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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #422333

Research Project: MaizeGDB - Database and Computational Resources for Maize Genetics, Genomics, and Breeding Research

Location: Corn Insects and Crop Genetics Research

Title: Maize and wild relatives show distinct patterns of genome downsizing following polyploidy

Author
item SNODGRASS, SAMANTHA - Iowa State University
item Woodhouse, Margaret
item STITZER, MICHELLE - Cornell University
item HUFFORD, MATTHEW - Iowa State University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 12/25/2024
Publication Date: 12/25/2024
Citation: Snodgrass, S.J., Woodhouse, M.R., Stitzer, M., Hufford, M.B. 2025. Maize and wild relatives show distinct patterns of genome downsizing following polyploidy. bioRxiv. https://doi.org/10.1101/2024.12.24.630189.
DOI: https://doi.org/10.1101/2024.12.24.630189

Interpretive Summary: Plant genomes undergo a great deal of genome duplication. However, many of the duplicated genes from these events become deleted, or fractionated, over time. Research in domesticated maize suggests that most of these deletion events occurred right after the genome duplication event. To precisely identify the timeline of gene deletion after the duplication event, we studied the deletion events in the recently sequenced genomes of maize wild relatives. We found that the majority of gene deletion occurred in a common ancestor of modern maize, but that one of the maize relatives, Tripsacum, had unexpectedly undergone less gene deletion than maize. We believe this is related to the fact that the Tripsacum genome appears to undergo less genome disruption and rearrangement than maize. We also found that ~35% of the duplicated genes examined underwent deletion in some maize lines but not others. These results suggest that gene deletion in plants is more dynamic than previously predicted.

Technical Abstract: Plant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, until genomes return to a diploid-like state, though some duplicates remain from the polyploid ancestor. Fractionation can affect the copies of ancestral diploid genomes (i.e., subgenomes) differently, resulting in one being preferentially retained and the other preferentially lost. While previous work suggested fractionation occurs shortly after a polyploidy event, few studies have been able to densely sample descendent genomes from the same whole genome duplication event. The Tripsacinae subtribe of grasses, which includes the genera Tripsacum and Zea and the economically and culturally important maize (Zea mays ssp. mays), originates from an ancient allopolyploid (~5-12 MYA). We use publicly available genome assemblies from the Tripsacinae subtribe of grasses to investigate the patterns and timing of fractionation relative to the outgroup sorghum, which does not share the allotetraploidy event. Our results show the majority of fractionation following polyploidy occurred in a common ancestor of modern species and that one subgenome is preferentially retained, in keeping with previous studies of maize. However, Tripsacum retains a greater proportion of duplicate genes (homoeologs) than Zea, potentially related to the fewer chromosomal rearrangements observed in this genus. Multiple, nested deletion events were commonly observed in alignments to a single sorghum reference exon, and some homoeologs show fractionation of different exons across genomes. Further, ~35% of homoeologous pairs of exons show differential fractionation, where fractionation patterns differ between species. Altogether, this suggests multiple origins of fractionation for a given homoeolog may be common. We demonstrate that fractionation is a much more dynamic process in the Tripsacinae than previously predicted.