVY resistance. Field observations of late blight resistance were conducted during three seasons under high infection pressure. A part of plant material was screened in laboratory tests. PCR tests employed 9 DNA markers of genes associated with resistance to Ph. infestans, PVY and PCN of Ro1 pathotype used in our previous study. Results. In field evaluation, hybrid clones mostly expressed high, and a part of them moderate late blight resistance. Of the 6 markers of the used Rpi genes, at least two were detected in most clones, while some had 3 or 4 markers. Some clones were found to have markers of PCN resistance genes and of several genes for resistance to PVY. The cytoplasm type was determined for all plant material. Conclutions. Within a small but pedigree-diverse set of interspeсific hybrids, the markers of resistance genes to all three pests were found. A part of clones obtained by using the sources of PVY and late blight resistance which we had identified, were found to contain two or more resistance genes to these pathogens. According to the results of molecular tests, the clones were found to carry several markers of late blight and PVY resistance genes. Original interspecific potato hybrids with determined late blight resistance levels, cytoplasm type and availability of markers of genes for resistance to three pests can be used in further hybridization.

Background. Identification of duplicates in the collections of genetic resources is the most important problem of seed gene bank management. Duplicate accessions expand the collection size, thus raising the costs of germplasm maintenance without broadening the genetic diversity.Materials and methods. The studied material included 17 pairs of Pisum sativum L. accessions from the VIR collection which presumably had been erroneously registered twice in the VIR catalogue; however, they had identical introductory numbers. The accessions entered the collection in 1922–1996 and to date they have been reproduced 2 to 16 times. After a field assessment, 15 pairs of putative duplicate accessions of various uses were selected for molecular analysis. A RAPD analysis was performed using five primers from the Operon Series. Total seed proteins were analyzed by SDS-polyacrylamide gel electrophoresis.Results. The following criteria were used to ascertain identity of the accessions or their difference: 1) similarity of morphological characters (habitus, and anthocyanin pigmentation of flowers and vegetative organs) and flowering dates; 2) identity or polymorphism of RAPD profiles; and 3) identity or difference in electrophoretic banding patterns of seed storage proteins. Seven pairs of duplicates were identified according to the results of a comparative analysis. Among them, the accessions in the pairs k-81/k-1199, k-8331/k-8645, k-8719/k-8760, and k-8757/k-8825 turned out to be completely identical, while k8464/k-8472, k-8740/k-8873, and k-8689/k-8723 were heterogenic, but had similar RAPD profiles and seed proteins patterns.Conclusions. An integrated assessment involving in-field plant phenotyping and analyzing polymorphism of amplified DNA fragments and components in electrophoretic banding patterns of seed proteins is promising for detecting identical or heterogenic accessions in genebank collections.

DNA markers are used as a size reference and sample loading control during gel electrophoresis. Most markers are designed for conventional gel electrophoresis to separate DNA smaller than 20 kb. For larger molecules, pulsed-field gel electrophoresis (PFGE) marker is required. Limited PFGE markers are available because large DNA are prone to nicking and degradation, causing smeary bands. Here, we developed a robust marker based on bacterial artificial chromosomes (BACs) with bands up to 184 kb. This marker could consistently confer intense and distinct bands for accurate gel analysis in molecular biology studies, laboratory validations or clinical diagnosis. [Display omitted] • PFGE marker is prone to DNA degradation, which gives smeary banding patterns, causing difficulties in gel analysis. • We have developed a set of low-range PFGE markers based on restriction endonuclease fragments of bacterial artificial chromosomes. • Instead of giving only single banding pattern, this method offers almost endless possible combinations of customizable bands up to 184 kb. • It gives distinct band distribution and accurate quantification of nucleic acid compared to traditional markers. [ABSTRACT FROM AUTHOR]

We benefited from the availability of a species-specific DNA marker to describe the morphometry of T. cordata × platyphyllos hybrids of an impressive age (ca. 150 years) grown in the Pazaislis baroque monastery yard in Central Lithuania. In an earlier study on a country-wide set of 543 T. cordata individuals from natural forest populations in Lithuania, we detected a nuclear microsatellite locus Tc8 well-differentiating between T. cordata and T. platyphyllos. The Tc8 locus contained a 140 bp allele in T. cordata (541 sampled individuals) and alleles above 160 bp in the two trees with a T. platyphyllos-like morphology (sampled in a national park). To verify the Tc8 locus as species specific, we sampled a further four T. platyphyllos-like individuals, which all contained the Tc8 locus alleles above 160 bp. We subsequently genotyped the six old-growth individuals from the Pazaislis monastery with mixed T. cordata × platyphyllos morphology. Results revealed that all six old-growth Tilia individuals from the Pazaislis monastery were heterozygous for the Tc8 locus with alleles of 140 bp (indicative of T. cordata) and 162 bp (indicative of T. platyphyllos). This finding confirms the morphological observations that these individuals are hybrids between T. cordata and T. platyphyllos. Additionally, the genotyping of a set of 14 nuclear microsatellite loci revealed that all six trees from the Pazaislis monastery are clones, possessing identical microsatellite genotypes. After the molecular identification, we morphotyped leaves, bracts, twigs, and nuts of the 6 old-growth T. cordata × platyphyllos hybrids from the Pazaislis monastery, 16 T. cordata old-growth trees, 4 T. × europaea var. europaea ‘Pallida’ trees growing near the Pazaislis monastery, and 4 mature T. platyphyllos trees from a nearby Girionys park. The morphotyping showed that T. cordata × platyphyllos hybrids may be the easiest to distinguish from T. cordata by raised and horizontally tertiary veins of leaves.

The climbing cucurbit Echinocystis lobata, native to North America and alien to many European countries, was assessed for its genetic diversity and differentiation across its introduced range of populations by applying markers of amplified fragment length polymorphism (AFLP). Various tests, including an evaluation of the intrapopulation diversity, principal coordinate, and molecular variance analyses, showed that the Central and Eastern European populations differing in geography and arrival history are also distinct in the genetic parameters. Genetic diversity, defined as the percentage of polymorphic AFLP loci, ranged within 28–62% (on average 51%) at the regional scale (in Romanian, Baltic State, and Central Russian populations), and was very similar to this parameter at the local scale (on average 52% for Lithuanian populations). The differentiation was significant among the populations of the regions (Ф = 0.125, p = 0.001) and at the local scale (among the Lithuanian populations of the different river basins, Ф = 0.058, p = 0.010). The Bayesian results suggested the presence of three genetic clusters among the 29 sites, with populations from Romania, Latvia, Estonia, and the northern part of Lithuania comprising one prevailing cluster, populations from the Nemunas river basin of Lithuania comprising either the former mentioned cluster or the second cluster, and populations of Central Russia comprising the third genetic cluster. Overall, E. lobata in Europe has probably originated from multiple introductions. The intentional anthropogenic seed dispersal by marketing accompanied by hydrochory might have an impact on such a profile of genetic clusters.

Tomato yellow leaf ... (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant. [ABSTRACT FROM AUTHOR]

The genus Coffea comprises more than 100 species, of which the most commercially important are Coffea arabica and Coffea canephora. The latter is a self-incompatible plant with high natural genetic variability. The detection of polymorphism at the DNA level by molecular markers allowed significant progress with the selection of superior plants. The objective of this study was the molecular characterization of C. canephora using microsatellite markers. To this end, a population of forty-four C. canephora genotypes and one C. arabica genotype, was evaluated with 21 primers. These primers identified 61 alleles in the population and between 2 and 5 alleles per locus. The information index indicated a high level of polymorphism of the analyzed markers. According to the observed and expected heterozygosity, the genetic diversity in the population is high. The overall inbreeding coefficient of the population detected high heterozygosity and zero inbreeding within this population. Genetic diversity among the accessions was also evaluated by the unweighted pair-group method based on arithmetic averages (UPGMA). Six groups were formed based on Mojena's cutting rule and three using the Bayesian approach. These results confirmed the existence of genetic diversity, genetic variability and a potential for selection in future breeding efforts involving the 45 genotypes studied. [ABSTRACT FROM AUTHOR]

The target capture GBS has been described to be advantageous over PCR-based GBS as oligonucleotides in target capture have less specificity compared to PCR primers. Additionally, to overcome the drawbacks of hybridization-based and PCR-fragment-based markers, the use of single nucleotide polymorphism (SNP) markers has been adopted in rice genetics research, as advances in chemistry have allowed cost-effective multiplex sequencing. One of the benefits of integrating GBS to GS programs is that it can effectively use genome-wide molecular markers from GBS. PCR-Based GBS Although RE-based GBS approaches have been utilized in marker-assisted studies, the need for high quality and quantities of DNA has become their limiting factor to being widely adopted. [Extracted from the article]

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.

The introduction of pharmacogenetic tests among the Russian population faces a fundamental limitation — pronounced genetic differences between populations. The genetic geography of pharmacogenetic markers of deoxyribonucleic acid (DNA) helps to remove these limitations.Aim. To reveal the spatial variation of the gene pools of the indigenous European Russian population in terms of DNA markers that are significant for the pharmacotherapy of cardiovascular diseases (CVDs) using the population biobank collections.Material and methods. A total of 3170 samples from 61 populations of the Biobank of Northern Eurasia, which represents the gene pools of the indigenous Eastern Europe population, were studied using two pharmacogenetic DNA marker arrays as follows: 60 most significant markers and 24 markers associated with CVDs. Using the multivariate statistics and genetic geography, a comparison of gene pool variation was made.Results. A cartographic atlas has been created that includes maps of the distribution among the Eastern Europe population of 24 pharmacogenetic CVD markers. These cartographic models allow various specialists to analyze patterns in the distribution of pharmacogenetic markers. General patterns are supplemented by regional studies in the North Caucasus, the Cisurals and the Russian Plain, which identify population groups with similar pharmacogenetic status. For each region, a comparison of gene pool variation for two arrays of above-mentioned DNA markers was made.Conclusion. The created atlas is the basis for the development of pharmacogenetic studies conducted by genetic geography methods using a single panel of markers and representative samples provided by population biobanks. The reliability of the results is ensured by a detailed genealogical and population annotation of each biobank sample and representative samples from the populations.