https://www.cs.rpi.edu/~leen/publications/LanderGreenAbrahamsonBarlowDalyLincolnNewberg1987.pdf

MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

We discuss the physical and enzymatic bases of carbone isotope discrimination during photosynthesis, noting how knowledge of discrimination can be used to provide additional insight into photosynthetic metabolism and the environmental influences on that process

Carbon Isotope Discrimination and Photosynthesis

Evolution of Protein Molecules

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na+(Li+)/H+ antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.

Metagenomics: Application of Genomics to Uncultured Microorganisms

Here, the state of the art of the application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology will be presented. Furthermore, the potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.

/pdf/application-of-denaturing-gradient-gel-electrophoresis-dgge-uzz5t0jk0x.pdf

Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology

A culture-independent survey of the soil microbial diversity in a clover-grass pasture in southern Wisconsin was conducted by sequence analysis of a universal clone library of genes coding for small-subunit rRNA (rDNA). A rapid and efficient method for extraction of DNA from soils which resulted in highly purified DNA with minimal shearing was developed. Universal small-subunit-rRNA primers were used to amplify DNA extracted from the pasture soil. The PCR products were cloned into pGEM-T, and either hypervariable or conserved regions were sequenced. The relationships of 124 sequences to those of cultured organisms of known phylogeny were determined. Of the 124 clones sequenced, 98.4% were from the domain Bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Two of the 124 sequences were of nuclear origin, one being fungal and the other a plant sequence. No sequences of the domain Archaea were found. Within the domain, Bacteria, three kingdoms were highly represented: the Proteobacteria (16.1%), the Cytophaga-Flexibacter-Bacteroides group (21.8%), and the low G+C-content gram-positive group (21.8%). Some kingdoms, such as the Thermotogales, the green nonsulfur group, Fusobacteria, and the Spirochaetes, were absent. A large number of the sequences (39.4%) were distributed among several clades that are not among the major taxa described by Olsen et al. (G.J. Olsen, C.R. Woese, and R. Overbeek, J. Bacteriol., 176:1-6, 1994). From the alignments of the sequence data, distance matrices were calculated to display the enormous microbial diversity found in this soil in two ways, as phylogenetic trees and as multidimensional-scaling plots.

Molecular microbial diversity of an agricultural soil in Wisconsin.

Genetic linkage maps were constructed for both maize and tomato, utilizing restriction fragment length polymorphisms (RFLPs) as the source of genetic markers In order to detect these RFLPs, unique DNA sequence clones were prepared from either maize or tomato tissue and hybridized to Southern blots containing restriction enzyme-digested genomic DNA from different homozygous lines A subsequent comparison of the RFLP inheritance patterns in F2 populations from tomato and maize permitted arrangement of the loci detected by these clones into genetic linkage groups for both species

Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms.

Restriction Fragment Length Polymorphism Analysis of Loci Associated with Insect Resistance in Tomato 1

More than 60% of common bean production worldwide is derived from cultivars of Middle American origin. Understanding the diversity of these will facilitate their use in genetic improvement. The objective of this study was to analyze a collection of 269 landraces of common bean (Phaseolus vulgaris L.) by correspondence analysis of random amplified polymorphic DNA (RAPD) data to determine the genetic structure of the Middle American gene pool of cultivated bean. One hundred eighty landraces originating in Mexico, the remainder in Central America and secondary centers of diversity within the Americas, and two checks were studied. DNA was extracted, RAPD reactions carried out, and polymorphic bands were scored as present or absent on the basis of 39 primers. Groups were formed which in part corresponded to races defined previously by morphological and agroecological criteria. However, tropical small-seeded Race M was composed of two groups: one largely Mexican that included most small-seeded black beans of upright plant habit, and one Central American with landraces of various seed colors. Most non-black small-seeded germplasm of Race M phenotype from secondary centers grouped with the Central American landraces, except for cream-seeded and purple-seeded accessions from Brazil. Races D and J could be distinguished and within races D and J further divisions could be recognized which were related to geographic origin. The more commercial Race D landraces formed a genetic group that was predominant in the western part of the Mexican highland plateau. Another Race D group was concentrated at the eastern extreme of the neovolcanic axis and was differentiated morphologically as well. Guatemalan germplasm contained accessions of climbing bean that did not group with any of the previously defined races and should be considered a separate race. Thus, Middle American germplasm of common bean is more complex than previously thought, and contains diversity that remains to be explored for its practical value.

Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD.

Improvement of crop water use efficiency (WUE) has not been successful because evaluation for this component of drought resistance is unreliable in field-grown plants. The composition of stable isotopes of plant carbon (δ13C) was earlier shown to be an excellent indicator of WUE in tomato and other species. It is now reported that δ13C can be satisfactorily predicted from three restriction fragment length polymorphisms (RFLPs), which are genetic markers for discrete DNA sequences within the genome. An additive type of gene action was observed for all three RFLP markers, and for one of them there also was a significant nonadditive component. Combining the δ13C and RFLP technologies may aid in identifying genes associated with WUE and in studying mechanisms contributing to WUE. These technologies will also be useful for crop improvement.

https://science.sciencemag.org/content/sci/243/4899/1725.full.pdf

James Nienhuis

Papers

Molecular microbial diversity of an agricultural soil in Wisconsin.

Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms.

Restriction Fragment Length Polymorphism Analysis of Loci Associated with Insect Resistance in Tomato 1

Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD.

Restriction fragment length polymorphisms associated with water use efficiency in tomato.