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From fundamental insights to better plants, sustainably grown, serving the world

Six students complete Plant Science Undergraduate Research Honors Program

Congratulations to the six Plant Science majors who successfully completed honors theses as part of the Plant Science Undergraduate Research Honors Program (PSURHP). The PSURHP Committee  is composed of Margaret Smith, Toni DiTommaso, Taryn Bauerle, Teresa Pawlowska, and Tim Setter (chair).

The Research Honors Program provides students with the opportunity to experience the research process with a faculty mentor. Successful completion of the honors program requires a research report, written in the style of a master’s thesis or scholarly journal article. Students meeting this and additional honors requirements receive a Bachelor of Science degree with “distinction in research”.


Preprocessing germination and GxE factors effects on α-amylase/ trypsin inhibitors on wheat
Marlie Lukach
Supervisor: Mark Sorrells
Section of Plant Breeding and Genetics, School of Integrative Plant Science

The objective of this study was to better understand environmental and genetic variables that impact alpha-amylase trypsin inhibitor (ATI) accumulation in wheat. ATIs have become a health concern causing illnesses that range from irritable bowel syndrome to severe allergic reactions. Studies have shown that during early germination ATIs decline to non-detectable amounts as they are used in plant development. Partially germinating wheat kernels has the potential to be used to deplete ATIs before processing the grain. Wheat kernels of Genesee Giant and Glenn were germinated in a range of time periods, temperatures, and pH value to test the if these variables significantly affected ATI depletion from the kernels. The 3,5-dinitrosalicylic acid (DNS) technique was used to measure mg of maltose released in each germination treatment. The maltose released was used to indirectly measure ATI reduction in the kernel. A time of about 6 hours at 20°C was found to have the highest reduction of ATIs. The pH value of the germination water was not shown to be significant in ATI reduction. To evaluate the potential for breeding to decrease ATI, regional wheat lines from Cornell’s Small Grains Breeding Program were used to see the effects of year, location, seed color, and entry. Year, entry, and the interaction of entry:location and year:seed color were found to significantly affect ATI accumulation. Using the variability from the regional wheat lines broad sense heritability was found to be 0.075. A GWAS was done to a secondary set of wheat lines that identified three main markers associated with ATIs that corresponded with known locations of ATI related genes on chromosome 3D and 4D. Heritability was calculated based on trait variance components to be about 4.4%. In conclusion, this study identified conditions to deplete ATIs as a pre-processing step for wheat; however, the low heritability of ATI accumulation may limit the potential for breeding low ATI cultivars.


Investigating the role of replication factor C (RFC) genes during arbuscular mycorrhizal symbiosis
Cassandra Proctor
Supervisor: Maria Harrison
Boyce Thompson Institute, School of Integrative Plant Science

The arbuscular mycorrhizal (AM) symbiosis is an ancient association between the roots of vascular plants and the fungi of the Glomeromycotina. In exchange for a carbon source, the fungus provides the plant with mineral nutrients, mainly phosphorus. The ability to support the symbiosis is highly conserved in many plant families. A phylogenomic study resulted in a set of genes conserved exclusively in AM plant hosts, two of which were annotated as AM specific replication factor C genes (RFCa and RFCb). RFCa and RFCb are homologous to subunit 3 of the well characterized replication factor C complex (RFC), the complex used to load Proliferating Cell Nuclear Antigen (PCNA) onto the DNA during replication. However, RFCa and RFCb have additional domains of unknown origin, almost doubling their size compared to RFC3. The spatial expression patterns of both genes were investigated using promoter-GUS fusions, which showed GUS expression in colonized root cells. Mutant rfcb plants were shown to have a small but significant reduction in the amount of colonization as compared to wildtype plants. A double rfca rfcb mutant was generated, and mycorrhiza phenotyping experiments revealed that, while the double mutants did not show an overall reduction in colonization levels, they did exhibit a significant reduction in arbuscule size. Finally, the ability of RFCa and RFCb to interact with five subunits of the replication factor C complex was tested using a yeast two hybrid system. These data provide the first information about the potential functions that the AM-conserved RFC genes may play during the symbiosis.


Computational Modeling and Optimization Applied to Controlled Environment Agriculture Lighting Systems
Daniel Santander
Supervisor: Neil Mattson, School of Integrative Plant Science, Cornell University
Supervisor: Kale Harbick, Application Technology Research, US Department of Agriculture

Supplemental lighting is integral to year‐round production of greenhouse crops; however, the location of lights within the greenhouse and its effects on lighting uniformity in the growing space is often not considered. This research was conducted to assist Controlled Environment Agriculture (CEA) producers and researchers in identifying the optimum lighting layout for improved lighting uniformity. The methodology outlines the development of an algorithm for modelling supplemental lighting, based on standardized goniophotometric data, and optimizing the location of lighting fixtures within the CEA environment. This resulted in the production of a software package in the Python Programming Language that could model and optimize lighting uniformity for unique CEA environments based on their physical dimensions and specified lighting fixture. Through the implementation of this novel software, the lighting uniformity for hypothetical CEA environments with a small number of supplemental lighting fixtures were optimized.


Genetic Basis for Enhancing Carotenoid Stability in Arabidopsis thaliana Seeds
Ziqing Wei
Supervisor: Li Li
USDA-Agricultural Research Service, and Section of Plant Breeding and Genetics, School of
Integrative Plant Science

Carotenoids play crucial roles in plant growth and human health. Worldwide vitamin A deficiency has aroused many breeding efforts to enhance provitamin A carotenoid (such as β- carotene) levels in crops. Due to non-optimal conditions during post-harvest storage and transportation, many carotenoids are lost before the harvested crop products reach the consumer. β-carotene instability has been a major barrier to the supply of this vital carotenoid for human nutrition. In this research, I utilized a set of Arabidopsis thaliana (L.) Heynh. genetic transformants with enhanced β-carotene stability and accumulation. We hypothesized that increased expression of certain enzymes in the carotenoid pathway would enhance the flux and stability of β-carotene and improve its accumulation. Through the use of stacking multiple gene constructs, we demonstrated that overexpression of phytoene synthase (PSY), ORANGE (OR) and homogentisate geranylgeranyl transferase (HGGT), and knock-out of hydroxylases BCH, increase the accumulation of β-carotene by improving metabolic flux and increasing stability (decrease degradation). I made major contributions to the selection of positive transformants, examination of seed germination rate, and assay of carotenoid content. A germination rate test confirmed that our genetic manipulations did not have a negative influence on seed development. Our analysis of carotenoid content indicated that the total amount and composition of carotenoids are substantially improved after 8-week post-harvest storage. These findings will provide new insights in understanding carotenoid metabolism and help plant scientists enhance the nutritional value of plant products.


The CITF1-mediated Regulatory Network of Copper Homeostasis in A. thaliana
Yihe Zhang
Supervisor: Olena Vatamaniuk
Section of Soil and Crop Science, School of Integrative Plant Science

Copper is a micronutrient involved in important biological processes including respiration, photosynthesis, reproduction, hormone perception, and lignin synthesis, and thus, is essential for the growth and development of all organisms including plants. Copper deficiency, occurring in alkaline and high organic matter soils that occupy more than 30% of the world’s arable land, can reduce plant growth, fertility and, in acute cases, cause total crop failure. In contrast, excessive copper accumulation in cells is toxic, because free copper ions cause oxidative stress. Therefore, the precise regulation of copper uptake and internal transport is needed to ensure successful growth, development, and fertility of plants. The transcription factor, SPL7, is a master regulator of copper homeostasis in Arabidopsis thaliana. A novel regulator of copper homeostasis, CITF1, was identified recently in A. thaliana and found to control the expression of genes mediating copper uptake into plant roots and internal transport and delivery to flowers. CITF1 was shown to act, in part, independently of the SPL7-mediated pathway. However, the upstream regulators of CITF1, the protein function of CITF1, and the downstream targets of CITF1 are still largely unknown. This thesis focuses on the identification of two putative upstream regulators of CITF1, ATHB2 and ATHB4, the copper dependent CITF1 turnover, and the downstream targets of CITF1 in A. thaliana. Specifically, I found that the transcription factor ATHB2 functions as the positive regulator of CITF1, whereas its homolog, ATHB4, can be a possible negative regulator of CITF1. I also found that the stability of CITF1 is regulated by copper availability. This conclusion was based on finding that copper deficiency has led to CITF1 accumulation in roots and shoots, while excess copper accelerated the turnover of CITF1 most likely via the 26S proteasome degradation pathway. Finally, I also present initial data on the identification of the downstream targets of CITF1.


QTL Analysis and Fine-Mapping of a Grain Morphology Kernel Length Locus in W7984×Opata Spring Wheat Reference Populations
Elizabeth J. De Meyer
Supervisor: Mark Sorrells
Section of Plant Breeding and Genetics, School of Integrative Plant Science

In wheat (Triticum aestivum L.), kernel morphology traits hold value for their association with milling quality and grain yield. Kernel morphology is largely determined by the rate and duration of grain fill resulting in variation in kernel length, width, and thickness. Although yield increases are difficult to attain by improving kernel size alone due to trade-offs with other yield components, understanding the genetics of kernel morphology remains important for increasing yield potential. The aim of this research was to initially map and compare contributions of QTL on chromosomes 2D and 5A to kernel morphology traits in the W7984 × Opata spring wheat doubled haploid (SynOpDH) reference population, then to fine-map within the chromosome 2D QTL using the W7984 × Opata spring wheat recombinant inbred line (SynOpRIL) reference population. We identified multiple quantitative trait loci (QTL) for kernel length, width, and weight in the SynOpDH population. Best linear unbiased predictor (BLUP) values for each SynOpDH line indicated that the QTL on chromosome 2D increased mean kernel weight by 6.26% and mean kernel length by 4.33%. We identified lines from the SynOpRIL reference population segregating at the 2D QTL, and we advanced these lines to develop heterogeneous inbred families for fine-mapping the 2D QTL for kernel length and weight. These developed lines, along with 11 KASP markers developed within the 2D QTL, provide potential for further population development and fine-mapping, with an ultimate goal of characterizing and cloning the causal variant of the gene within the 2D QTL and integrating the gene into commercial varieties.

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