2009 Summer Internship Program
Undergraduates: McCouch RiceLab at Cornell University
Diane Wang is a dual major in Biology and Entomology, with a minor in Plant Science in the College of Agriculture and Life Sciences at Cornell. She has done undergraduate research in the McCouch RiceLab since her freshman year (spring 2006), focusing on genotypic and phenotypic characters that can be used to interpret the genetic relationships among wild and cultivated rice species. During her 2009 summer internship, she undertook a QTL analysis using an interspecific backcross population to identify regions of the genome associated with the production of awns, a character related to seed dispersal that is found predominantly in wild accessions. She genotyped large numbers of segregating offspring using SSRs and indel markers, phenotyped the plants for the presence or absence of awns, and identified several QTLs related to the trait. She compared her findings to reports in the literature and to the results emerging from our large association mapping studies, and decided to fine-map and clone the gene(s) underlying the phenotype in order to gain a deeper understanding of the pathway or network of genes involved. Over the course of the summer, she observed that the trait was strongly influenced by environment; under crowded conditions, plants generally produce short or no awns, while they may produce long awns under non-crowded conditions. This insight heightened her interest in understanding how genes controlled awn production in response to environment. She is continuing her work in the McCouch RiceLab during her senior year at Cornell.
Ben Conway is a biology major at Temple University in Philadelphia. He came to the McCouch RiceLab in 2009 through the Boyce Thomson Institute REU summer internship program. During his time in the lab, he undertook a backcross conversion program using BC2 and BC3 progeny derived from a cross between the US cultivar, Jefferson, and a wild/weedy accession of O. rufipogon (IRGC#105491). His objective was to develop a near isogenic line containing a single O. rufipogon introgression across the yield-QTL on chromosome 6. The BC2 progeny was segregating for both the target QTL on chromosome 6 and several background introgressions that had been identified using a 1536-SNP Illumina assay. Lines containing the target introgression and as few background introgressions as possible had been backcrossed to generate a BC3 population. Ben screened this population using SSR markers across the regions known to carry introgressions to identify a line that carried only O. rufipogon DNA across the target QTL region on chromosome 6. He extracted DNA from leaf tissue collected from each plant and genotyped the DNA samples using SSR markers. His analysis allowed him to identify a plant that was identical to the Jefferson recurrent parent across the entire rice genome except for a ~10-13 Mb region across the target yield QTL on chromosome 6. This NIL will be selfed and seed will be amplified in the winter nursery during Nov 2009-Feb. 2010. Along with the Jefferson parent and other yield-NIL, this yld6.1_NIL will be grown out in multi-location trials in the southern US during summer 2010 to determine whether the O. rufiopogon introgression(s) continue to confer a yield advantage once background introgressions have been eliminated.
Undergraduates: Eizenga Lab at Dale Bumpers National Rice Research Center
Chance Jackson and Grant Brock assisted with most aspects of the phenotyping work from planting the seed in the field, to growing the accessions in the field, to collecting heading notes. They collected data on the panicle and seed traits using a seed counter and barcode reader, as well as, preparing samples for the chemical analyses. Both are seniors and the first in their families to attend college.
High School Students:
Eliza Sherpa entered the McCouch RiceLab in January 2009 as a high school intern. When she started, she had just completed one year of high school-level science and was recommended by her teacher, Dan Flerlage, who described her as having "an innate curiosity with all things related to biology". She was mentored by graduate student, Michael Kovach, and spent about 6 hours per week during spring semester working in the lab and greenhouse. Over the course of the semester, she assisted with the harvesting of rice leaf tissue from greenhouse grown plants and extracted DNA on a large scale (ie, dozens of plates of 96 samples each). She learned to perform PCR, set up and run agarose and polyacrylamide gels and to call alleles. She became familiar with genetic mapping, and has assisted with the mapping of a gene controlling hull color in rice. She also contributed to a molecular cloning project, where several PCR- amplified fragments were sub-cloned into a pCAMBIA plasmid for transformation. Eliza participated in the enzyme digestion, ligation, and bacterial transformation activities, assisted with colony selection, mini-preps to obtain plasmid DNA, and confirmation of transformed plasmids by PCR and enzyme digestion. By May 21, 2009, at the end of 16 weeks in the lab, Eliza was proficient enough to perform most regular laboratory activities without supervision, and shewas selected for an NSF-funded summer internship at the Boyce Thompson Institute.