Source: UNIVERSITY OF NEBRASKA submitted to
DETECTION AND ASSESSMENT OF GENETIC VARIATION IN ECONOMICALLY IMPORTANT WEED SPECIES.
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0195217
Grant No.
(N/A)
Project No.
NEB-12-294
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jan 2, 2003
Project End Date
Jan 31, 2008
Grant Year
(N/A)
Project Director
Lee, D. J.
Recipient Organization
UNIVERSITY OF NEBRASKA
(N/A)
LINCOLN,NE 68583
Performing Department
AGRONOMY & HORTICULTURE
Non Technical Summary
Herbicides initially effective in eliminating weed problems in crop production are now less effective. DNA analysis of a specific region of single genes can explain this observation. Biocontrol of noxious weeds in rangelands is influenced by genetic variation among populations. These examples illustrate the need for understanding the role of genetic variation in weed management. The purpose of this project is to learn more about the role of genetic variation in the managment of weed species.
Animal Health Component
(N/A)
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
21323001080100%
Knowledge Area
213 - Weeds Affecting Plants;

Subject Of Investigation
2300 - Weeds;

Field Of Science
1080 - Genetics;
Goals / Objectives
1) Determine the weed species and individuals for genetic analysis using field observation and genetic databases. 2) Assemble information and protocols appropriate for the plant species to be studied and the specific genes to be analyzed. 3) Identify and collect individuals and populations that represent the weed management situation. 4) Design preliminary studies that will test and optimize procedures to reliably target desired gene sequences. 5) Apply genetic analysis procedures to the population representatives. 6) Analyze gene sequence information to identify the genotype of individuals or compare the relationships and genetic composition of individuals and populations.
Project Methods
The motivation for our project will start with the work of the field biologist that points to the need for genetic information on a plant species. The second phase will be to assign specific genetic targets for analysis. Based on field observations, the literature and genetic database information, the genetic target may be as narrowly defined as a small region of a single gene or may be targets that provide a genome-wide analysis. When specific genes controlling specific traits will be logical candidates for study, the search for targets and procedures is focussed to a few hundred nucleotides. In cases where the physiological function of the genes controlling weed success in a management system are not known, genetic markers combined with phenotypic analysis of individuals and families will be used to track sequence variation associated with fitness. We will prioritize expressed genes in our work. The procedure of choice in DNA analysis uses the polymerase chain reaction (PCR). Single stranded primers must be designed to target the gene region to be analyzed and not generate PCR products from additional loci. Sequencing of the purified product can be used to verify the targeted gene was amplified with the procedures developed. Once primer combinations and PCR protocols that generate multiple products are eliminated, attributes of the amplified product can be assessed. In studies using genome markers, introns will be targeted because they are more likely to contain nucleotide sequence variation and serve as genetic markers to track the biogeographical difference in populations. When genes with specific functions are used, exon sequence differences that result in amino acid sequence variation in the encoded protein will be the emphasis. Finally, whether the primers target a specific gene region that includes an intron or make a copy entirely of exon sequence, we must be able to detect nucleotide sequence variation in this region. Gene sequencing is the utlimate method to detect nucleotide sequence differences. However, gene sequencing is too expensive for application to populations. Thus in our study, sequence variation is detected through a sampling of sequences in the amplified products with restriction endonucleases. After restriction endonuclease digestion, DNA fragments are separated by size with agarose gel electrophoresis to detect restriction fragment length polymorphisms. Analysis of the data is done with the specific statistical method to address different questions.

Progress 01/02/03 to 01/31/08

Outputs
OUTPUTS: manuscript in preparation for "Biological Control" PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Genetic variation among North American (NA) populations of leafy spurge was found and this has implications on the use of biological control. We were testing the hypothesis that NA populations represent distinct introductions from different Eurasian origins. Comparing DNA differences within and between populations tells us the story is more complex. A subset of the variation found in Leafy spurge populations in their native range exists in North America as expected. However, NA populations represent a mixture of genetic types found in various Eurasian populations. NA populations have been mixed, probably from migration. Biological control success may be attributed to the genetics of the NA population and the biocontrol insect. Establishment of successful insects on a given population may require more attempts. One clear relationship from our analysis was the lack of genetic similarity between NA and Italian leafy spurge. This suggests that collection of more insects to build diversity in the biocontrol agent populations should be directed to locations other that Italy.

Publications

  • No publications reported this period


Progress 10/01/06 to 09/30/07

Outputs
OUTPUTS: Revealing, quantifying and evaluating the genetic variation in weeds and economically important native plants provides insights on both their past and their future. Our project asks the same questions and undertakes the same line of investigation on both categories of plants. The answers we uncover can either be good news or bad news, depending on the plant and what you want to do with the plant. Our primary output has been information about the genetic status and genetic history of the plants we study. We disseminate this information through peer reviewed publication, through extension and outreach teaching and in academic courses. The communities of interest are peers in research, the general public and undergraduate and graduate students. The most significant outputs are likely to be research publications.. however our work in this area coupled with access to hundereds of science students in academic courses means this area of investigation gains tremendous exposure to people who can relate to the importance of pushing science in a direction to know more about this part of our natural world. TARGET AUDIENCES: Biological control professionals and practitioners. Native plant breeders.

Impacts
Approaching agriculture from an ecosystem management prespective is the mission of our work. Relatively few resources are committed to a better understanding of weeds and native plants. Our work will help move our understanding of the value of model system genetic information in addressing questions about plants in important production and natural ecosystems. Our work will also provide the opportunity for ecosystem managment decision making to be based on facts rather than assumptions. For example, our analysis of leafy spurge variation demonstrates the plants in North America are likely to have origins from Europe and Russion that are not in the focus areas for biological control agent collection. The information we publish can help make this aspect of ecosystem management for systematic.

Publications

  • Gulsen, O., R.C. Shearman, T.M. Heng-Moss, N. Mutlu, D.J. Lee, and G. Sarath. 2007. Peroxidase gene polymorphism in buffalograss and other grasses. Crop Science 47: 767-772.
  • Clark, P. L., J. Molina-Ochoa, S. Martinelli, S. R. Skoda, D. J. Isenhour, D. J. Lee, J. T. Krumm, and J. E. Foster. 2007. Population variation of the fall armyworm, Spodoptera frugiperda, in the Western Hemisphere. J. Insect Science. Vol. 7: number 5 1-10


Progress 10/01/05 to 09/30/06

Outputs
Leafy spurge plants from five North American and eight Eurasian populations have been compared using differences in expressed DNA sequences. Sequence variation is based on differences in DNA fragment lengths generated by restriction enzyme cutting from these expressed DNA regions.

Impacts
1) The restriction fragment length polymorphisms (RFLPs) discovered are reliable DNA markers that mark genes with known or proposed functions. These should provide advantages as markers when used between populations or between researchers. 2) The markers are PCR-based and can be used in population level studies. 3) The markers reveal considerable genetic variation in leafy spurge. This variation reflects the gene family nature of the target sequences and the occurence of within and between population variation in this species.

Publications

  • No publications reported this period


Progress 10/01/04 to 09/30/05

Outputs
Genetic variation in leafy spurge has been investigated with the use of DNA markers. We use two kinds of DNA markers in our investigations. One is a chloroplast DNA specific marker that allows us to detect differences in DNA sequences that are passed from the female parent to the seed. These markers help us track maternal parent origins of leafy spurge plants. These chloroplast markers are used in many kinds of plants and were developed as Universal markers by other researchers. They are useful to track variation in leafy spurge. The other kind of marker we use is based on nuclear DNA differences we can detect among expressed genes in leafy spurge. We have developed these markers from the sequence of cDNAs provided by other leafy spurge researchers. The markers we have developed are unique and help us track variation among leafy spurge that previous DNA markers could not find. The markers have been used to help us compare leafy spurge plants found in three North American areas (Nebraska, Montana and North Dakota) and three Eurasian areas (France, Italy and Russia). One of the most important questions is where did our (North American) leafy spurge come from? Our analysis tells us it probably did not come from Italy. The analysis also tells us that there is abundant genetic variation in all the leafy spurge populations we have looked at.

Impacts
The impact of these results is two fold. First, genetic variation is likely to impact the success of biocontrol approaches use for leafy spurge control and this variation contributes to the success of this invasive weed in North America. Second, many biocontrol insects that are used in North America to control leafy spurge populations were first collected on leafy spurge plants in Italy. Russia would be a better choice for future biocontrol agent collection based on the relationships revealed by these DNA markers.

Publications

  • No publications reported this period


Progress 10/01/03 to 09/30/04

Outputs
Our most recent progress has been on a project designed to establish PCR-based DNA markers for leafy spurge. The goal is to establish DNA markers that can be reliably used to provide DNA fingerprints for this noxious weed. The project has been successful. We have developed several marker systems that target nuclear genes in leafy spurge and reveal genetic variation. Of the approximately 230 plants from North American and Eurasian populations, 210 unique types can be identified with these markers. Use of the markers to assess both within and between population variation reveals some insights on the natural history of leafy spurge. The populations from Montana, Nebraska and North Dakota are at least as variable as the Eurasian populations. This suggests that the North American populations have been mixed since the plant was first introduced. The populations from Italy are the most unique. This fact is of important since much of the biocontrol agent collection has focussed on these Italian populations and it is known that genetic variation has an influence on biocontrol agent establishment. A paper is being developed for submission to the journal "Biological control".

Impacts
These marker systems can be used by groups looking systematically at the deployment of biocontrol insects.

Publications

  • No publications reported this period