The use of retrotransposon-based molecular markers to analyze genetic diversity

Molecular markers play an essential role in all aspects of genetics, modern plant breeding, in human forensics, for map-based cloning of genes, ranging from the identification of genes responsible for desired traits to the management of backcrossing programs. Retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their “copy and paste” life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Following the demonstration that retrotransposons are ubiquitous, active, and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of genetic diversity in plants and the way for the rapid isolation of retrotransposon termini.Peer reviewe

A major gene for grain cadmium accumulation in oat

A population of 150 F2 plants was derived from a cross between two spring oat individuals, one from cv. Aslak (Boreal Plant Breeding LTd., Finland) and the other from cv. Salo (Svalöf-Weibull AB, Sweden). Cadmium was tested by inductively coupled plasma mass spectrometry (ICP-MS) method

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.Non Peer reviewe

Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides

Background: The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n=2x=14), a wild cross-pollinated relative of cultivated wheat. Results: The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of LTR retrotransposon intraspecific variability in Ae. speltoides and closely related species of sect. Sitopsis. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the same population significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species’ range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element in populations of Ae. speltoides significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis of WIS2, Wilma, and Daniela elements revealed a grouping similar to groupings determined by other methods, with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. Conclusions: IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population-specific, ultimately leading to the separation of small stressed populations from the main bunch.Peer reviewe

Application of five DNA marker techniques to distinguish between five apple (Malus x domestica Borkh.) cultivars and their sports

Peer reviewe

Application of five DNA marker techniques to distinguish between five apple (Malus x domestica Borkh.) cultivars and their sports

Peer reviewe

Assessment of genetic diversity in Nordic timothy (Phleum pratense L.)

Timothy (Phleum pratense L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers.Peer reviewe

Characterization of water and wildlife strains as a subgroup of Campylobacter jejuni using DNA microarrays.

Campylobacter jejuni is the leading cause of human bacterial gastroenteritis worldwide, but source attribution of the organism is difficult. Previously, DNA microarrays were used to investigate isolate source, which suggested a non-livestock source of infection. In this study we analysed the genome content of 162 clinical, livestock and water and wildlife (WW) associated isolates combined with the previous study. Isolates were grouped by genotypes into nine clusters (C1 to C9). Multilocus sequence typing (MLST) data demonstrated that livestock associated clonal complexes dominated clusters C1-C6. The majority of WW isolates were present in the C9 cluster. Analysis of previously reported genomic variable regions demonstrated that these regions were linked to specific clusters. Two novel variable regions were identified. A six gene multiplex PCR (mPCR) assay, designed to effectively differentiated strains into clusters, was validated with 30 isolates. A further five WW isolates were tested by mPCR and were assigned to the C7-C9 group of clusters. The predictive mPCR test could be used to indicate if a clinical case has come from domesticated or WW sources. Our findings provide further evidence that WW C. jejuni subtypes show niche adaptation and may be important in causing human infection

Development and Evaluation of Let\u27s Eat Smart: a Pilot School-Based Nutrition Intervention for Elementry School Children in Kuwait

Due to nutrition transition, the prevalence of childhood obesity is increasing significantly worldwide especially in affluent developing countries such as Kuwait. Obesity is associated with adverse chronic health conditions and financial burdens which provides an incentive for prevention. The objective of the study was to examine the effectiveness of a multi-component school-based nutrition intervention designed to improve healthy eating knowledge, attitudes, self efficacy and dietary behaviors among fourth and fifth graders in Kuwait. The Let\u27s Eat Smart program was based on the social cognitive theory and used short interactive lessons, DVD sessions, posters, food models and parental letters to promote a healthy lifestyle message among fourth and fifth graders. Let\u27s Eat Smart was delivered to 110 students in the English Playgroup and Primary School. Surveys and 3-day food-records were collected on pre- and post-intervention. Surveys assessed nutrition knowledge, attitudes, dietary behaviors and self efficacy while diet records were analyzed to examined intake of food groups. Additionally, program evolutions were collected on post-intervention. A paired t-test was used to analyze the change from pre- to post-intervention. Eighty four students completed all requirements of the program and were included in the quantitative analysis, while 95 students were included in the qualitative analysis of the program evaluation. After the intervention, students reported high levels of knowledge (p \u3c .0001), positive attitude toward a healthy lifestyle (p \u3c .04) and higher levels of self efficacy toward healthy eating (p \u3c .01). There was no significant change in dietary practices assessed in the survey except for fast food consumption where there was a significant decrease in consumption after the intervention (p \u3c .001). Diet-records analysis shoa significant increase in fruits intake (p \u3c .02) and vegetables intake (p \u3c .001) after the intervention. The overall students\u27 evaluation of the program was positive as 90.5% were satisfied and would like to have more nutrition lessons. Due to its apparent impact on children, Let\u27s Eat Smart is an effective school-based intervention approach to address prevention of childhood obesity in Kuwaiti schools