McKain, M. R. | Search bioRxiv

bioRxiv2018

Ancestry of the two subgenomes of maize

Maize (Zea mays ssp. mays) is not only one of the worlds most important crops, but it also is a powerful tool for studies of genetics, genomics, and cytology. The genome of maize shows the unmistakable signature of an ancient hybridization event followed by whole genome duplication (allopolyploidy), but the parents of this event have been a mystery for over a century, since studies of maize cytogenetics began. Here we show that the whole genome duplication event preceded the divergence of the entire genus Zea and its sister genus Tripsacum. One genome was donated, in whole or in part, by a plant related to the modern African genera Urelytrum and Vossia, although genomic rearrangement has been extensive. The other genome donor is less well-supported, but may have been related to the modern Rottboellia-Hemarthria clade, which is also African. Thus Zea and Tripsacum together represent a New World radiation derived from African ancestors.

plant biology↗

bioRxiv2016

Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower.

The importance and applications of polyploidy have long been recognized, from shaping the evolutionary success of flowering plants to improving agricultural productivity. Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. How quickly one subgenome dominates within a newly formed polyploid, if immediate or after millions of years, and the genomic features that determine which genome dominates remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and that subgenome expression dominance significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within transposons in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and submissive subgenomes in the natural allopolyploid. Our analyses reveal that the subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following the hybridization. These findings not only provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events, but may also contribute to uncovering the mechanistic basis of heterosis and subgenomic dominance.

genomics↗