Restriction fragment length polymorphism in plants and its implications

Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism

Restriction fragment length polymorphism (RFLP) is a difference in DNA sequences of organisms belonging to the same species. RFLPs are typically detected as DNA fragments of different lengths after digestion with various restriction endonucleases. The comparison of RFLPs allows investigators to analyze the frequency of occurrence of mutations, such as point mutations, deletions, insertions, and gross chromosomal rearrangements, in the progeny of stressed plants. The assay involves restriction enzyme digestion of DNA followed by hybridization of digested DNA using a radioactively or enzymatically labeled probe. Since DNA can be digested with methylation sensitive enzymes, the assay can also be used to analyze a methylation pattern of a particular locus. Here, we describe RFLP analysis using methylation-insensitive and methylation-sensitive enzymes.

Chromosomal and phylogenetic context for conglutin genes in Arachis based on genomic sequence

Comparative genomic and cDNA sequence analysis of ara h 2, a major peanut allergen, and a related conglutin ara h 6 were performed in Arachis hypogaea L. and its putative progenitors, Arachis duranensis and Arachis ipaensis. The complete identity between sequences encoding Ara h 2 isoforms demonstrated that these are homeologous genes and represent orthologs from diploid ancestors. Three copies of ara h 6 were identified in A. hypogaea, one of them located in the A-genome and the other two in the B-genome. Expression analysis showed higher levels of ara h 2 transcripts compared with ara h 6. Dual-labeled genomic in situ hybridization permitted identification of two subgenomes, each of which contained one pair of ara h 2-ara h 6 signals localized by fluorescence in situ hybridization. Characterization of genomic clones showed close genetic linkage between Ara h 2.02 and one copy of ara h 6 in the B-genome. The physical linkage may have arisen by tandem duplication and divergence of an ancestral gene. A gene duplication event specific to the B-genome progenitor has resulted in ara h 6 paralogs. These data provide further evidence for progenitor relationships and genomic organization of the conglutin gene family in the genus Arachis and could contribute to the development of a hypoallergenic peanut.

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.

Biotechnology domain

Biotechnology and the use of biologically based agents for the betterment of mankind is an active field which is founded on the interaction between many basic sciences. This is achieved in coordination with engineering and technology for scaling up purposes. The application of modern recombinant DNA technology gave momentum and new horizons to the field of biotechnology both in the academic setting and in industry. The applications of biotechnology are being used in many fields including agriculture, medicine, industry, marine science and the environment. The final products of biotechnological applications are diverse. In the medical applications of biotechnology, for example, the field has been evolving in such a way that the final product could be a small molecule (e.g. drug/antibiotic) that can be developed based on genetic information by drug design or drug screening using a cloned and expressed target protein.

Restriction polymorphisms and fingerprint patterns from an interspersed repetitive element of Plasmodium falciparum DNA

A recombinant DNA clone, pC4.H32, identifies distinguishable restriction fragment patterns from different Plasmodium falciparum clones. Analysis of these DNA fingerprint patterns from parasites cultivated over several years and from progeny of a P. falciparum cross showed the fingerprints to be mitotically and meiotically stable. Restriction fragments from the parents of the cross possessed sufficient polymorphism and number to generate 14 unique fingerprint patterns in 16 independent recombinant progeny. The pC4.H32 insert contains a 0.5-kb imperfectly repeated sequence found in subtelomeric regions of multiple chromosomes. Restriction site variations both within and outside of the 0.5-kb repeat contribute to the fingerprint polymorphisms. Fingerprint analysis can serve to type P. falciparum clones and can detect mislabeling and cross-contamination of parasite stocks.