Plant Molecular Biology Reporter

An assay was performed to identify the antibiotics that are most effective againstAgrobacterium tumefaciens strains EHA101 and LBA4404, and to determine if these antibiotics inhibited tobacco callus and shoot formation. We tested ten antibiotics: cefotaxime, carbenecillin, erythromycin, spectinomycin, polymixin B, chloramphenicol, methicillin, Augmentin 500, Augmentin 250, and moxalactam. The effectiveness of each antibiotic against the two strains was determined by measuring the zones of inhibition of bacterial growth in a disk-diffusion assay. The five antibiotics that generated the largest zones of inhibition for each strain were assayed to determine their effects on callus formation. Cefotaxime was the most active antibiotic tested against strain LBA4404, and moxalactam was the most effective antibiotic against EHA101. Both cefotaxime and moxalactam had little or no effect on callus development.

Nếu các lạp thể được tinh chế trên các gradient sucrose được xử lý trong 10 phút ở 4°C với 2 M NaCl, sau đó được ly tâm với lực 1000-g, ô nhiễm DNA từ nhân tế bào giảm từ 1.5 đến 3 lần như được ước tính bằng phương pháp đo mật độ quang.

Somaclonal variant CIEN BTA-03 resistant to yellow Sigatoka was obtained from a susceptible banana clone (Williams clone), by increasing the production of adventitious buds using 6-Belcilaminopurine at high concentrations. This somaclone has exhibited yellow Sigatoka resistance in the field for five consecutive years of asexual reproduction. We used RAPD markers to generate characteristic “fingerprints” for each probe, concluding that they are reliable tools for evaluating the genetic variability ofMusa regenerants obtained byin vitro culture.

The improvement of commercial maize lines via biotechnological approaches is limited by the lack of a transformation system that is tissue culture free. In this paper, the development of a genetic transformation system is presented using electroporation for gene delivery and seed-derived embryo as the gene target. Plasmid DNA (pBARGUS), which contained the selectablebar gene for resistance to the herbicide Basta and the screenablegus gene, was delivered into enzymatically wounded mature maize embryos via electroporation. Transformed plants were identified by their ability to grow on a selective medium containing 30 mg/L of phosphinothricin. Southern hybridization, plant resistance to the application of Basta, GUS expression, and segregation analysis indicated that a functionalbar gene had integrated into the maize genome and was inherited in a mendelian fashion by the progeny.

Mitochondrial (mt) DNA structure in higher plants is still unclear as to the circularity or linearity of the genome. We have developed a system to electrophoretically separate distinct populations of mtDNA, with some populations enriched for networked linear and circular DNA molecules. Using field inversion gel electrophoresis (FIGE) and electron microscopy (EM), we have identified four distinct populations of mtDNA from two Brassica species. Using FIGE, two slow migrating mtDNA populations ran faster than a 66 kbp Escherichia coli circular plasmid marker, while these same populations comigrated in the compression zone in contour-clamped homogeneous electrophoretic field (CHEF) gels. A fast-migrating mtDNA population was also resolved by FIGE as a diffuse band between 20 to 70 kbp when compared with linear lambda (λ) markers. FIGE resolved the 66 kbp circular marker into several multimers, while CHEF resolved only open-circular monomers and linears. In agreement with FIGE results, EM analysis indicated the two slow migrating mtDNA populations contained circular (both supercoiled and relaxed circles) and free linear molecules of 10-60 kbp, and networked linear molecules of 45–140 kbp total size that may represent recombination intermediates. The fast migrating population consisted of 10–50 kbp linear molecules. Well-bound mtDNA showed only long linear molecules of 40–150 kbp with no detection of circles or complex/rosette molecules. This report shows that FIGE has clear advantages over CHEF for separating large DNA molecules with different conformations, and may be very useful for studies to characterize genome structure in complex systems such as plant mitochondria.

We developed six pipelines (TBSPG) for mapping Illumina sequence reads to reference genomes, refining unique mapping, and computing the mapped read number and coverage. These pipelines provide the options of conducting multi-mapping or unique mapping, inputting with paired-end read files or a single-end read file, removing or not removing nucleus-organelle shared sequences, and mapping with the full-length reads or with the two halves of each read to refine the detection of unique and non-unique sequences. These TBSPG pipelines were based on (and named after) publicly available tools: Trimmomatic, the Burrows–Wheeler Aligner (BWA), SAMtools, Picard, and the Genome Analysis Toolkit (GATK). We developed several Perl scripts to fill the gaps between the tools, connect the tools, recognize half-length reads, select uniquely mapped reads, and compute and output data in a Microsoft Excel-recognizable format for studying the read number and the coverage per chromosome and organellar genome. In a potato 100-bp paired-end sequence file (Illumina TruSeq), approximately 6.75 % of uniquely mapped full-length reads were found to actually contain non-unique sequences at the half-length-read level. These freely available TBSPG pipelines can be used for many read-based applications, including repetitive sequence analysis and organellar genome copy number estimation.

Peanut (Arachis hypogaea L) is one of the wide cultivated plants with a narrow genetic base, hence the interest in prospecting, rescuing, and characterizing germplasm of this species is continuously carried out. In this work, eleven microsatellite markers were used to assess the genetic diversity and population structure of 68 Algerian peanut accessions originated from four geographic regions in the north and south of Algeria. A total of 83 alleles were amplified with a mean number of 7.545 alleles per locus and polymorphic information content (PIC) ranged from 0.625 to 0.874. The observed and expected heterozygosity varied from 0.31 to 1.00 and from 0.61 to 0.84 with a mean of 0.704 and 0.732, respectively. Genetic structure analysis showed a strong population at K = 2, separating accessions according to their subspecies affiliation (hypogeae ssp. and fastigiata ssp.). It was also able to quantify the genetic correlations between genotypes using principal component analysis (PCA) and the method of groups of unweighted pairings with arithmetic means (UPGMA). Analysis of molecular variance (AMOVA) revealed high genetic variation within individuals (90.7%) and low genetic differentiation between subspecies (10.3%) and among populations (8.9%) from different geographical origin. Genetic diversity analysis in this study provides useful information for the exploration and utilization of these peanut cultivars.