Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination

Authors: GARCIA, NELSON - University Of Minnesota; YIN, LU - Arizona State University; DUKOWIC-SCHULZE, STEFANIE - University Of Regensburg; MILSTED, CLAIRE - University Of Minnesota; KIANIAN, PENNY - Pepsico; Kianian, Shahryar; PAWLOWSKI, WOJCIECH - Cornell University; CHEN, CHANGBIN - University Of Minnesota

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2022
Publication Date: 10/12/2022
Citation: Garcia, N., Yin, L., Dukowic-Schulze, S., Milsted, C., Kianian, P.A., Kianian, S., Pawlowski, W.P., Chen, C. 2022. Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination. BMC Genomics. 23:702. https://doi.org/10.1186/s12864-022-08922-w.
DOI: https://doi.org/10.1186/s12864-022-08922-w

Interpretive Summary: A major determinant of the genetic diversity present in sexually reproducing species is the ability of their homologous chromosomes to exchange DNA during meiosis – a process called meiotic recombination. A reciprocal exchange of large chromosomal segments is called a crossover, and the cytological manifestation of the point of exchange is called chiasma. Meiotic recombination starts as a highly conserved process in sexually reproducing organisms and begins as a programmed double-strand break (DSB) in the DNA created by the SPO11 enzyme. Cellular events during meiosis can differ between inbred lines in maize. To determine if gene expression might play a role in these observed differences, an RNA-Seq experiment was performed on meiocytes from CML228 and compared to both B73 and Mo17. Results from this study reveal new potential genes that may be involved in meiosis in maize and suggest new lines of investigation into their potential role.

Technical Abstract: Cellular events during meiosis can differ between inbred lines in maize. For example, substantial differences in the average numbers of chiasmata and double-strand breaks (DSBs) per meiotic cell have been documented among diverse inbred lines of maize. CML228, a tropical maize inbred line, forms significantly fewer chiasmata per bivalent, when compared to temperate maize lines B73 and Mo17. To determine if gene expression might play a role in these observed differences, an RNA-Seq experiment was performed on meiocytes from CML228 and compared to both B73 and Mo17. Overall, the degree of similarity in expression patterns between the three maize lines reflect their genetic relatedness. Many of the genes that were expressed at higher levels in CML228 were related to small molecule metabolic processes, protein folding, response to stimuli, and meiotic recombination. On the other hand, genes that were expressed higher in B73 and Mo17 were related to regulation of transcription and nucleic acid metabolic processes. In addition, genes with inbred line specific expression patterns were uncovered, which implies that some cellular processes during meiosis might be different from inbred to inbred. Many of these sequences also have no functional annotation and appear to be unique to maize. Interestingly, the expression of Atm, a gene involved in DNA damage repair, was higher in CML228 compared to the other two inbred lines. Atm's role in regulating DSBs and crossover interference implies that naturally occurring gene expression differences of specific meiotic genes might have a potential impact on genome-wide patterning of crossovers. Taken together, our results reveal new potential genes that may be involved in meiosis in maize and suggest new lines of investigation into the potential role of Atm in fine tuning DSBs and crossovers.