ABSTRACT

Genetic information in plants and animals is carried in the DNA of pairs of chromosomes that are carried forward from generation to generation. Change in the numbers, or doses, of individual chromosomes is known to occur, usually with detrimental effects on the stature and health of the affected organism. Surprisingly, there are no obvious differences if the entire set of chromosomes change. This phenomenon has puzzled scientists for decades: what features of the genome maintain balance when fully altered, but are imbalanced when only some chromosomes are affected? This project will examine how and why this partial change in the chromosomes has such an impact on plants. Maize is an ideal model for this study due to its global crop importance and also because of the powerful genetic resources available to test how the so-called genome balancing act occurs. One hypothesis is that the relative expression of regulatory genes, which are the factors that control the expression of other genes, has a significant impact on development and vigor of plants. The research identifies the underlying molecular mechanisms involved in maintaining genomic balance. This knowledge is essential to understand how plant vigor is controlled and will provide information about the traits needed for improving agriculture. Students and educators of all levels are engaged in addressing this problem through direct hands-on research, via social media outlets and outreach workshops. Understanding how regulatory dosage effects operate will guide breeding programs for crop improvement and will answer basic questions about how plant genomes function.

This project is based on a synthesis emerging from the idea of genomic balance known from classical genetics and more recent molecular studies. The overall hypothesis is that the stoichiometry of assembly of multisubunit gene regulatory complexes affects the function of the whole, which will impact global gene expression and ultimately the phenotype. The analysis of genomic balance issues will address: (1) how genomic imbalance affects gene expression levels of mRNA, siRNA, and miRNA as the baseline for understanding the circuitry involved; (2) how small RNAs are involved with genomic balance in modulating mRNA levels and how genomic balance affects small RNA levels; (3) how genomic imbalance impacts and/or operates through chromatin modifications; and (4) how genomic imbalance works on the single gene level by examining the effect of varying the dosage of single subunits on whole complex formation and function. These aspects will be studied in a set of aneuploids generated by translocation with the supernumerary B chromosome of maize that can be used to vary selected chromosome arms in haploid and diploid plants. By examining more complex changes in dosage with greater or lesser genomic imbalance, how the interactions of regulatory processes alter various aspects of gene expression will be tested. Single regulatory gene candidates responsible for target gene modulations will be examined in a transgenic dosage series to gain insight into the mechanism of genomic balance. Together, the information from all of these fields will contribute to an understanding of genomic balance and allow this information to be applied to issues of world food production.

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