Mendelian genetic principles guide our understanding of how traits are defined by specific gene variants (alleles) and are inherited into future generations, like how the human brown eye color trait is due to the inheritance of a single "dominant" allele. However, certain alleles - like some responsible for defining flower or seed colors in corn - exhibit inheritance patterns at variance with Mendelian laws. Previous studies show that some of these exceptional behaviors are influenced by temperature during early seedling development, causing heritable changes in seed coloring. Because modern breeding applies Mendelian rules to adapt agriculturally relevant species to increasing environmental extremes, it is imperative to understand why some alleles exhibit non-Mendelian behaviors and how plant genomes are heritably influenced by the environment.

The project goals were to define the regions of a highly-studied corn genome that are copied into ephemeral bioactive messages, identify other alleles that can be heritably changed from one generation to the next, and investigate the heritable changes occurring to this genome copying process caused by extreme temperatures during seedling stages. Additionally, the project synergistically generated a set of educational corn cob sets suitable for hands-on classroom experiences to learn about both classical Mendelian genetic concepts and exceptional inheritance behaviors, including those defined by inheritance from male vs female parents.

This project adapted a protocol (Global Run-On sequencing - GROseq) for identifying specific regions of the corn genome that are copied/transcribed to RNA messages and the rates at which these transcription events occur. The sequence-based datasets generated from this protocol defined regions previously known to be copied, as well as novel areas of the genome that presumably make RNA molecules that are rapidly degraded. These datasets now facilitate a high-confidence annotation of the B73 inbred corn genome for regions that are copied by a highly-conserved cellular enzyme known as RNA polymerase II (RNAP II). We found that a related, but plant-specific RNA polymerase (RNAP IV), impacts precisely where RNAP II engages DNA to make RNA copies. In the absence of RNAP IV, RNAP II copies alternative regions of the genome and some of these novel patterns persist into the next generation. Thus, we found that RNAP IV action and/or its copied RNAs in the parental generation define the way in which the DNA-based blueprint is interpreted and executed during corn development in the subsequent generation.

Our results identified hundreds of alleles, and other regions, whose normal copying patterns are heritably altered either in the absence of RNAP IV or after heat stress in early development. These alleles represent labile targets of corn improvement strategies that do not conform to canonical Mendelian laws, particularly the concept that alleles remain unchanged from one generation to the next. The project used differences in both seedling temperature and RNAP IV function to show that the corn genome blueprint being copied in future generations is dependent on both paternal parameters. These findings add to a growing list of organisms, and examples, in which paternal environmental experiences have heritable consequences to their offspring, and provide a clear example in which some of these changes are due to the actions of RNAP IV. The specific alleles identified in this project provide a targeted dataset with which to discover the types of chromosome organizations and/or molecular hallmarks that characterize these unusual and highly dynamic genomic regions. The datasets and corn materials developed by this project facilitate our greater understanding of both Mendelian and non-Mendelian inheritance in student education, chromosome biology, evolution, and applied plant sciences.

Last Modified: 07/30/2023
Modified by: Jay B Hollick