Intraspecific hybrids between the Arabidopsis thaliana accessions C24 and Landsberg erecta have strong heterosis. The reciprocal hybrids show a decreased level of 24-nt small RNA (sRNA) relative to the parents with the decrease greatest for those loci where the parents had markedly different 24-nt sRNA levels. The genomic regions with reduced 24-nt sRNA levels were largely associated with genes and their flanking regions indicating a potential effect on gene expression. We identified several examples of genes with altered 24-nt sRNA levels that showed correlated changes in DNA methylation and expression levels. We suggest that such epigenetically generated differences in gene activity may contribute to hybrid vigor and that the epigenetic diversity between ecotypes provides increased allelic (epi-allelic) variability that could contribute to heterosis.

The heterotic hybrid offspring of Arabidopsis accessions C24 and Landsberg erecta have altered methylomes. Changes occur most frequently at loci where parental methylation levels are different. There are context-specific biases in the nonadditive methylation patterns with ^m CG generally increased and ^m CHH decreased relative to the parents. These changes are a result of two main mechanisms, Trans Chromosomal Methylation and Trans Chromosomal deMethylation, where the methylation level of one parental allele alters to resemble that of the other parent. Regions of altered methylation are enriched around genic regions and are often correlated with changes in siRNA levels. We identified examples of genes with altered expression likely to be due to methylation changes and suggest that in crosses between the C24 and Ler accessions, epigenetic controls can be important in the generation of altered transcription levels that may contribute to the increased biomass of the hybrids.

Significance: Hybrids are extensively used in agriculture to deliver increases in crop yields, yet the molecular basis of their superior performance (heterosis) is not well understood. We report that someArabidopsisF1 hybrids show changes to salicylic acid- and auxin-regulated defense and stress response gene expression. These changes could be important for generating the greater growth of some hybrids given the antagonistic relationship between plant growth and defense responses. Hybrids showing different levels of heterosis have changes in the salicylic acid- and auxin-regulated pathways that correlate with differences in the enhanced leaf growth. The larger leaves, and thus greater capacity for energy production, support the increased growth vigor and seed yields of the hybrids.

The dynamics of leaf photosynthesis in fluctuating light affects carbon gain by plants. Mesophyll conductance (g_m) limits CO₂ assimilation rate (A) under the steady state, but the extent of this limitation under non-steady-state conditions is unknown. In the present study, we aimed to characterize the dynamics of g_m and the limitations to A imposed by gas diffusional and biochemical processes under fluctuating light. The induction responses of A, stomatal conductance (g_s), g_m, and the maximum rate of RuBP carboxylation (V_cmax) or electron transport (J) were investigated in Arabidopsis (Arabidopsis thaliana (L.)) and tobacco (Nicotiana tabacum L.). We first characterized g_m induction after a change from darkness to light. Each limitation to A imposed by g_m, g_s and V_cmax or J was significant during induction, indicating that gas diffusional and biochemical processes limit photosynthesis. Initially, g_s imposed the greatest limitation to A, showing the slowest response under high light after long and short periods of darkness, assuming RuBP-carboxylation limitation. However, if RuBP-regeneration limitation was assumed, then J imposed the greatest limitation. g_m did not vary much following short interruptions to light. The limitation to A imposed by g_m was the smallest of all the limitations for most of the induction phase. This suggests that altering induction kinetics of mesophyll conductance would have little impact on A following a change in light. To enhance the carbon gain by plants under naturally dynamic light environments, attention should therefore be focused on faster stomatal opening or activation of electron transport.