Hybrid vigor or heterosis refers to the superior performance of F 1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.heterosis | hybrid vigor | Arabidopsis | DNA methylation | DDM1

F1 hybrids in Arabidopsis and crop species are uniform and high yielding. The F2 generation loses much of the yield advantage and the plants have heterogeneous phenotypes. We generated pure breeding hybrid mimic lines by recurrent selection and also selected a pure breeding small phenotype line. The hybrid mimics are almost completely homozygous with chromosome segments from each parent. Four particular chromosomal segments from C24 and 8 from Ler were present in all of the hybrid mimic lines, whereas in the F6 small phenotype line, the 12 segments were each derived from the alternative parent. Loci critical for promoting hybrid vigor may be contained in each of these 12 conserved segments. We have identified genes with similar altered expression in hybrid mimics and F1 plants but not in the small phenotype line. These genes may be critical for the generation of hybrid vigor. Analysis of transcriptomes indicated that increased expression of the transcription factor PHYTOCHROME-INTERACTING FACTOR (PIF4) may contribute to hybrid vigor by targeting the auxin biosynthesis gene YUCCA8 and the auxin signaling gene IAA29. A number of auxin responsive genes promoting leaf growth were up-regulated in the F1 hybrids and hybrid mimics, suggesting that increased auxin biosynthesis and signaling contribute to the hybrid phenotype. The hybrid mimic seeds had earlier germination as did the seeds of the F1 hybrids, indicating cosegregation of the genes for rosette size and the germination trait. Early germination may be an indicator of vigorous hybrids.heterosis | transcription factor | biomass | transregulation | germination T wo features common to hybrids in many crops are the increased yield and phenotypic uniformity of the F1 hybrid generation and the reduced yield and phenotypic heterogeneity of the F2 generation (1). These characteristics also apply to the F1 and F2 populations in Arabidopsis hybrids (2). The processes of capture of light and assimilation of CO 2 into photosynthate are the same in the hybrid and parents and as the hybrids have larger leaves than their parents, they produce more photosynthate (3).In a previous paper (2), transcriptome analyses showed that in the hybrids, most genes are expressed at the same levels as in the parents. Compared with the average level of gene expression in the parents, ∼2,000 genes (6% of the genome) have altered expression in the hybrids and are likely to be involved in the generation of the hybrid vigor phenotype. Many of the differentially expressed genes (DEGs) encode proteins in key metabolic pathways such as the plant hormone systems auxin and salicylic acid (SA) and the basal defense response, suggesting that these pathways contribute to the development of hybrid vigor (4). Altered hormone abscisic acid (ABA) and defense response have also been reported in rice hybrids (5). Despite the contrasting phenotypes of the F1 and F2 populations, we were able to develop "pure breeding" F5/F6 lines with phenotypes comparable to the F1 hybrids (hybrid mimics) (2). The hybrid mimic...

F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.I n Arabidopsis some ecotypes with similar genome sequences produce F1 hybrids with large increases in vegetative and reproductive yields (1, 2). These results appear to be at variance with the generalization that the larger the genetic distance between parents, the greater the hybrid vigor (3); however, the Arabidopsis ecotypes have different epigenomes that may be important for hybrid vigor (4). In hybrids between C24 and Ler, we found altered levels in two epigenetic systems: 24nt siRNAs and DNA methylation (4, 5). These epigenetic changes appear common among hybrid systems with similar observations being made in maize and rice hybrids (6). The epigenetic changes can correlate with changes in gene expression and contribute to the unique gene expression profile of the F1 hybrid (7). Not all crosses result in hybrid vigor (heterosis); some result in decreased vigor and yield referred to as "hybrid weakness" (8).Heterotic F1 hybrids are featured in agricultural and horticultural crops, and in all species, the yield gains are restricted to the F1 generation. The F2 and subsequent selfed generations are discarded because of reduced yields and heterogeneity of morphological and developmental traits. A hybrid crop system requires an efficient method of F1 hybrid seed production dependent on male sterility in the female parent and synchronous flowering of the male and female parents.QTL analysis in maize and rice has confirmed that hundreds of genome segments contribute to the heterotic phenotype, but the main m...

Hybrid breeding is of economic importance in agriculture for increasing yield, yet the basis of heterosis is not well understood. In Arabidopsis, crosses between different accessions produce hybrids with different levels of heterosis relative to parental phenotypes in biomass. In all hybrids, the advantage of the F1 hybrid in both phenotypic uniformity and yield gain is lost in the heterogeneous F2. F5/F6 Hybrid Mimics generated from a cross between C24 and Landsberg erecta (Ler) ecotypes demonstrated that the large plant phenotype of the F1 hybrids can be stabilized. Hybrid Mimic selection was applied to Wassilewskija (Ws)/Ler and Col/Ler hybrids. The two hybrids show different levels of heterosis. The Col/Ler hybrid generated F7 Hybrid Mimics with rosette diameter and fresh weight equivalent to the F1 hybrid at 30 DAS; F7 Ws/Ler Hybrid Mimics outperformed the F1 hybrid in both the rosette size and biomass. Transcriptome analysis revealed up‐regulation of cell wall biosynthesis, and cell wall expansion genes could be a common pathway in increased size in the Arabidopsis hybrids and Hybrid Mimics. Intercross of two independent Hybrid Mimic lines can further increase the biomass gain. Our results encourage the use of Hybrid Mimics for breeding and for investigating the molecular basis of heterosis.