C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants

Abstract

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) seedlings of A. thaliana. The genetically identical reciprocal 3x genotypes had either an excess of maternally inherited 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 DNA methylation patterns at CCGG sites were analysed, which revealed that paternal-excess F1 triploid seedling C(m)CGG sites are overall hypermethylated. However, no correlation exists between C(m)CGG methylation polymorphisms 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 C(m)CGG methylation polymorphisms. Such findings have implications for understanding parental effects and genome-dosage effects on gene expression and phenotypes in polyploid plants.

Keywords: DNA methylation; epigenetic; parent-of-origin effect; polyploidy; triploid.

Figure 1.

Generation of isogenic F1 reciprocal triploid plants. (A) Generation of tetraploid A. thaliana Col-0 using colchicine treatment. (B and C) Generation of maternal- and paternal-excess reciprocal F1 triploids by crossing diploid and tetraploid A. thaliana plants.

Figure 2.

(A) Percentage methylation of constitutive (orange) and polymorphic (blue) methylation in a C^mCGG context across the five chromosomes of A. thaliana. (B) LOWESS smoothing of constitutive methylation d scores using 200 kb discrete windows. LOWESS smoothing of constitutive methylation (orange), or a null distribution (black) obtained by shuffling by 1 kb blocks then LOWESS smoothing. (C) LOWESS smoothing of polymorphic methylation d scores using 200 kb discrete windows. LOWESS smoothing of polymorphic methylation (blue), or a null distribution (black) obtained by shuffling by 1 kb blocks then LOWESS smoothing. X-axis represents the position across the chromosomes.

Figure 3.

Percentage of methylated sites (C^mCGG) across genomic features for constitutive (orange) and polymorphic (blue) methylation. CDS: coding sequence; 5′ and 3′ UTRs: untranslated regions; up 1 kb: 1 kb region upstream of the genes; down 1 kb: 1 kb region downstream of the genes.

Figure 4.

Percentage methylation (C^mCGG) across genic regions. (A) Constitutive methylation between reciprocal triploids and (B) polymorphic methylation between reciprocal triploids. Gene regions split into percentiles from 5′ to 3′ end of genes. Genes were further split into sizes ranges from <1, 1–2, 2 and >3 kb.

Figure 5.

Association between constitutive methylation (C^mCGG) across genomic features (y-axis) and the absolute gene expression of associated genes (x-axis). Gene expression levels from all arrays [3x(m) and 3x(p)] were used and genes were split into percentiles.

Figure 6.

Boxplots of the distribution of small RNA accumulation across genomic features associated with genes differentially expressed between 3x(m) and 3x(p). n = the number of genes differentially expressed represented in each boxplot. (A) Boxplots of 24-ht small RNA accumulation. (B) Boxplots of 24-ht small RNA accumulation.