Thelytokous Reproduction of Onion Thrips, Thrips tabaci Lindeman 1889, Infesting Welsh Onion and Genetic Variation among Their Subpopulations

Parthenogenesis is not uncommon in thrips. This asexual reproduction produces males (arrhenotokous) or female (thelytokous). Only females are found in the onion thrips (Thrips tabaci Lindeman 1889) infesting Welsh onion (Allium fistulosum) in several areas of Korea. To determine the reproduction mode of T. tabaci, thrips infesting Welsh onion were collected from different localities in Korea. Cytochrome oxidase I (COI) sequences were then assessed. Results showed that all test local populations had signature motif specific to a thelytokous type. These COI sequences were clustered with other thelytokous populations separated from arrhenotokous T. tabaci populations. In a laboratory test, individual rearing produced female progeny without any males. These results support that Korean onion thrips infesting Welsh onion have the thelytokous type of parthenogenesis. Local thrips populations exhibited significant variations in susceptibility to chemical and biological insecticides. Random amplified polymorphic DNA (RAPD) analysis indicated genetic variations of local populations. However, the genetic distance estimated from RAPD was independent of the actual distance among different local populations. These results suggest that genetic variations of T. tabaci are arisen from population subdivision due to asexual thelytokous reproductive mode.

The Efficiency of Long Primers Compared to The Short Primer for RAPD Technique in Date Palm

Random Amplified Polymorphic DNA (RAPD) applies single arbitrary short primers (8-12nucleotides) to produce many amplified discrete DNA. Limited reports and studies were done onthe use of long primers (over 12 bases). This study was performed to investigate the potential valueof long primers (15-21 bases) for generating RAPD polymorphisms. We compared both short andlong primers in RAPD assays of two date palm cultivars grown in Malaysia: Ajwa and Barhi. Thenumber of produced polymorphic fragments ranged in order from 2 and 38 bands for short andlong primers in Ajwa. Meanwhile, more polymorphic fragments were generated by long primersin Barhi, which were 50 and only five bands for short primers. 18-mer GY107 and 20-mer CO4primers yielded 100% polymorphism in Ajwa and Barhi, respectively. Moreover, long primersproduced more DNA fragments and a wider range of DNA fragment sizes (from 140-1600 bp,with respect to 300-1000 bp obtained with 10-mer primers). Hence, a significant correlation wasobserved between primer length and the number of polymorphic fragments within the long primergroup, suggesting that increasing primer length above 15 bases may demonstrate enhancedproduction of more polymorphism.

Morphoagronomic and molecular characterization of Euterpe oleracea accessions from eastern Brazilian Amazon

Açaí (Euterpe oleracea Mart.) - a common tropical palm has high social, economic, and environmental importance in the Amazon region. In the light of increasing exploration to obtain the fruit and heart of this palms, comprehensive studies are warranted for conservation and genetic improvement. Here, we characterized açaí accessions using phenological, morphological, and agronomic descriptors and random amplified polymorphic DNA (RAPD) molecular markers for joint selection of accessions with greater productivity. Hundred accessions were analyzed using 18 morphoagronomic descriptors and 13 RAPD markers. The spathe and inflorescence emission phases during flowering and fruiting showed seasonality. Based on the coefficient of variation and mean squared error, the accessions exhibited high variability in the tested morphoagronomic descriptors and were distributed into seven groups. Fruit, seed, and pulp weights were important descriptors for the distinction of accessions and identification of those with greater productivity. The accessions presented >85% similarity, and 85 accessions, distributed in nine subgroups, could not be differentiated using RAPD markers. There was no correlation between grouping based on morphometric descriptors and RAPD markers. Panicle weight was 3.9-9.0 kg in 15 accessions and 100-fruit pulp weight was 35-50 g in six accessions. Therefore, accessions with high productivity could be selected.

Bacillus cytotoxicus Genomics: Chromosomal Diversity and Plasmidome Versatility

Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.

A Study on the Clustering of Extra Virgin Olive Oils Extracted from Cultivars Growing in Four Ionian Islands (Greece) by Multivariate Analysis of Their Phenolic Profile, Antioxidant Activity and Genetic Markers

Background: The phenolic fraction of extra virgin olive oil (EVOO) has disease preventive and health-promoting properties which are supported by numerous studies. As such, EVOO is defined as a functional food. The aim of the present study was to characterize the phenolic profile of olive oil from cultivars farmed in the Ionian Islands (Zakynthos, Kefalonia, Lefkada, and Kerkyra) and to investigate the association of phenols to antioxidant activity, which is central to its functionality. Furthermore, the study investigates whether multivariate analyses on the concentration of individual biophenolic compounds and genetic population diversity could classify the olive oil samples based on their geographic origin. Methods: Phenols were determined in 103 samples from different Ionian Island tree populations by 1H nuclear magnetic resonance (NMR), and sample antioxidant activity was measured by their capacity to reduce the free radical 2,2-diphenyl-1-picrylhydrazyl) (DPPH). Genetic diversity was measured by estimating Nei’s population genetic distance using 15 reproducible bands from random amplified polymorphic DNA (RAPD) genotyping. Results: Principal component analysis (PCA) of the secoiridoid concentrations clustered samples according to cultivar. Clustering based on genetic distances is not concordant with phenolic clustering. A cultivar effect was also demonstrated in the association between the concentration of individual phenols with DPPH reducing activity. Conclusions: Taken together, the study shows that the olive oil phenolic content defines “cultivar-specific phenolic profiles” and that environmental factors other than agronomic conditions contribute more to phenotype variance than genetics.

Functional Characteristics and Molecular Identification of Interspecific Hybrids from Genus Capsicum

The taxonomy of the genus Capsicum has distinguished more than twenty species of peppers with only C. annuum L. being a vegetable of economic importance. The remaining species can, however, be used in breeding via interspecies hybridization as a source of valuable functional traits. The aim of the study was to obtain interspecific hybrids of peppers with increased agronomic potential and their molecular identification. Based on their agromorphological characteristics, the obtained hybrids (‘Anchi’ × C. frutescens L.)F1 and (‘Anchi’ × C. baccatum var. pendulum)F1 formed fruits that had the combined functional traits typical of the cultivar ‘Anchi’, with a high content of soluble solids, and the wild species, with dry matter. To identify hybrids and their parental forms, the random amplified polymorphic DNA polymerase chain reaction (PCR-RAPD) and inter simple sequence repeat polymerase chain reaction (PCR-ISSR) techniques were used. The polymorphic products obtained in both methods totalled 65% and 59%, respectively, and they allowed for the identification of all tested genotypes, excluded the possibility of self-pollination of ‘Anchi’ plants, and confirmed the hybrid characteristics of the crossbreed (‘Anchi’ × C. frutescens L.)F1.

Biodiversity of Soil Bacterial Communities from the Sasso Fratino Integral Nature Reserve

The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable and the total bacterial community of soil samples from the reserve in terms of taxonomy, composition, and structure. Seven soil samples were collected at different altitudes, and the chemical composition, the total and the cultivable microbiota, and the antibiotic resistance profiles of isolates were investigated. Total bacterial communities, studied through Next Generation Sequences analysis, included 390 genera. Samples differed in terms of microbial composition basing on the different altitude/vegetation of collection points. Random Amplified Polymorphic DNA Analysis (RAPD) allowed to identify 82 haplotypes out of 158 bacterial isolates. The taxonomic identification through 16S rDNA sequencing revealed that the strains were affiliated to 21 genera. Antibiotic resistance profiles of bacteria were also investigated, highlighting a high resistance against streptomycin and kanamycin. This work represents the first description of the soil bacterial community from the Natural Reserve of Sasso Fratino, and it is the first study considering the soil microbiota of an Italian integral nature reserve.

Establishment of an Efficient Micropropagation System for Humulus lupulus L. cv. Cascade and Confirmation of Genetic Uniformity of the Regenerated Plants through DNA Markers

The demand for virus-free hop planting material has increased in the last few years due to its multipurpose uses. The present study aimed to establish an effective protocol for clonal propagation of cv. Cascade using only the cytokinins as PGRs in all stages of micropropagation: (i) in vitro culture initiation using single-node micro-cuttings inoculated on modified Murashige and Skoog (MSm) medium solidified with Plant agar and supplemented with 0.5 mg L−1 6-benziyladenine (BA) with 76% recorded viability of nodal explants; (ii) in vitro multiplication of multinodal shoots on MSm medium gelled with Plant agar and supplemented with different types and concentrations of cytokinins: 2 mg L−1 kinetin (KIN), 0.7 mg L−1 1-(2-Chloro-4-pyridyl)-3-phenylurea) (1 CPPU), 2 mg L−1 meta-topoline (mT) and 0.5 mg L−1 BA, which was the best variant for shoot proliferation (9.48 ± 0.78 shoots/explant); (iii) rooting and acclimatization with the best results obtained by ex vitro rooting and acclimatization of plants in the same stage in perlite (96.00 ± 0.60% acclimatized rooted plants with 100% survival under greenhouse conditions). The true-to-type nature of in vitro raised plants with the mother plant was assessed by Random Amplified Polymorphic DNA (RAPD) and Start Codon Target Polymorphism (SCoT) molecular markers, and then their genetic uniformity were confirmed.

Genetic diversity analysis of lactic acid bacteria isolated from regional yogurt samples

Probiotics are live, non-pathogenic microorganisms which have enormous health benefits. Yogurt is a potential source of probiotic bacteria. Lactic acid bacteria are the most common and major group of probiotic bacteria that can be found easily in different dairy products. The aim of study was the genetic diversity analysis using random amplified polymorphic DNA (RAPD) marker from regional yogurt samples of Bangladesh. Ten probiotic isolates from yogurt samples of different sweet meat shops of Sylhet and Mymensingh Divisions of Bangladesh were used. Morphological and biochemical tests were performed to ensure the presumptive probiotic characteristics of isolated bacteria. All isolates were cultured in De Man, Rogosa, and Sharpe (MRS) medium to exhort the growth of lactic acid bacteria. Genomic DNA was extracted by Ampicillin Lysozyme Tandem method. Four random RAPD primers were used in this study for detecting genetic diversity of these isolated bacteria. Among them, OPA 18 showed the maximum number of reproducible bands. Nei’s genetic distance was performed for determining Pair-wise Genetic Distance. UPGMA and NJ dendrogram were performed based on molecular data showing that all the isolates could be divided into two major clusters. Data analysis revealed that isolates from the same location were closely related and showed less genetic variation whereas, isolates from geographically different regions exhibited more genetic diversity. Bang. J. Livs. Res. Vol. 27 (1&2), 2020: P. 55-63

RAPD primer screening as a preliminary study to analyze the genetic diversity of Citrus spp. in South Sulawesi, Indonesia

The typical citrus germplasm collection in South Sulawesi has not been thoroughly characterized, especially in several citrus development centers, which have begun to be promoted again after the decline in productivity due to CVPD infection. The study of citrus diversity is very important to support future citrus breeding programs. Random amplified polymorphic DNA (RAPD) has been widely used for the analysis of genetic diversity among species in populations. In this study, 23 RAPD primers were used on Citrus cultivated in Selayar and Pangkep Regencies, which are citrus development areas in South Sulawesi. A total of 19 primers (OPA-05, OPA-09, OPA-17, OPC-09, OPC-17, OPE-04, OPH-04, OPH-15, OPN-14, 0PN-16, OPR-08, OPR-20, OPW-06, OPW-09, OPX-07, OPX-11, OPX-17, UBC-18, and UBC-51) can form polymorphic bands in randomly selected DNA samples. Monomorphic bands were formed by OPA-12 and OPD-07 primer in 12 samples. The primers OPX-13 and OPX-16 produced unclear bands. These 19 primers can be used to amplify DNA and determine the genetic diversity of Citrus in further analysis.