Journal of Plant Molecular Breeding
Volume:1 Issue: 2, Summer and Autumn 2013

Expressed sequence tags simple sequence repeats (EST-SSRs) are important sources for investigation of genetic diversity and molecular marker development. Similar to genomic SSRs, the EST SSRs are useful markers for many applications in genetics and plant breeding such as genetic diversity analysis, molecular mapping and cross-transferability across related species and genera. In spite of low polymorphism, these markers show variation in the expressed part of the genome. In this study, Medicago truncatula EST-SSRs were used for investigation of transferability between M. truncatula and some chickpea (Cicer arietinum L.) genotypes, also genetic diversity between used chickpea genotypes was determined. In this research, 650 M. truncatula ESTs were searched to find simple sequence repeats (SSRs). A total of 131 EST-SSRs were contained di-and trinucleotide motif SSRs. In this study, thirty pairs of primers were designed to amplify over 10 chickpea genotypes. Thirteen primer pairs (43%) generated reproducible bands in at least one chickpea genotype that eight bands (61.5%) were polymorphic in the chickpea genotypes. A total of 24 alleles were amplified with an average of 3 alleles per primer. The average of polymorphism information content (PIC) was 78.75% and transferability across M. truncatula and C. arietinum was 43.32%. The results indicate that the developed EST-SSR markers from M. truncatula as a model plant are valuable genetic markers for legume species such as chickpea. In addition to suitability of EST-SSR markers for genetic diversity analysis, their broad range of transferability also proved their potential for comparative genomics studies.

Identification of genes with invariant levels of gene expression is a prerequisite for validating transcriptomic changes accompanying development. Ideally expression of these genes should be independent of the morphogenetic process or environmental condition.We report here the validation of internal control gene i.e.TPS (trehalose 6-phosphate-synthase) in cotton (Gossypium spp), using TaqMan system in quantitative Real Time PCR (qRT-PCR). The Gene expression was tested in five different G. hirsutum cultivars including Coker 312, Acala SJ, ZETA 2, Taghva, Neishabour and a diploid wild type; G. barbadense. Identical amplicons were obtained within these cultivars. No amplifications was achieved when DNA samples from barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), Fig (Ficus carica), pistachio (Pistacia vera), yew (Taxus baccata), wheat (Tirticum aestivum), rose (Rosa hybrida) and soybean (Glycine max) were used as template. Therefore, it was confirmed that the primers and probes designed in this study were specific for the identification and quantification of internal control gene. These results reveal the possibility of using the TPS gene as an internal control in cotton. In another word, this gene would be a suitable candidate as a reference gene in examination of gene expression, detection of transgenic cotton and determining e the zygosity as well as the copy number of the transgene.

Narrow genetic variability may lead to genetic vulnerability of field crops against biotic and abiotic stresses which can cause yield reduction. In this study a set of 37 wheat microsatellite markers linked with identified QTLs for salinity tolerance were used for the assessment of genetic diversity for salinity in 30 promising lines of hexaploid bread wheat (Triticum aestivum L.). A total of 438 alleles were detected with an average allele number of 11.84 per locus using 37 microsatellite markers. The number of alleles per locus ranged from two to twenty, the maximum number of alleles was observed at Xgwm312. Gene diversity statistic for 37 microsatellite loci was varied from 0.66 to 0.94 and also polymorphic information content value was varied from 0.64 to 0.93 for Xgwm445 and Xgwm312 respectively. Result showed Xgwm312 SSR marker with the highest PIC value was distinguished as the best marker for genetic diversity analysis to improve of salinity tolerance. Obtained dendrogram by UPGMA method categorized genotypes in to 3 different groups, which had different reaction to salinity. A wide range of genomic diversity was observed among all the genotypes. Principal Coordinates Analysis (PCoA) also confirmed this pattern of genetic diversity, proving them can be use as the prime candidates in order to improve of salinity tolerance in breeding programs of wheat. The present study also indicates that microsatellite markers permit the fast and high throughput fingerprinting of numbers of genotypes from a germplasm collection in order to assess genetic diversity.

Chamomile (Matricaria chamomilla), an important medicinal plant belonging to the Asteraceae family, has a wide distribution in Iran and other parts of the world. The medicinal and pharmacological effects of chamomile are mainly associated with its essential oil content and it is widely used in food, cosmetics and pharmaceutical industries. Despite its wide geographical distribution in Iran, little is known about its molecular genetic diversity and distribution. In this study, intron-exon splice junction (ISJ) markers, including both intron-targeted (IT) and exon-targeted (ET) primers, were used to assess the genetic diversity of thirty-one chamomile populations, including 28 populations from different parts of Iran, one Hungarian population, and two of unknown origin. Twenty-six out of thirty-five primers used in the study, were reliable, producing a total number of 566 sharp and precise bands, of which 557 bands were polymorphic (98%). The average polymorphic information content (PIC) and the average marker index (MI) were calculated at 0.33 and 7.34, respectively. The average total genetic diversity (HT), average genetic diversity within population (HST) and gene differentiation coefficient (Gst) were 0.293, 0.219, and 0.251, respectively. The diversity data revealed that the Matricaria chamomilla species exhibited the closest relationship with the Tripleurospermum disciforme and Tripleurospermum sevanense species.

Drought stress is one of the serious problems that restricted agronomic plant production worldwide. In molecular level, the harmful effect of drought stress is mostly caused by producing of large amount of reactive oxygen species (ROS). Catalase and Metallothionein genes have a crucial role to mope the hydrogen peroxide (H2O2) resulting reducing oxidative damage. In this research the gene expression pattern of Catalase and Metallothionein was studied in response to drought stress treatments. The treatments included - 0.3 bar, - 0.9 bar, - 8 bar and -12 bar and wheat varieties included Zagros (drought tolerant), Moghan (semi- tolerant) and Tajan (drought sensitive). The amount of cellular oxidative levels (TBARM) increased steady by intensify of drought stress levels. Real time PCR analysis showed different expression pattern for catalase and metallothionein encoded genes. Catalase gene expression was increased during drought stress up to -8 bar and reduced in -12 bar treatment, in all cultivars specially in Tajan cultivar. Metallothionein gene expression was linearly reduced during different levels of drought treatments especially in Zagros and Tajan cultivars. The most activity for both genes has observed in Zagros cultivar at -0.9 bar treatment. Whereas, Moghan cultivar showed most transcription for both genes at -8 bar treatment. Overall gene activities, content of chlorophyll (a, b) and whole plants appearance declined by high level of drought stress e.g. -12 bar treatment in all cultivars particularly in Tajan variety. Whereas, the moderate levels of drought stress treatments induced genes activitiy.

Mutation induction is considered as an effective way to enrich plant genetic variation, particularly for traits with a very low level of genetic variation. This research was conducted to assess genetic variation induced by gamma radiation in M2 and M3 mutant lines of canola (Brassica napus L.) by SSR and morphological characteristics and to identify useful mutants in terms of agronomic traits. Sixty-two mutant lines derived from gamma mutagenesis and their wild-type progenitors (‘RGS003’ and ‘Sarigol’ cvs) were used. Twenty-five polymorphic SSR primers were used in this study. Results of cluster analysis based on both morphological traits comprising plant height, days to flowering, days tomaturity, number of pods/plant, number of seeds/pod, 1000-seed weight and seed yield/plant and SSR data revealed a separate grouping of mutant lines from control cultivars. SSR data analysis of mutant lines and controls demonstrated a considerable genetic variation among mutant lines, where 83% of primers generated polymorphic bands with 3.32 alleles per locus. The genetic distance calculated between mutant lines and their controls indicated a significant difference between mutant lines and controls. Although both morphological and SSR markers successfully discriminated mutant lines from controls, SSR primers could further discriminate between the mutant lines derived from the related cultivar. Mutant lines 24 derived from ‘RGS003’ and 16 and 26 from ‘Sarigol’ were considered as superior for breeding canola, which could be utilized in future genetic and breeding programs. Distinct classification of genotypes based on agromorphological and SSR data in the present study implies that morphological and SSR markers reflected different aspects of genetic variation among mutant lines.

Leaf senescence constitutes the last stage of leaf development in plants and proceeds through a highly regulated program in order to redistribution of micro- and macro-nutrients from the senescing leaves to the developing/growing plant organs. Initiation and progression of leaf senescence is accompanied by massive sequential alterations at various levels of leaf biology including leaf morphology and physiology, cell metabolism and structure, and gene transcription. In this regard, comprehensive expression analysis of senescence-associated genes (SAGs) and the identification of leaf senescence related mutants has revealed that leaf senescence is a complex genetically controlled program. In this review, we present important findings about the molecular genetic mechanisms underlying leaf senescence in various plants with a main focus on the model plant Arabidopsis thaliana. Functional analysis of leaf senescence mutants has provided new insights into the key processes that regulate the onset and progression of leaf senescence, thus allowing categorization of the various regulatory factors into several signalling pathways.