Faculty mentors: Asa Ben-Hur, Hari Iyer, Nora Lapitan

Project Objectives and Aims:

The objective of this project is to provide an opportunity for students to learn about molecular genetic mechanisms of susceptibility/resistance of plants to insect attack, through a hands-on project requiring both basic biological knowledge and the development and use of bioinformatics tools and statistical analyses.

Project Background:

For more than two decades Colorado's multi-million dollar wheat industry has been damaged by the Russian wheat aphid (Diuraphis noxia). Chemical control is costly and may be environmentally threatening. Dr. Lapitan and colleagues have identified several genes in wheat that confer natural resistance to the aphid, and molecular genetic maps have been developed for these genes. DNA markers for resistance genes have been provided to the wheat breeding program to use in marker-assisted-selection of resistant cultivars.

Recently, populations of D. noxia have overcome existing resistance genes in the United States. These new biotypes present a difficult challenge, and new solutions depend on understanding how the aphid and plant interact, and how and why new biotypes evolve. Studies ongoing in Dr. Lapitan’s laboratory address these questions, including transcript profiling studies and identification of elicitor proteins from the aphid that are recognized by resistant plants (Botha et al. 2005; Lapitan et al. 2007). Recently, genomic resources have become available for wheat, with more than 900,000 ESTs and an oligonucleotide microarray. The Wheat Gene Chip array® contains 61,000 probe sets representing 55,000 wheat transcripts. The rice genome also provides an important resource for wheat because of conservation of gene order between parts of the genomes of rice and wheat (Gale et al. 1998). Additionally, pairs of wheat genetic lines differing in the presence or absence of genes conferring different types of resistance have been developed and are available for this project.

Project Description:

Our hypothesis is that host plant genes conferring resistance to D. noxia will be differentially expressed by resistant and susceptible plants during aphid infestation. During the summer following the Team Research Seminar the student team will design a microarray experiment incorporating RNA collection and hybridization to Affymetrix gene-chip arrays, data analysis, and identification of differentially expressed genes. The data collection phase of the project will be completed during the first summer, data analysis and manuscript writing will occur during the following summer.

Students will attempt to identify genes that are involved in different types of resistance response of the plant hosts by identifying differentially expressed genes between different pairs of resistant and susceptible genotypes. Additional experiments will be conducted to test any further hypotheses generated during the data analysis stage. These may include reverse transcription quantitative PCR (RT-qPCR) or silencing of candidate genes using virus-induced gene silencing. Students may also use comparative genomics analysis between rice and wheat to identify candidate genes for resistance loci in wheat that had been previously genetically mapped (Anderson et al. 2003; Lapitan et al. 2007).