Genetic analysis of the grapevine genotypes of the Russian Vitis ampelographic collection using iPBS markers

Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

Use of retrotransposon based iPBS markers for determination of genetic relationship among some Chestnut Cultivars (Castanea sativa Mill.) in Türkiye

BACKGROUND

The aim of this study was to reveal the genetic relationships among some economically important chestnut cultivars for Türkiye by using retrotransposon-based inter primer binding site (iPBS) markers.

METHODS AND RESULTS

In this study, a total of 19 iPBS markers were used to determine the genetic relationships among 11 chestnut cultivars (Castanea sativa Mill.). In the study, chestnut cultivars named Hacıömer, Osmanoğlu, Sarıaşlama, Erfelek, Kemer, Işıklar, Şekerci, Siyah Bursa, Tülü, Bouche De Betizac and Marigoule were the preferred cultivars utilised. Using the online marker efficiency calculator (iMEC), some indices of polymorphism, such as the mean heterozygosity, polymorphism information content, marker index and discriminating power, were determined. In addition, the size ranges of alleles, number of average alleles, number of total alleles, number of polymorphic alleles, and polymorphism rate were determined at a successful level. The chestnut cultivars of Hacıömer and Şekerci were determined to be the most similar cultivars with a similarity coefficient value of 0.924, and they formed a subgroup together with the chestnut cultivars Osmanoğlu and Erfelek, showing close similarity with these two cultivars.

CONCLUSIONS

The use of iPBS markers in chestnuts in Türkiye was carried out for the first time in this study. The power of iPBS markers to evaluate the genetic relationship for our preferred chestnut cultivars was revealed. For this reason, it has emerged that it will be useful in the molecular characterization of both genotypes in natural chestnut populations and chestnut breeding materials such as varieties and cultivars in chestnut breeding programs.

Exploring the genetic diversity and population structure of upland cotton germplasm by iPBS-retrotransposons markers

BACKGROUND

Upland cotton is one of the utmost significant strategic fiber crops, and play a vital role in the global textile industry.

METHODS AND RESULTS

A total of 128 genotypes comprised Gossypium hirsutum L, Gossypium barbadense L., and pure lines were used to examine genetic diversity using iPBS-retrotransposon markers system. Eleven highly polymorphic primers yielded 287 bands and 99.65% polymorphism was recorded. The mean polymorphism information content was estimated at 0.297 and the average diversity indices for the effective number of alleles, Shannon's information index, and overall gene diversity were 1.481, 0.443, and 0.265, respectively. The analysis of molecular variance (AMOVA) revealed that 69% of the genetic variation was within the population. A model-based STRUCTURE algorithm divided the entire germplasm into four populations and one un-classified population, the genotypes G42 (originating in Egypt) and G128 (originating in the United States), showed the highest genetic distance (0.996) so these genotypes could be suggested for breeding programs as parental lines.

CONCLUSIONS

This is the first investigation using an iPBS-retrotransposon marker system to examine the genetic diversity and population structure of upland cotton germplasm. The rich diversity found in upland cotton germplasm could be exploited as a genetic resource when developing breeding programs and could also help with efforts to breed cotton around the world. These findings also show the applicability and effectiveness of iPBS-retrotransposons for the molecular characterization of cotton germplasm.

Genetic variation of Cerastium alpinum L. from Babia Góra, a critically endangered species in Poland

Babia Góra massif is the only site of occurrence of the Cerastium alpinum L. in Poland, an arctic-alpine perennial plant with a wide distribution in North America, northwestern Asia, and Europe. To determine whether the isolated Polish populations are genetically distinct, we have performed an evaluation of C. alpinum from Babia Góra with the use of iPBS markers. A total number of 133 individuals of C. alpinum from seven populations representing four localizations of the species were analyzed, i.e., from Babia Góra (Poland), Alps (Switzerland), Nuolja massif (Sweden), and Kaffiøyra (Svalbard, Norway). Genetic analysis of all C. alpinum samples using eight PBS primers identified 262 bands, 79.4% of which were polymorphic. iPBS markers revealed low genetic diversity (average H_e = 0.085) and high population differentiation (F_ST = 0.617). AMOVA results confirmed that the majority of the genetic variation (62%) was recorded among populations. The grouping revealed by PCoA showed that C. alpinum from Svalbard is the most diverged population, C. alpinum from Switzerland and Sweden form a pair of similar populations, whereas C. alpinum from the Babia Góra form a heterogeneous group of four populations. Results of isolation by distance analysis suggested that the spatial distance is the most probable cause of the observed differentiation among populations. Although significant traces of a bottleneck effect were noted for all populations of C. alpinum from Babia Góra, the populations still maintain a low but significant level of genetic polymorphism. These results are of great importance for developing conservation strategies for this species in Poland.

Agrobiological evaluations of newly introduced grapes varieties under climatic conditions of the south of Kazakhstan

Variety assortment enhancement is a normal task that involves enhancing the assortment's quality and upgrading varieties. The findings of a research of imported grape varieties in the southeast of Kazakhstan, namely in the Almaty region's bottom-mountain zone, are presented in this article. The onset and conclusion of the main phenological phases of a grape plant throughout the vegetative period were directly influenced by the climatic and meteorological conditions of this district. In comparison to the recognized variety Almaty early-maturing, it has been proven that types Priusadebny, Iyulsky, and Kuibyshevsk early-maturing have a high degree of eyes wintering buds and may provide a high-quality crop in this location.

Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity

Retrotransposable elements (RTEs) are highly common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The "copy-out and paste-in" life cycle of replicative transposition in these dispersive and ubiquitous RTEs leads to new genome insertions without excision of the original element. RTEs are important drivers of species diversity; they exhibit great variety in structure, size, and mechanisms of transposition, making them important putative components in genome evolution. Accordingly, various applications have been developed to explore the polymorphisms in RTE insertion patterns. These applications include conventional or anchored polymerase chain reaction (PCR) and quantitative or digital PCR with primers designed for the 5' or 3' junction. Marker systems exploiting these PCR methods can be easily developed and are inexpensively used in the absence of extensive genome sequence data. The main inter-repeat amplification polymorphism techniques include inter-retrotransposon amplified polymorphism (IRAP), retrotransposon microsatellite amplified polymorphism (REMAP), and Inter-Primer Binding Site (iPBS) for PCR amplification with a single or two primers.

Genetic Diversity and Pathogenicity of Rhizoctonia spp. Isolates Associated with Red Cabbage in Samsun (Turkey)

A total of 132 Rhizoctonia isolates were recovered from red cabbage plants with root rot and wirestem symptoms in the province of Samsun (Turkey) between 2018 and 2019. Based on the sequence analysis of the internal transcribed spacer (ITS) region located between the 18S and 28S ribosomal RNA genes and including nuclear staining, these 124 isolates were assigned to multinucleate Rhizoctonia solani, and eight were binucleate Rhizoctonia. The most prevalent anastomosis group (AG) was AG 4 (84%), which was subdivided into AG 4 HG-I (81%) and AG 4 HG-III (3%), followed by AG 5 (10%) and AG-A (6%), respectively. The unweighted pair group method phylogenetic tree resulting from the data of 68 isolates with the inter-PBS amplification DNA profiling method based on interspersed retrotransposon element sequences confirmed the differentiation of AGs with a higher resolution. In the greenhouse experiment with representative isolates (n = 24) from AGs on red cabbage (cv. Rondale), the disease severity index was between 3.33 and 4.0 for multinucleate AG isolates and ranged from 2.5 to 3.17 for AG-A isolates. In the pathogenicity assay of six red cabbage cultivars, one isolate for each AG was tested using a similar method, and all cultivars were susceptible to AG 4 HG-I and AG 4 HG-III isolates. Redriver and Remale were moderately susceptible, while Rescue, Travero, Integro, and Rondale were susceptible to the AG 5 isolate. The results indicate that the most prevalent and aggressive AGs of Rhizoctonia are devastating pathogens to red cabbage, which means that rotation with nonhost-crops for these AGs may be the most effective control strategy. This is the first comprehensive study of Rhizoctonia isolates in red cabbage using a molecular approach to assess genetic diversity using iPBS-amplified DNA profiling.

DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan's Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

Differences between microbiota, phytochemical, antioxidant profile and dna fingerprinting of cabernet sauvignon grape from Slovakia and Macedonia

This study aimed to evaluate the microbiota, phytochemical, antioxidant profile and DNA fingerprinting of Cabernet Sauvignon grapes from Slovakia and R. North Macedonia. There were used two samples of grape berries (one sample from Slovakia and one from Macedonia). Each sample was analyzed in triplicate. The bacteria were cultivated on Plate count agar (PCA), microscopic filamentous fungi were cultivated on Malt extract agar (MEA). MALDI-TOF MS Biotyper mass spectrometry was used for the identification of microorganisms (bacteria and yeasts) and microscopic filamentous fungi with manuals. DPPH method was used to determine of antioxidant activity of grape berries. Phytochemical and antioxidant profiles were evaluated in grape berries samples. Total genomic DNA was extracted from mature grapes by GeneJET Plant Genomic DNA Purification Kit. The number of bacteria was higher in the sample of Macedonian grape (4.13 log CFU.g-1) in comparison to the grape from Slovakia as well as the number of yeasts was also higher in the Macedonian sample (2.57 log CFU.g-1). Antioxidant activity of Slovak grape berries was 0.55 mg TEAC.g-1 and of Macedonian grape, berries was 0.51 mg TEAC.g-1. Total polyphenol content was higher in grape from Slovakia (0.81 mg GAE.g-1) than in grape from Macedonia (0.77 mg GAE.g-1), while total flavonoid content was 0.57 and 0.17 mg QE.g-1 in Slovak grape and Macedonian grape, respectively. Total phenolic acid content was higher in the sample from Macedonia (0.40 mg CAE.g-1) compared to the grape from Slovakia (0.24 mg CAE.g-1). Total anthocyanin content was also higher in Macedonian grape (0.46 mg.g-1) compared to the Slovak sample (0.05 mg.g-1). The total polymorphism for all of the used primers of 87.5% was obtained for the Macedonian sample of Cabernet Sauvignon and 89.4% for the Slovak sample.

DNA-based genealogy reconstruction of Nebbiolo, Barbera and other ancient grapevine cultivars from northwestern Italy

Northwestern Italy is a wine region of the world with the highest of reputations, where top quality wines of remarkable economic value are produced from traditional, long-cultivated varieties. Kinship analyses were performed using 32 microsatellite loci and more than 10 K single-nucleotide polymorphism markers on 227 traditional grapes mostly from Northwestern Italy—including those that have been neglected or are threatened. This was done to better understand the genetic grapevine origins and history of this reputable wine producing area, thus enhancing its cultural value and the marketing appeal of its wines. The work revealed a complex network of genetic relationships among varieties, with little contribution of genotypes from other areas. It revealed the major role played by a few ancient grape varieties as parents of numerous offspring, including some that are endangered today. The ancestry of many cultivars is proposed. Among these are Dolcetto, Barbera and Riesling italico. Through the inference of parent–offspring and sibling relations, marker profiles of ungenotyped putative parents were reconstructed, suggesting kinship relations and a possible parentage for Nebbiolo, one of the most ancient wine grapes worldwide. Historic and geographic implications from the resulting kinships are discussed.

Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India

10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.

Genetic diversity of Alternaria species associated with black point in wheat grains

The genus Alternaria is a widely distributed major plant pathogen that can act as a saprophyte in plant debris. Fungi of this genus frequently infect cereal crops and cause such diseases as black point and wheat leaf blight, which decrease the yield and quality of cereal products. A total of 25 Alternaria sp. isolates were collected from germ grains of various wheat cultivars from different geographic regions in Kazakhstan. We investigated the genetic relationships of the main Alternaria species related to black point disease of wheat in Kazakhstan, using the inter-primer binding site (iPBS) DNA profiling technique. We used 25 retrotransposon-based iPBS primers to identify the differences among and within Alternaria species populations, and analyzed the variation using clustering (UPGMA) and statistical approaches (AMOVA). Isolates of Alternaria species clustered into two main genetic groups, with species of A.alternata and A.tennuissima forming one cluster, and isolates of A. infectoria forming another. The genetic diversity found using retrotransposon profiles was strongly correlated with geographic data. Overall, the iPBS fingerprinting technique is highly informative and useful for the evaluation of genetic diversity and relationships of Alternaria species.

High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

Maize is one of the world's most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.