Use of an adsorbent and antioxidants to reduce the effects of leached phenolics in in vitro plantlet regeneration of faba bean

Development of a reliable in vitro regeneration protocol is necessary to facilitate genetic transformation of faba bean. However, leaching of phenolics from the explants of most genotypes of faba bean to theculture medium causes browning, and eventually kills the explants, hindering in vitro regeneration. This study is aimed to minimize the effect of phenolics and to identify the most suitable types of explants forin vitro regeneration. We pre-treated faba bean seeds in polyvinylpyrrolidone (PVP), then cultured different types of explants on tissue culture media supplemented with an adsorbent (activated charcoal) and antioxidants (ascorbic acid, cysteine and silver nitrate). Our results showed that treating the over night soaked seed (after removing the seed coat) with PVP solution (1000 mg/l) for 1 h, followed by culturing in Murashige and Skoog medium (MS medium) with 3% (w/v) sucrose, 0.8% (w/v) agar, 2 mg/l 6-benzylaminopurine and 2 mg/l thidiazuron, supplemented with ascorbic acid (1 mg/l) or activatedcharcoal (10 g/l), greatly reduced lethal browning in explants and improved shoot regeneration. The shoots rooted on half-strength MS medium supplemented with 0.5 mg/l -naphthaleneacetic acid. Thecotyledonary node is the most suitable type of explant for regeneration. Regenerated plantlets were successfully established in pots and set seeds in the green house

Genotype x Environment interaction for quality traits in durum wheat cultivars adapted to different environments

The quality traits of durum wheat are important for the utilization by the industries. These traits may be influenced by genotype and interaction of genotype and environment (GxE). To evaluate the effects of genotype, environment and genotype x environment interaction on quality traits such as vitreousness, SDS sedimentation test, yellow pigment index, protein content and test weight, twelve Moroccan durum wheat cultivars representing a range of agronomic adaptation were tested in five locations representing a range of environments in three growing seasons. The results indicated significant effects of genotype, environment and GxE for all the quality traits. The extent of these effects differed; for SDSsedimentation volumes, yellow pigment and test weight, the component of variation due to genotype was larger than due to the environment, indicating the greater influence of genotypes on these traits. However, for vitreousness and protein content, the effect of environment was higher than the effect due to genotypes. Thus, these traits are controlled greatly by environmental effects than genetics. The variation due to GxE was higher than that of genotype for vitreousness and test weight, indicating high GxE interaction effect and less genotypic stability for these traits. For protein content, where the environmental effect was greater than that of genotype and GxE effect, multiple environmental trials are necessary in order to determine protein content of a cultivar. For other traits,  preliminary evaluations can be done in one environment and good performing ones can be selected for multiple environmental trials

Design, fabrication and performance evaluation of a 22-channel direct reading atomic emission spectrometer using inductively coupled plasma as a source of excitation

The indigenous design, fabrication and performance evaluation of a polychromator, using inductively coupled plasma (ICP) as a source of excitation, are described. A concave holographic grating is used as the dispersing element and a Paschen-Runge mount is chosen to focus the spectra over a wide range along the Rowland circle. Twenty-two exit slits, mounted along the circle, precisely correspond to the wavelengths used for determination of up to twenty elements present in the plasma. Radiations emerging from the exit slits are detected by photomultiplier tubes placed behind them. The photomultiplier signal is recorded by an electronic system consisting of an integrator and a PC-based data acquisition system. The performance of the spectrometer has been evaluated with an ICP excitation source. Synthetic standards in deionized water containing a mixture of twenty impurities have been analysed. Typical determination limits observed for elements range from sub-ppm to ppm levels. All the elements present as impurities can be detected simultaneously. It is also observed that each element has a different emitting region in the ICP flame for which the maximum signal to the background is obtained. The determination limits obtained corresponding to these zones are the lowest. A study of the sensitive emitting zones for several elements has been carried out and the results are demonstrated by photographs of the ICP flame. The study will help in achieving the minimum value of determination limit for an impurity element

Genetic diversity and population structure of Ascochyta rabiei from the western Iranian Ilam and Kermanshah provinces using MAT and SSR markers

Knowledge of genetic diversity in A. rabiei provides different levels of information that are important in the management of crop germplasm resources. Gene flow on a regional level indicates a significant potential risk for the regional spread of novel alleles that might contribute to fungicide resistance or the breakdown of resistance genes. Simple sequence repeat (SSR) and mating type (MAT) markers were used to determine the genetic structure, and estimate genetic diversity and the prevalence of mating types in 103 Ascochyta rabiei isolates from seven counties in the Ilam and Kermanshah provinces of western Iran (Ilam, Aseman abad, Holaylan, Chardavol, Dareh shahr, Gilangharb, and Sarpul). A set of 3 microsatellite primer pairs revealed a total of 75 alleles; the number of alleles varied from 15 to 34 for each marker. A high level of genetic variability was observed among A. rabiei isolates in the region. Genetic diversity was high (He = 0.788) within populations with corresponding high average gene flow and low genetic distances between populations. The smallest genetic distance was observed between isolates from Ilam and Chardavol. Both mating types were present in all populations, with the majority of the isolates belonging to Mat1-1 (64%), but within populations the proportions of each mating type were not significantly different from 50%. Results from this study will be useful in breeding for Ascochyta blight-resistant cultivars and developing necessary control measures

Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae)

This is the author's accepted manuscript, made available with the permission of the publisher.This research was supported by NIH grant GM073990 and NSF grant DEB-0543052 to J. K. Kelly, NSF grants DEB-9629457 and DEB-9981891 to R. G. Shaw, and NSF DEB-0108242 to M. Orive. M. E. Mort acknowledges DEB-0344883

Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64

The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis

Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance “QTL-hotspot” region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis