Jacob D. Alsdurf
Ecological and Genomic Effects of Drought on Black Hills Native Perennial Plants
Overview of Research
The David Siemens Plant Ecological Genetics lab group at Black Hills State University is currently researching a variety of questions concerning range limit development in wild upland perennial plants. This research may also increase our understanding of the effects of climate change on range distributions.
We work with a small native mustard species, commonly called “Rock Cress,” whose genome has just been sequenced. The sequenced genome provides a huge advantage when searching for genes that matter. Much of my work has included conducting growth chamber experiments, where I plant, water, and care for 448 plants simultaneously. My research for the master’s thesis is on a functional genomic level, where I am asking questions about effects of the parent’s environment on offspring development. I am using DNA methylation detection techniques to help identify drought response genes and/or gene regions.
In previous lab experiments, we observed that plants whose parents were raised in a drought environment were more drought tolerant. We believe that this observation could be an epigenetic effect. Epigenetics includes the inheritance of environmental effects that cause changes in gene expression without changes to the DNA sequence.
DNA methylation is one of many epigenetic mechanisms that can regulate gene expression trans-generationally. The assay we used to detect differences in DNA methylation is called a methylation sensitive amplified polymorphism (MSAP or MS-AFLP). This method generates thousands of DNA fragments. Consequently, I am also learning about the statistical analysis of huge data sets. I received funding to attend a statistical genetics workshop this summer at the Fred Hutchinson Cancer Research Center, Seattle, WA.
DNA is composed of varied sequences of only four different molecules called bases. One of the bases is called cytosine. The MSAP protocol uses enzymes that are sensitive to methylated cytosine. The enzymes cut the DNA and produce fragments. The fragments can be separated electrophoretically, which means that the fragments travel different distances on a gel with an electric current running through it. The separated DNA fragments can then be excised from gels, amplified, sequenced, and compared to annotated reference sequences. The Rock Cress is a close wild relative of the model organism for plant molecular biology. Because their DNA sequences are similar, I will be able to understand the function of genes in the fragments that I sequence.
Thus far, I have extracted DNA from plants in a drought growth chamber experiment, completed the MSAP, and analyzed fragments on a genetic analyzer in BHSU’s DNA core facility. The data analysis of date has consisted of analyzing the methylation patterns using various statistical methods, including discriminant functional analysis, principal component analysis, and analysis of molecular variance, all of which we do within our lab group. This fall will involve lab intensive work, involving gel extraction and sequencing of fragments that are differentially methylated, which I believe to be functional drought responsive genes or gene regions.
My own story is not as exciting as the research I am involved with. I was raised in Rapid City, SD and have life experiences ranging from cooking in France to being a United States Marine running around the jungles of Okinawa. My educational background is a B.S. History/English from Minot State University, ND and then after more science training at BHSU, admittance into BHSU’s Masters of Science in Integrative Genomics program in the fall of 2012. After graduation I plan to work on a Ph.D. in a related genomics field.