Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

Population genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

Exploring Project-Based Teaching for Engaging Students' Mathematical Learning

The declining interest of learners in mathematics in the learning process has resulted in poor achievement (Yeh et al., 2019). To get rid of these poor achievements, we explored project-based teaching in four topical areas (e.g., mathematical concepts of coordinate geometry, trigonometry, sequence, and series) in the school mathematics. This paper results from observing changes in engagement of learners in learning mathematics by motivating them through the project-based learning (PBL) guided by two theories – knowledge constitutive interests (Habermas, 1972), and collaborative and cooperative learning under the paradigms of interpretivism and criticalism. In this ethos, PBL is an “engaging and learner-directed approach that provides equal opportunities for students to explore their knowledge and understanding” (Thomas, 2000, p. 12). More specifically, we adopted the 'action research' method with the secondary level students (Grade IX) of one of the institutional schools in their classrooms. The information was collected by observing and recording the changes seen in consecutive seventeen days. The research landed that project-based learning is an appropriate pedagogy for engaged learning. The study revealed that the students were motivated while they got opportunities to interact in the projects. Moreover, the findings show that PBL is helpful to engage the learners through questioning, pair/group discussion, discovery learning, and concept mapping.

Revealing Genetic Diversity, Population Structure and Cultivar-Specific SSR Alleles in Pistachio Using SSR Markers

Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and one of the most important nut crop in terms of production. Pistachio cultivars have significant level of variation in their phenotypic appearance and productivity. Understanding the genetic diversity between pistachio cultivars could facilitate breeding programs. Simple sequence repeat (SSR) markers are powerful tools in genetic diversity and germplasm collection studies. However, published information about the characterization of large scale pistachio cultivar germplasm with adequate number of SSR markers is limited. In this study, sixty-six pistachio cultivars and genotypes originated from six different countries were characterized and fingerprinted by 74 genomic and 18 genic SSR markers. SSR analysis identified 576 alleles for all 66 cultivars and genotypes. The number of alleles per locus ranged from 2 to 20 (CUPOhBa1592) alleles with a mean value of six alleles per locus. The polymorphism information content (PIC) values ranged from 0.07 (CUPVEST2939) to 0.87 (CUPSiOh2460) with a mean PIC value of 0.58. The pistachio cultivars and genotypes were divided into five clusters according to Structure and UPGMA (Unweighted Pair Group Method with Arithmetic Average) analysis. Total of 61 cultivar specific alleles were detected in 34 cultivars, among them three primers (CUPOhBa1592, CUPBaPa1606 and CUPOhBa2127) produced more than four cultivar-specific loci therefore very promising for cultivar identification, fingerprinting and breeding studies in pistachio.

Characterization of Fusarium Spp. Inciting Vascular Wilt of Tomato and Its Management by a Chaetomium-Based Biocontrol Consortium

Though the vascular wilt of tomato caused by the species of Fusarium is globally reported to be a complex disease in certain countries, for example, India, our studies indicated that the disease is caused by either Fusarium oxysporum f. spp. lycopersici (Fol) or Fusarium solani (FS) with the Fol being widely prevalent. In assessing the genetic diversity of 14 Fol strains representing the four Indian states by the unweighted pair group method with arithmetic averaging using Inter Simple Sequence Repeat (ISSR) amplicons, the strains distinguished themselves into two major clusters showing no correlation with their geographic origin. In pot experiments under polyhouse conditions, the seed dressing and soil application of a talc-based formulation of a biocontrol treatment, TEPF-Sungal-1 (Pseudomonas putida) + S17TH (Trichoderma harzianum) + CG-A (Chaetomium globosum), which inhibited Fol, was equally effective like the cell suspensions and was even better than the fungicidal mixture (copper oxychloride-0.25% + carbendazim-0.1%) in promoting the crop growth (52.3%) and reducing vascular wilt incidence (75%) over the control treatment, despite the challenge of inoculation with a highly pathogenic TOFU-IHBT strain. This was associated with significant expressions of the defense genes, indicating the induction of host resistance by a biocontrol consortium. In field experiments on two locations, the bioconsortium was highly effective in recording maximum mean fruit yields (54.5 and 60%) and a minimum mean vascular wilt incidence (37.5%) in comparison to the untreated control. Thus, Chaetomium-based bioconsortium demonstrated consistency in its performance across the two experiments in 2 years under the two field conditions.

Variation and Phenetic Relationship of Tobacco (Nicotiana tabacum L.) In Central Java and Yogyakarta Based on Morphological Characters

Tobacco (Nicotiana tabacum L.) is a plant used as a mixture of cigarettes, and recreational media especially for men. This study aimed to identify variations, and determine the relationship between tobacco cultivars in Central Java and Yogyakarta based on macromorphological and micromorphological characters. Sampling locations are determined by surveying locations in both regions. Tobacco samples found include 5 cultivars in Central Java namely 'Mantili', 'Uler Magetan', 'Garut', ‘Gober Boyolali’, 'Manila', and 3 cultivars in Yogyakarta namely 'Siluk', 'Java', and 'Virginia'. Characterization with 23 qualitative macromorphological characters including leaves, and stems, with 9 qualitative and quantitative micromorphological characters including trichome and stomata. Descriptive data analysis is done to obtain the typical character of each cultivar, followed by numerical analysis including scoring characters processed with MVSP (Multi Variate Statistical Package), clustering with UPGMA (Unweighted Pair Group Method with Averages), and calculation of similarity coefficients with Simple matching formula. The results showed variations in the macromorphological characters including the shape of the leaf lamina, the base of the leaf, the absence of leaf stalks, and type of leaf venation. Tobacco has anisositic stomata, and varies in terms of length, width, and density of stomata. Tobacco trichomes are glandular. The result dendrograms form two clusters (A and B) with the similarity index of each cluster above 0.80. Cultivars with close relationships such as 'Siluk'-'Java', and far relationship like 'Java'-'Manila'.

Number of Experiments that Should be Considered in the Cluster Analysis of Common Bean Genotypes for Plant Architecture and Grain Yield Traits

The number of experiments that allows the choice of parents to be used in controlled crossings in a more assertive way in cluster analysis is unknown for plant architecture and grain yield traits in common bean. Therefore, the objective of this work was to determine the number of experiments that should be considered in Tocher's and the unweighted pair group method with arithmetic mean (UPGMA) cluster analyses to identify promising common bean parents for several plant architecture and grain yield traits. Four experiments were carried out in different years and growing seasons, in the same site. The randomized block design was used and 17 common bean genotypes with carioca (beige seed coat with brown streaks) and black grains were evaluated in relation to 12 traits related to plant architecture and five traits related to grain yield. Statistical analyses were performed with data obtained from individual and combined experiments. Significant genotype × experiment interaction was observed for most of the evaluated traits. When Tocher's and UPGMA cluster analyses was performed from data obtained in individual experiments different groups were formed. The use from data obtained in two, three ou four experiments allowed greather reliability in the formation of groups. Three and two experiments are sufficient in the Tocher's and the UPGMA cluster analyses, respectively, to identify promising carioca and black common bean parents for several plant architecture and grain yield traits in a more assertive way.

Microbial Community Structure and Its Driving Environmental Factors in Black Carp (Mylopharyngodon piceus) Aquaculture Pond

This study focused on monitoring the dynamics of bacterial communities and assessment of the influences of physicochemical parameters during a culture cycle in black carp polyculture ponds. Our results showed high variation in microbial diversity and microbial composition in the water column during the culture period. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla, while the abundances of the phyla Cyanobacteria, Firmicutes, and Bacteroidetes changed in different months. Moreover, 13 abundant genera with significant difference were found between different months. Thus, samples in different months were divided into three groups according to principal coordinate analysis (PCoA) and unweighted pair-group method (UPGMA) clustering results. RDA showed that total nitrogen (TN), total phosphorus (TP), phosphate (PO43−-P), nitrate (NO3−-N), temperature (T), dissolved oxygen (DO), and pH significantly shaped the microbial community composition in different months. While Pearson correlation coefficient showed that T, SD, and pH were strongly correlated to the dominant genera. Considering some genera are potential pathogenic bacteria, we could manage the black carp pond by quickly monitoring the water temperature and SD in the future.

GENETIC DIVERSITY OF LIMA BEAN (PHASEOLUS LUNATUS L.) FROM TIMOR ISLAND BASED ON MOLECULAR MARKER INTER-SIMPLE SEQUENCE REPEATS (ISSR)

Lima bean (Phaseolus lunatus L.) is one of the important legume vegetables in Indonesia. However, genetic information for these plants is still minimalized, especially on Timor Island. This study aims to analyze the genetic diversity of lima beans from Timor Island based on ISSR molecular markers. A total of 4 accessions of lima beans were analyzed using 3 ISSR primers to produce 15 polymorphic bands with an average of 68.18% polymorphism. The cluster analysis results use the Unweighted Pair Group Methods using Arithmetic averages (UPGMA) method to create a dendrogram that produces two main clusters. There were plain seed and pattern seed group with a similarity coefficient of 0.52. These results indicated that the genetic variation of the lima beans from Timor Island was high. Moreover, the result provides a sutable method for evaluating the genetic diversity of lima beans using the ISSR marker and important information of future lima bean breeding programs.

Geographical Survey and Genetic Variation Studies of Few Chilly Varieties Collected from Different Regions of Karnataka, India

Chillies are widely used throughout the world in the form of spice and are also used in making beverages and medicines. They are rich in vitamins, especially in vitamin A and C. Chillies contain lots of minerals like potassium, magnesium, and iron. They have been employed for pain relief as they are known to inhibit pain messengers and hence their extracts are used to alleviate the pain of arthritis, headaches, burns, and neuralgia. It is also claimed that they have the power to boost the immune system and lower cholesterol. They are also helpful in getting rid of gut parasites. In this regard we attempted to do a geographical survey about the chilly varieties and chilly growing states in India. We collected the local varieties of chillies available in Karnataka and performed genetic variation studies to understand their relationship at the genetic level. PCR analysis was done using the selected random amplified polymorphic DNA (RAPD) marker to identify the polymorphic loci between the genotypes taken. DNA Barcoding was done to validate the species using basic local alignment search tool (BLAST) and Clustal Omega, further dendrogram was constructed which guide the joining linkage rule of unweighted pair group average (UPGMA) and the genetic distance to compute from matrix table. The results obtained highlight the relationship between species of Capsicum annum, Capsicum frutescens which are closely related followed by Capsicum pubescens and Capsicum baccatum providing knowledge about its application in genetics and plant breeding in developing efficient hybrid variety.

Analysis of Genetic Variability Amongst Polyploid Genotypes of Pteris vittata L. From Various Geographic Locales of India

Pteris vittata L. is very common and a widely distributed species belongs to the family Pteridaceae. Various cytotypes from diploid to octaploid is available in this fern species. The present work has been carried out for genetic diversity in this fern both within and between the cytotypes. The molecular analysis at inter- as well as intra-species has been carried out with 57 accessions of P. vittata as well as of other species of Pteris with Microsorium punctatum considered as an out group taxon. For the present study 48 P. vittata (36 tetraploid and 12 pentaploid) and five of other species (four P. cretica, one P. pellucida, one P. tremula, one P. quadriaurita, and two P. ensiformis) accessions were used. The UPGMA (unweighted pair group method with arithmetic mean) dendrograms were generated for each method separately, as well as for all methods cumulatively, after a 1000 replicate bootstrap analysis. In order to determine the utility of each of the method, a comparative statistical assessment was done and marker index (MI), expected average heterozygosity, fraction of polymorphic loci and effective multiplex ratio (EMR) were calculated in case of each of the methods used in the present study. At the level of individual methods highest MI was obtained for directed amplification of minisatellites DNA (DAMD) method. Our findings of the present study concluded that out of the three methods Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR), and Directed Amplification of Minisatellite DNA (DAMD), DAMD was the best in term of polymorphism and heterozygosity as scores exhibited highest MI. The different accessions of P. vittata collected from different phytogeographical regions falls into six groups. Out of six clusters, one cluster is of pentaploid cytotype, four clusters are of tetraploid cytotype and one for outgroup taxon (M. punctatum). The result thus showed that within tetraploid, heterozygosity with variable genomic structure exists.