Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations

Authors: LI, BO - Chinese Academy Of Agricultural Sciences; KREMLING, KARL - Cornell University; WU, PENGHAO - Cornell University; BUKOWSKI, ROBERT - Cornell University; ROMAY, MARIA CINTA - Cornell University; XIE, EN - Chinese Academy Of Sciences; Buckler, Edward - Ed; CHEN, MINGSHENG - Chinese Academy Of Sciences

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2018
Publication Date: 8/30/2018
Citation: Li, B., Kremling, K., Wu, P., Bukowski, R., Romay, M., Xie, E., Buckler IV, E.S., Chen, M. 2018. Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations. Genome Research. https://doi.org/10.1101/gr.229716.117.
DOI: https://doi.org/10.1101/gr.229716.117

Interpretive Summary: Cells need ribosomes to make proteins, yet modern research focused on the diversity of the regions of the genome coding of the DNA that makes them has been sparse. This study focused on the variations of the sequence and expression of those regions in maize. Through this study, we found that rRNA expression variation is probably a source of functional diversity that affects expression of thousands of genes, and thus phenotypes.This information can be used in breeding programs to guide selection and potentially improve the rate of genetic gain.

Technical Abstract: Ribosomal repeats occupy 5% of a plant genome, yet there has been little study of their diversity in the modern age of genomics. Ribosomal copy number and expression variations present an opportunity to tap a novel source of diversity. In the present study, we estimated the ribosomal DNA copy (rDNA) number and ribosomal RNA (rRNA) expression for a population of maize inbred lines, and investigated the potential role of rDNA and rRNA dosage in regulating global gene expression. Extensive variations were found in both ribosomal DNA copy number and ribosomal RNA expression among maize inbred lines. However, rRNA abundance was not consistent with the copy number of the rDNA. We confirmed the rDNA gene dosage has no regulatory role in gene expression; however, thousands of genes are co-regulated with rRNA expression, including genes participating in ribosome biogenesis and other functionally relevant pathways. We investigated the potential roles of copy number and the expression level of rDNA on agronomic traits, and found that both correlated with flowering time, but probably through different regulatory mechanisms. This comprehensive analysis suggested that rRNA expression variation is probably a source of functional diversity that affects gene expression variation and field-based phenotypic changes.