CmCGGMethylation-Independent Parent-of-Origin Effects on Genome-Wide Transcript Levels in Isogenic Reciprocal F1 Triploid Plants

Triploid F1 hybrids generated via reciprocal interploidy crosses between genetically distinct parental plants can display parent-of-origin effects on gene expression or phenotypes. Reciprocal triploid F1 isogenic plants generated from interploidy crosses in the same genetic background allow investigation on parent-of-origin-specific (parental) genome-dosage effects without confounding effects of hybridity involving heterozygous mutations.Whole-genome transcriptome profiling was conducted on reciprocal F1 isogenic triploid (3x) seed-lings of A. thaliana. The genetically identical reciprocal 3x genotypes had either an excess of maternally inher-ited 3x(m) or paternally inherited 3x(p) genomes. We identify a major parent-of-origin-dependent genome-dosage effect on transcript levels, whereby 602 genes exhibit differential expression between the reciprocal F1 triploids. In addition, using methylation-sensitive DNA tiling arrays, constitutive and polymorphic CG DNAmethylationpatterns atCCGGsiteswereanalysed,whichrevealed thatpaternal-excess F1 triploid seedling CmCGG sites are overall hypermethylated. However, no correlation exists between CmCGG methylation poly-morphisms and transcriptome dysregulation between the isogenic reciprocal F1 triploids. Overall, our study indicates that parental genome-dosage effects on the transcriptome levels occur in paternal-excess triploids, which are independent of CmCGG methylation polymorphisms. Such findings have implications for under-standing parental effects and genome-dosage effects on gene expression and phenotypes in polyploid plants. Key words: triploid; DNA methylation; parent-of-origin effect; polyploidy; epigenetic 1