HORT 484 Blog: UGA Crop Genetics and Genomics REEU

Finemapping of Chlorophyll Content Locus in Tomato (S. lycopersicum) Katie Toomey, Yasin Topcu, & Ester van der Knaap Chlorophyll are the color-capturing pigments found in plants that allow them to photosynthesize. Chlorophyll A is considered the main pigment that absorbs UV in the orange-red and violet-blue range (430-660 nm) while the accessory pigment, chlorophyll B, absorbs orange-red UV (470 nm). To map chlorophyll B content genes in tomato, we worked with tomatoes of a known genetic background: BGV007900 and BGV007936 which are known to have high and low chlorophyll B contents respectively. Using with these two accessions from the sol genomics varitome project, one F4 and three F7 populations were created and F3:4 and F6:7 plants were selected using marker assistant selection using Kompetitive Allele Specific PCR (KASP). Populations along with parental checks were grown in a greenhouse and plants were phenotyped weekly for chlorophyll content index (CCI) using an apogee chlor

After finishing the last week of scanning, we will be throwing away the majority of my plants which no longer serve a purpose. So to honor their service, I took one last photo with them. Above are images of the plants in the third and sixth week post sowing. Their growth is astonishing to me; Two plants (after all data was collected thank goodness) fell off the bench due to their sheer height and weight. I've overall enjoyed working with tomatoes though because I am grateful I got to work on such an important crop. It was extremely rewarding to be on this project as we were successful in narrowing the region of interest where our locus can be. Above shows how the previous and current knowledge concerning the region of the chlorophyll content gene in tomato. The genotypes are 21S237, 21S238, 21S239, & 21S240 reading from top to bottom. We are able to lower the region of interest to 31.5 thousand base pairs because we saw both 237 and 240 separate phenotypically that correlated t

This week has involved me working with other researchers to aid in their projects in my free time. I helped a post-doc take cross-section images of her fruit shape project and I personally found the tomatoes to be adorable. She is studying the genes that affect fruit shape in the longjohn variety of tomato and the images below prove that they live up to their name. She will use specified metrics such as height to width ratio to be able to compare such strangely shaped fruit.  Furthermore, I also got a working rough draft of my poster organized for this program. I have gotten feedback from a PhD student in the lab, but will discuss the poster with my mentor soon enough. In the meantime though, I am proud of the flow and organization of it.

This week in the REEU we visited the Sundance Organic Farm in Danielsville, Georgia. There we met farmer Ed who grows everything on his farm organically. This means that he must abide by certain regulations and avoid the use of certain pesticides and GMO crops in order to meet the organic requirements. Instead of pesticides, he relies on planting small portions of crops and rotating them often to avoid getting a severe infestation. He said he once got an insect problem and had to go squish them by hand and spray with neem oil (an organic bug deterrent) to fight them off. He also avoids the use of herbicides and picks weeds by hand. He says farming is better this way, rather than spraying "poision" on your crops and then feeding it to your family. He did admit though, he would potentially be open to planting editted tomatoes if they still contain only the tomato genome. However, this would breach the organic regulations and would therefore be impossible for him. Nonetheless, h

Using the Apogee CCM-200, I took multiple scans chlorophyll content of every plant in our experiment to help phenotype the plants. Happily enough, I got a clear, statistical separation between the phenotypes  Here is a rough JMP snapshot of the 21S240 So the 237 and 240 both segregated in terms of phenotypic expression which indicate that the gene of interest (the one they are segregating for) must lie somewhere in the unfixed region that 237 and 240 have in common. This means that we have effectively narrowed down the region of interest for the gene and we will continue to do so over the summer.  The unfixed areas of 237 and 240 show where we believe the gene of interest to be.

Background for PCR:  DNA is the recipe cells use to create and sustain life. A location on a strand of DNA is called the gene locus and the different variations of the gene are called alleles. So a designated parking spot would be similar to the gene locus and the car parked there would be akin to an allele. If scientists want to study a particular locus in a set of samples, polymerase chain reaction (PCR) can be used to produce multiple copies of a specific region. The basic steps to PCR: First, the sample's DNA must be mixed with a combination of primers, a buffer, and a special enzyme named Taq that is heat resistant. Then the mix is heated and cooled repetitively to allow the primers and enzyme to create new copies of the DNA in a cycle. When finished, the DNA is multiplied/amplified and can be used for forensics, the detection of viruses, genotyping(observing which samples have which alleles), etc.  How PCR will help my project: I learned PCR this summer because we have used i