In the past decade there have been major advances in molecular genetics research. A wide variety of DNA-based markers have been developed. These include random amplified polymorphic DNAs (RAPD), amplified fragment polymorphisms (AFLP) and DNA microsatellites. These markers are used to map genes, study population genetics and produce DNA fingerprints. The advantage of these new tools is that the number of genetic markers is potentially unlimited for many species. In addition, these biotechnology-based tools can be applied to a wide range of topics and species.
One molecular genetics project involves mapping genes in longleaf pine. This species of pine has many desirable qualities, including excellent wood quality, insect and disease resistance, and is associated with fire-managed ecosystems in the southeastern United States. Longleaf pine, however, has an extended juvenile phase, called the grass stage, during which height growth does not occur. The unpredictable nature of the grass stage contributes to limited use of longleaf pine in forests managed intensively.
The increased use of other pine species and a reduction in the frequency of fires have reduced the area of longleaf pine forests in the Southeast and have affected other species, such as the red-cockaded woodpecker and the gopher tortoise, both of which are dependent upon longleaf pine forests.
In conjunction with U.S. Department of Agriculture Forest Service scientists in Mississippi, LSU AgCenter researchers are mapping genes that regulate early height growth in longleaf pine. To date, we have mapped 11 genes using RAPD markers and are using this information in a breeding program. The end result should be that with the use of DNA markers, we may be able to breed longleaf pine trees without the grass stage in about half the time that would be required in a traditional breeding program. The successful integration of genetic mapping with the breeding program may result in increased use of longleaf pine in industrial forests. This work is continuing, and we have expanded our research to include several other tree and wildlife species.
Louisiana Black Bear
The Louisiana black bear is a federally listed endangered species that survives in several small populations in Louisiana. LSU AgCenter researchers used DNA microsatellites to estimate abundance of the bears in different locations of the state. The traditional method is to catch the bears, tag them and then see how often a different bear or a previously captured bear is caught. With the ratio of previously caught to newly caught bears, it is possible to estimate the number of bears in an area. In addition to being expensive, this technique is potentially hazardous to both the bears and the researchers.
Instead of capturing the bears, we now put out traps in bear habitat that snag hair samples from passing bears. Then, using the polymerase chain reaction to analyze the DNA in the hair follicles, we can identify each bear caught in the hair snare. By determining a recapture rate, we are able to provide accurate population size estimates. Because of the increased efficiency of the DNA-based techniques, many more bears were sampled than would be possible with traditional methods, and this has provided the best estimates of population sizes to date.
With these techniques, it will be possible to monitor genetic diversity within and among populations and to minimize the chances of inbreeding in the new population while, at the same time, following the genetic health of the current populations.
Eastern cottonwood is the fastest growing tree in the eastern United States and is increasingly being used in short-rotation, high-intensity forestry operations. In addition to their fast growth rate, cottonwood trees are easily propagated by using rooted cuttings. This allows the best ones to be rapidly cloned. LSU AgCenter researchers have used AFLP markers to estimate the amount of genetic diversity in southeastern populations and to assist in an eastern cottonwood breeding program coordinated by Mississippi State University. Because AFLP markers are so highly variable, scientists can easily identify each individual in our breeding program by its DNA fingerprint. This allows us to improve the efficiency of breeding by increasing the accuracy of the data and to assure proprietary rights by producing a DNA fingerprint for each clone.
Henslow’s sparrow is a small bird commonly found in prairie and pine habitats in Louisiana. In recent decades, this species has suffered a significant decline in population. One problem in studying Henslow’s sparrows is that it is impossible to accurately distinguish between the two sexes in the field. The inability to determine the sex of the birds makes monitoring the health of breeding populations difficult and imprecise. However, by using DNA markers to determine the sexes of captured birds, the researcher needs only to gather a small blood sample and can determine the sex of the bird in the laboratory.
These diverse research projects have all benefited from the application of molecular genetics. Basically, once the DNA is extracted from the leaves, blood or hair, the methods of analysis are the same and can be applied to such diverse topics as breeding trees and managing endangered wildlife species.
Michael Stine is an associate professor in the School of Renewable Natural Resources.
(This article appeared in the fall 2003 issue of Louisiana Agriculture.)