Isolation, identification, and study of the genetic diversity between three entomopathogenic nematodes belonging to Heterorhabditis sp. using ISSR technique

Background Entomopathogenic nematodes (EPNs) are widely used in biological control for soil-dwelling stages of many insect pests that are characterized by their safety to most non-target organisms and to the environment. Results The objectives of the present study were isolation of EPNs from agricultural soil in Egypt for further use in biological control programs and study the genetic variation among them using the molecular marker inter-simple sequence repeats (ISSR). Three out of 25 soil samples collected from fields cultivated with strawberry, tangerine, and pumpkin were positive for the presence of EPNs, using the Galleria baiting technique. Sequencing of the internal transcribed spacer (ITS) region indicated that the isolates obtained belong to Heterorhabditis sp. The ITS sequences were submitted to the National Center for Biotechnology Information (NCBI) and registered under accession nos. MH553165, MH553168, and MH553169. Six ISSR primers were used. The numbers of polymorphic bands were 42 out of 56, and the polymorphism percentage was 75%. The highest number of bands was 12 bands generated by primer ISSR8 followed by UBC-809 (11 bands) while recorded the lowest band number (4 bands), the percentage of polymorphism ranged from 40% (ISSR1) to 100% (ISSR6). Conclusion ISSR marker can be considered a good marker to study genetic diversity and detecting the genetic polymorphism among the nematodes species.

Comparison of Sunn Pest Damage and Genotypic Differences in Bread Wheat Varieties by SDS-Page Analysis

The research was carried out in five different locations in 2010 and 2011 years under in the ecological conditions of Hayrabolu, Malkara, Suleymanpasa, sarköy and Saray district. Twenty-three bread wheat varieties were used as material in the study. the study carried out in the same area was made up of 2 different growing conditions, namely field conditions and a covered area covered with sunlight. The sunn pest damage rates in wheat varieties grown in the open area were ranged from of 6.0. to 0.10 %. The sunn pest damage rates in bread wheat varieties grown in closing area was changed between 10.37 to 23.17% with a significant increase. the average of the highest sunn pest damage in two years was observed the numbered 15, 10, 1, 11 and 16 cultivars, while the lowest values was obtained form 4, 13, 8 and 3 varieties According to the SDS-PAGE analysis in order to determine the genotypic differences of bread wheat varieties, protein band number in bread wheat varieties was ranged from 17 to 21, the density and molecular weight of protein bands were significant differences among the varieties. Protein bands are distributed predominantly in the omega region while in the gamma and beta regions a small number of bands were observed. There are no bands in bread wheat varieties in the alpha region.

Development of polymorphic EST-SSR markers and characterization of the autotetraploid in sainfoin (Onobrychis viciifolia)

Background: Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods: In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using denovo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results: Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion: Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

Development of polymorphic EST-SSR markers and characterization of the autotetraploid in sainfoin (Onobrychis viciifolia)

Background: Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods: In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using denovo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results: Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion: Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

Genotyping via Sequence Related Amplified Polymorphism Markers in Fusarium culmorum

Fusarium culmorum is predominating causal agent of head blight (HB) and root rot (RR) in cereals worldwide. Since F. culmorum has a great level of genetic diversity and the parasexual stage is assumed for this phytopathogen, characterization of isolates from different regions is significant step in food safety and controlling the HB. In this study, it was aimed to characterize totally 37 F. culmorum isolates from Turkey via sequence related amplified polymorphism (SRAP) marker based genotyping. MAT-1/MAT-2 type assay was also used in order to reveal intraspecific variation in F. culmorum. MAT-1 and MAT-2 specific primer pairs for mating assays resulted in 210 and 260 bp bands, respectively. 11 of isolates were belonged to MAT-1 type whereas 19 samples were of MAT-2. Remaining 7 samples yielded both amplicons. Totally 9 SRAP primer sets yielded amplicons from all isolates. Genetic similarity values were ranged from 39 to 94.7%. Total band number was 127 and PCR product sizes were in the range of 0.1-2.5 kb. Amplicon numbers for individuals were ranged from 1 to 16. According to data obtained from current study, SRAP based genotyping is powerful tool for supporting the data obtained from investigations including phenotypic and agro-ecological characteristics. Findings showed that SRAP-based markers could be useful in F. culmorum characterization.

Genetic Diversity in Haploid Nicotiana alata Induced by Gamma Irradiation, Salt Tolerance and Detection of These Differences by RAPD

Haploid plants of Nicotiana alata were cultured in vitro on MS medium with IAA + KIN. The resulting plantlets were irradiated using gamma radiation doses of 10, 15, 20 and 25 Gy. Single node pieces were cut and transferred onto fresh MS medium. Gamma radiation doses caused the death of 9% and up to 28% of explants. NaCl concentrations caused the death of 8% up to 36% of explants, while the combined effect between gamma radiation doses and salinity had an impact suffused on the percentage of survival. The combined effect of gamma radiation doses 20 Gy and 25 Gy on NaCl concentrations of 100, 150 and 200 mM were deadly. Even more, the combined effect of gamma radiation doses and salinity had a severe negative impact on both the proline content and total soluble protein. Random amplified polymorphic DNA (RAPD) analysis was used to determine the degree of genetic variation in treated haploid Nicotiana alata plants. Total genomic DNAs from different haploid plantlets treated were amplified using five arbitrary primers. Two hundred and seventy bands were detected from plantlets irradiated with doses of 15, 20 and 25 Gy, with polymorphic band number 226 (83.7%). The total number of bands resulted from plant grew on 150 mM and 200 mM NaCl were 260 bands with polymorphic bands 185 (85.6%). However, the total number of bands produced from combined effects between gamma rays and salinity (20 Gy X 50 mM NaCl, 20 Gy X 100 mM NaCl and 25 Gy X 50 mM NaCl) were 270, with polymorphic band number 231 (85.5%). High similarity between treatments was revealed. Treatments relationships were estimated through cluster analysis (UPGMA) based on RAPD data.

Design of Digital Channelizer Based on Source Number Estimation

Digital channelizer is used to separate the sub-band signals contained within a wideband intermediate frequency (IF) received signal. This paper presents a structure of digital channelizer which is built upon estimation of the sub-band signal number. The proposed structure is designed by employing nonuniform filter banks (NUFBs), which are implemented by merging the adjacent sub-branches of the perfect reconstruction (PR) cosine modulated filter banks (CMFBs). Using source number estimation algorithm, the estimated value of sub-band number can be obtained. By energy detection, the energy characteristic of the analysis filter banks (AFBs) can be acquired and another value of sub-band number is calculated. Comparing the estimated value and the calculated one, we can evaluate whether the design of the AFB is suitable for the received signal. The structure of digital channelizer proposed by this paper provides a potential way to channelize the unknown signal and suggests a solution for the dynamic channelizaiton. A design example is also presented to demonstrate the feasibility and simplicity of this method.