Thanks to a novel approach, researchers can now look at the DNA of a wide range of animals and even see how the genes in a population of oysters can change from yesterday to today. Dr. Chris Bird, Assistant Professor of Biology at Texas A&M University-Corpus Christi, and his colleagues, have introduced a simplified method for genotyping in non-model organisms. The process called ezRAD, is a unique approach to genotyping and allows labs to conduct research with little technical knowledge that could potentially save over $100 thousand in laboratory equipment.
ezRAD allows researchers at the Island University to ask questions on how human activities are affecting the genetic structure of an animal’s population. Bird says that because they can sequence so much of the genome in hundreds of individuals at a low cost, they can really tell how populations are responding to natural and human-induced pressures. This information can potentially affect the management of economically important species in Texas, like oysters and red snapper.
“Instead of asking what happened in a population’s genome over the past thousand years we can ask questions that are impacting populations today,” said Bird. “Because we can see so much of an animal’s DNA, we can now ask what has changed today compared to yesterday.”
With the assistance of his co-authors; Dr. Robert J. Toonen of the Hawaii Institute of Marine Biology, and Jonathan B. Puritz, a post-doctoral student at Texas A&M-Corpus Christi, Bird has developed an easy way for scientists to look at organism’s genes. Using traditional methods for genotyping required researchers to work with model organisms that have well-developed genomic resources. This makes finding markers, a DNA sequence with a known location, for non-model organisms a costly endeavor.
Bird and his colleagues use restriction enzymes that can recognize particular sequences of nucleotides in an organism’s DNA. They then sequence the DNA on either side of the restriction cut sites.
“Basically we chop up the genome at the GATC location and sequence next to the chopped sites,” said Bird. “We have sequenced everything from sea stars to dolphins and the new process worked. It worked the first time–it has worked every time.”
Future studies will lead to optimizing ezRAD and making it even less expensive. Assistant Professor Dr. Derek Hogan, Heart Research Institute Endowed Chair for Genetics and Biodiversity Dr. John Gold, Assistant Professor of Marine Biology Dr. David Portnoy, and a team of graduate students are currently working on the project. The study can be found published in the peer-reviewed academic journal “PeerJ.”
“We are really putting Texas A&M University-Corpus Christi on the map in the field of population genomics,” said Bird. “We are bringing high-tech, cutting edge research right here to Corpus Christi.”