Figure,1-8, retrotransposon based marker paper Final

Methods in Molecular Biology, 2012

Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction.

Retrotransposons (RTs) are major components of most eukaryotic genomes; they are ubiquitous, dispersed throughout the genome, and their abundance correlates with the host genome sizes. Copy-and-paste life style of the RTs consists of three molecular steps, which involve transcription of an RNA copy from the genomic RT, followed by reverse transcription to cDNA, and finally a reintegration event into a new locus of the genome. This process leads to new genomic insertions without excision of the original RT. The target sites of insertions are relatively random and independent for different plant taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the chromosome centromers and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular barcoding of RTs play an essential role in all fields of genetics and genomics, and represent a powerful tool for molecular barcoding. To detect RT polymorphisms, marker systems generally rely on the amplification of sequences between the ends of the retrotransposon, such as long terminal repeats (LTR) of LTR-retrotransposons (LTR-RT) and the flanking genomic DNA. In this Chapter, we review the utility of some commonly used PCR-based molecular barcoding methods of LTR-RTs, including RBIP(Retrotransposon-Based Insertion Polymorphism), REMAP (Retrotransposon-Microsatellite Amplified Polymorphism), SSAP (Sequence-Specific Amplified Polymorphism), IRAP (Inter Retrotransposon Amplified Polymorphism) and IPBS (Inter Primer Binding Sequence). Interspersed repetitive DNA sequences comprise a large fraction of the eukaryotic genomes. They predominantly consist of transposable elements (TEs) with two main families, Retrotransposons (Class I) and DNA transposons (Class II) (McClintock, 1984). Retrotransposons (RTs) are the most abundant class of TEs (IHGSC, 2001; Feschotte et al., 2002; Sabot and Schulman, 2006; Kalendar and Schulman, 2006). There are two major groups of RTs based on the presence vs. absence of long terminal repeats (LTRs), LTR-retrotransposons (LTR-RTs) and non-LTR-retrotransposons. LTR-RTs comprise two main subgroups, copia (with high copy number) and gypsy (with high transposing activity) (Fig. 1). Both, copia and gypsy LTR-RTs, carry regulatory sequences of gene promoters such as CAAT box (e.g., CCATT), TATA box (e.g., TGGCTATAAATAG), transcription start (e.g., CCCATGG), polyadenylation signal (e.g., AATAAG), and polyadenylation start (e.g., TAGT) (Ramallo et al., 2008). All these domains are required for replication and integration of RTs (Sabot and Schulman, 2006; Mansour, 2008). The large internal domain of the LTR-RTs encodes the structural proteins of the virus-like particle, which encapsulate the RNA copy of the RT, and the enzymes Reverse Transcriptase and Integrase (Fig. 1). The process is called transposition. There are three further non-autonomous, short derivative, recombinant LTR-RTs, LARD (Large Retrotransposon Derivatives), TRIM (Terminal Repeat Retrotransposon in Miniature) and solo-LTR (sequence carrying 5’ and 3’ LTRs only) (Xiong and Eickbush, 1990; Havecker et al., 2004; Jurka et al., 2007). The size of LTR-RTs varies from long (e.g., Bare1 copia LTR-RT at 13,271 bp, NCBI Z17327) to short (e.g., Bare1 copia solo-LTR-RT at 3,130 bp, NCBI AB014756; and the truncated RLC_Lara copia RT; at 735 bp, NCBI EF067844; TREP2298). In plants, LTR-RTs are more plentiful and active than non-LTR-RTs (AGI, Arabidopsis Genome Initiative, 2000; Rice Chromosome 10 Sequencing Consortium, 2003; Alzohairy et al., 2012; 2013; 2014a,b). Due to the induction of chromosome recombinational processes during the meiotic prophase, active retrotransposons tend to lose their activity due to sequence breakage (Mansour, 2007; 2008; 2009; Alzohairy et al., 2012; 2013; 2014a,b).

Molecular markers have become crucial part of genetics due to their use in various branches of it, such as positional cloning, which includes identification of genes responsible for desired traits and management of backcrossing programs, as well as in modern plant breeding, and human forensics. Retrotransposons are a major component of all eukaryotic genomes, which makes them suited as molecular markers. The retrotransposons comprise most of large genomes among plants; differences in their prevalence explain most of the variation in genome size. These ubiquitous transposable elements are scattered in all of genome and their replicative transposition allows insert itself into a genome without deletion of the original elements. Retrotransposon activity can occur during development, cell differentiation and stress, and a source of chromatin instability and genomic rearrangements. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. A high proportion of the retroelements have lost their autonomous transposition ability, either by point mutations and/or deletions, many of them seem to embody defective elements with deletions. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The utility of LTR-retrotransposon-based markers, not only for genetic analysis and map construction, in addition also for the isolation and characterization of LTR retrotransposons, such as the long terminal repeats or the internal genes they contain. This review encompasses description of the range of retrotransposon-based marker systems established for plants and evaluation of the role of retrotransposon markers in genetic diversity analysis of plant species.

Field and Vegetable Crops Research, 2011

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 the 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.

Genetica, 1997

The genomic organisation and diversity of the Ty1-copia group retrotransposons has been investigated in several crop plants and their relatives from both dicotyledonous and monocotyledonous families, including potato ( Solanum tuberosum), faba beans ( Vicia faba), Vicia melanops, Vicia sativa, barley ( Hordeum vulgare), rye ( Secale cereale), and onion ( Allium cepa). Extreme heterogeneity in the sequence of the Ty1-copia retrotransposons from all these plants was revealed following sequence analysis of reverse transcriptase fragments. The estimated copy numbers of the Ty1-copia group retrotransposons for the genomes of S. tuberosum, L. esculentum, A. cepa, S. cereale, and V. faba is highly variable, ranging from a few hundred to approximately a million copies per genome. In situ hybridisation data from metaphase and prophase chromosomes of V. faba, S. cereale, and H. vulgare suggest that retrotransposon sequences are dispersed throughout the euchromatic regions of the genome but are almost undetectable in most heterochromatic regions. In contrast, similar data from metaphase chromosomes of A. cepa suggests that although retrotransposon sequences are dispersed throughout the euchromatic regions of the genome, they are predominantly concentrated in the terminal heterochromatin. These results are discussed in the context of the role played by the Ty1-copia group retrotransposons in the evolution of the plant genome. Lastly, the application of retrotransposon sequences as genetic markers for mapping genomes and for studying genetic biodiversity in plants is presented.

Heredity, 2011

Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. 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 population diversity in plants.

Water, 2019

Hillslope viticulture has a long history in Mediterranean Europe, and still holds important cultural and economic value. Steep hillsides have widely been levelled by terraces, in order to control surface water flow and facilitate cultivation. However, under unsustainable management and growing rainfall aggressiveness, terraced vineyards have become one of the most erosion-prone agricultural landscapes. The Valcamonica valley in Lombardy (Italy) presents a typical example of an ancient wine production region where rural land abandonment has previously caused widespread degradation of the traditional terracing systems. Recently, a local revival of wine production led to restoration plans of the terraces and their drainage functioning, to safeguard productivity and hydrogeologic safety. In this study, an Unmanned Aerial Vehicle (UAV) survey was carried out to reconstruct an accurate and precise 3D terrain model of a Valcamonica vineyard through photogrammetry. The resulting high-resolution topographic data allowed insights of surface flow-induced soil erosion patterns based on the Relative Path Impact Index (RPII). Three diverse drainage networks were designed and digitally implemented, allowing scenario analysis of the costs and benefits in terms of potential erosion mitigation. The presented methodology could likely improve the time-efficiency and cost-effectiveness of similar restoration plans in degraded landscapes.

“Senza satisfare all’universale, non si fece mai alcuna repubblica stabile” (Niccolò Machiavelli) Tra i molti progetti progetti sviluppati nel corso della sua vita, solo negli ultimi anni Niccolò Machiavelli ha la possibilità di scrivere una costituzione per la sua città. L'occasione è data da un ampio dibattito che si apre a Firenze a partire dal 1519, dopo la morte di Lorenzo de' Medici il Giovane, duca di Urbino. Il Discursus florentinarum rerum, scritto tra il 1520 e il 1521, è l'ultima occasione per mettere in pratica le sue idee, incidendo sul destino della sua comunità. Contro l'accentramento del potere e della ricchezza nelle mani di poche famiglie, tipico delle repubbliche oligarchiche del suo tempo, Machiavelli progetta una costituzione in grado di tenere insieme ordine e conflitto valorizzando il ruolo del popolo (l'universale). Istituzioni come un nuovo tribunato della plebe e una larga assemblea popolare sono così lo strumento per controllare e limitare il potere delle élite. Un modello, ispirato alla storia repubblicana di Roma e Firenze, che non finisce di parlarci. Niccolò Machiavelli (1469-1527), scrittore e uomo politico fiorentino. Dopo un periodo come funzionario della Repubblica fiorentina (1498-1512) ha scritto dall’esilio alcune delle opere che hanno contribuito a fondare il pensiero politico moderno. L’avversione nei confronti delle oligarchie fiorentine lo ha condotto a teorizzare la figura di un innovativo capo politico popolare (Il principe) e a riproporre, sul modello della Roma repubblicana, un ordinamento misto fondato sul conflitto tra istituzioni aristocratiche e plebee (Discorsi sulla prima deca di Tito Livio).

differential calculus 1