Corn can be found all around us from our food to our fuel. Corn is the plant behind the scenes running the show. If you find yourself fascinated with this plant good news for you, read on to find out more about this a-maize-ing plant! Sorry, if that was a bit corny but I promise that was the last joke.
So this summer I have been investigating two different mutant genes found in corn known as teopod 1 (tp1) and teopod 2 (tp2) with Professor Wills. Teopod 1 is a mutation that affects both vegetative and reproductive structures. Plants with this gene will have the following phenotypes: many tillers, narrow leaves, and partially podded ears. Plants with the teopod 2 phenotype will have many of the same phenotypes: many tillers, narrow leaves, and many small partially podded ears. But tp2 differs from tp1 in that it has a more severe effect on vegetative and tassel phenotypes and has less of an effect on the ear phenotypes.
The following is an image of an ear of corn we grew in the greenhouse with the tp1 phenotype. Teopod gets it name because some kernels are podded meaning they have extra husk leaves that cover individual kernels not just the whole ear. In the following image below, this is an ear of corn with those extra husk leaves. The next image below shows one of the extra husk leaves from that ear. Notice how the leaf is attached to a single kernel this is a phenotype associated with the teopod gene and does not occur in plants without this gene.
The following is an image of the corn we had growing in the greenhouse from a few weeks ago. There are 5 different plant lines growing here, either W22 or B73, two of the main plant lines with lots of genetic information already mapped out. W22 and B73 do not contain the mutant genes. Another plant line, X contains tp1 gene and plant lines Y and Z contain tp2 gene. We pollinate plants so there will be a cross from a W22 or B73 plant to one of the X,Y,or Z plants that contains the mutant gene. So the F1 generation will be heterozygous for the mutant gene if the X,Y, and Z plants were homozygous for the mutant gene.
Our goal is to find the specific location of these genes in the genome through genetic mapping. Based on other research we know tp1 is on chromosome 7 and tp2 is on chromosome 10 so now we just need to find the exact location by developing genetic markers.
So what are genetic markers? They are basically locations where there are mutations to be found between two different plant lines. The plant lines we examined were W22 and B73, they did not contain our mutant genes but have a ton of genetic information available so we are able to find useful mutations. We tried to design markers for the two ends where we believed the teopod genes were located. We looked for mutations in either the W22 or B73 lines that have huge insertions or deletions that are easy to score. Hopefully, these markers can be used as well in our other plant lines but it will be lots of trial and error before we can find good genetic markers.
The genetic markers are indicators on specific regions of the genome. So each bar would represent a different plant that either has the mutation or does not. Yellow would be representative of the mutant gene DNA and green will be representative of DNA without the mutation. If the gene is say located between M1.5 and M1.6 we would be able to narrow it down to that location based on whether or not the plant shows the tp phenotype.
So basically these markers help us narrow down exactly where the gene is located through process of elimination. All the bars above the red line are green representing plants without the mutation and the bars below the red line are yellow representing plants with the mutation. This is why it is important to have markers to identify the 5 plant lines a part. If it a segment has B73 or W22 DNA in between the two markers then the gene is not located in that region but the plant has the tp phenotype the gene is located somewhere in the entire region.
Finally, here is a picture of some plant leaves we took for our DNA extraction.
We ground up these leaves and extracted DNA to use for polymerase chain reactions (PCR) which is a method to amplify DNA. Primers are included in this reaction to amplify the region that contains the insertions or deletions that we designed primers against. If the PCR goes smoothly then we should see a gel that has an obvious difference in the number of base pairs in the W22 and B73 plant samples. Successful primers meant to amplify DNA regions for tp1 should have bands for W22, B73, and X plant lines while successful primers meant to amplify DNA regions for tp 2 should have bands for W22, B73, Y, and Z plant lines.