Hydrogel: Preparation, characterization, and applications: A review

Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 x W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

https://www.genetics.org/content/genetics/149/4/2007.full.pdf

A microsatellite map of wheat.

Novel crosslinking methods to design hydrogels

A total of 57.8 Mb of publicly available rice (Oryza sativa L.) DNA sequence was searched to determine the frequency and distribution of different simple sequence repeats (SSRs) in the genome. SSR loci were categorized into two groups based on the length of the repeat motif. Class I, or hypervariable markers, consisted of SSRs > or =20 bp, and Class II, or potentially variable markers, consisted of SSRs > or =12 bp <20 bp. The occurrence of Class I SSRs in end-sequences of EcoRI- and HindIII-digested BAC clones was one SSR per 40 Kb, whereas in continuous genomic sequence (represented by 27 fully sequenced BAC and PAC clones), the frequency was one SSR every 16 kb. Class II SSRs were estimated to occur every 3.7 kb in BAC ends and every 1.9 kb in fully sequenced BAC and PAC clones. GC-rich trinucleotide repeats (TNRs) were most abundant in protein-coding portions of ESTs and in fully sequenced BACs and PACs, whereas AT-rich TNRs showed no such preference, and di- and tetranucleotide repeats were most frequently found in noncoding, intergenic regions of the rice genome. Microsatellites with poly(AT)n repeats represented the most abundant and polymorphic class of SSRs but were frequently associated with the Micropon family of miniature inverted-repeat transposable elements (MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was developed and integrated into the existing microsatellite map of rice, providing immediate links between the genetic, physical, and sequence-based maps. This contribution brings the number of microsatellite markers that have been rigorously evaluated for amplification, map position, and allelic diversity in Oryza spp. to a total of 500.

/pdf/computational-and-experimental-analysis-of-microsatellites-57ccrkraw8.pdf

Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential

Cloning and characterization of the

Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.

/pdf/the-genome-of-the-recently-domesticated-crop-plant-sugar-2hjx8u6sll.pdf

The genome of the recently domesticated crop plant sugar beet ( Beta vulgaris )

Plants from wide taxonomic groupings have similar genes and ordering of genes along the chromosomes. However, the repetitive DNA, much of no known function and often constituting the majority of the genome, varies extensively from species to species in absolute amount, sequence and dispersion pattern. Despite this, it is known that families of repeated DNA motifs each have a characteristic genomic location within a genus, and that there are different constraints on the evolution of repetitive DNA and genes. There are now enough data about different types of repetitive DNA—from sequencing, Southern analysis and in situ hybridization—to build a model of the organization of a typical plant genome, and apply it to gene cloning, evolutionary studies and gene transfer.

Genomes, genes and junk: the large-scale organization of plant chromosomes

A major part of the nuclear genome of most plants is composed of different repetitive DNA elements. Studying these sequence elements is essential for our understanding of the nature and consequences of genome size variation between different species, and for studying the large-scale organization and evolution of plant genomes. Sugar beet (Beta vulgaris L.) is an important crop and a suitable model for such investigations: with a genome size of 0-8 pg C (760 Mbp) it contains significant amounts of all major groups of repetitive sequences among its nine chromosome pairs, but analysis is not complicated by polyploidy or the huge size of some genomes, and there are valuable genetic data, recombinant DNA libraries and wild relatives to complement studies of sequence contribution to genome size in sugar beet. A sophisticated understanding of the structure of the genome will provide valuable data about the major factors responsible for genome size variation, useful aids in the development of a molecular understanding of genome evolution, and perhaps indicate strategies for crop improvement. Using molecular and cytological approaches, we have characterized a range of differentially organized repetitive DNA sequence elements from the genomes of cultivated and wild beet species, leading to an extensive model of the repetitive DNA, its organization and evolution. © 1998 Annals of Botany Company

/pdf/repetitive-dna-elements-as-a-major-component-of-plant-1v6gtfh5j6.pdf

Repetitive DNA Elements as a Major Component of Plant Genomes

/pdf/patterns-and-trends-of-early-successional-forests-in-the-4gb0ng4mvh.pdf

Patterns and trends of early successional forests in the Eastern United States

We have analysed a family of highly repetitive DNA from Arabidopsis arenosa (L.) Lawalree [syn. Cardaminopsis arenosa (L.) Hayck] composed of AT-rich tandem repeats of 166–179 bp in head to tail organization. Sequence comparison between several repeat units revealed a high level of divergence of 4.5% to 25%. The sequence family shows more than 58% homology to satellite sequences described in Arabidopsis thallana (L.) Heynh. but no homology to other satellite repeats in the Cruciferae. Within the genus Arabidopsis the satellite sequence was found to be present in A. thaliana and Arabidopsis suecica (Fries) Norrlin, but not in Arabidopsis griffithiana (Boiss.) N. Busch and Arabidopsis pumila (Stephan) N. Busch. In situ hybridization to metaphase chromosomes of A. arenosa (2n=4x=32) showed the sequence to be localized at the centromeres of all 32 chromosomes with substantial hybridization along the chromosome arms. Using Southern hybridization and in situ hybridization, we give evidence that A. suecica is a hybrid of A. thaliana and A. arenosa. A considerable reorganization of the A. thaliana satellite sequence pAL1 occurred in the hybrid genome while no molecular change of the A. arenosa repeat was observed in the hybrid. Analysis of related repeats enabled differentiation between closely related genomes and are useful for the investigation of hybrid genomes.

/pdf/analysis-of-a-repetitive-dna-family-from-arabidopsis-arenosa-1h9bf7oue0.pdf

Thomas Schmidt

Papers

The genome of the recently domesticated crop plant sugar beet ( Beta vulgaris )

Genomes, genes and junk: the large-scale organization of plant chromosomes

Repetitive DNA Elements as a Major Component of Plant Genomes

Patterns and trends of early successional forests in the Eastern United States

Analysis of a repetitive DNA family from Arabidopsis arenosa and relationships between Arabidopsis species