Role of DNA methylation in hybrid vigor in
            <i>Arabidopsis thaliana</i>

Kawanabe, Takahiro; Ishikura, Sonoko; Miyaji, Noriaki; Sasaki, Taku; Wu, Li Min; Itabashi, Etsuko; Takada, Shoji; Shimizu, Mitsuru; Takasaki-Yasuda, Takeshi; Osabe, Kenji; Peacock, W. James; Dennis, Elizabeth S.

doi:10.1073/pnas.1613372113

Cited by 72 publications

(65 citation statements)

References 37 publications

(45 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In Columbia-0 (Col)/C24 hybrids, an active copy of the chromatin remodeler DECREASE IN DNA METHYLATION (DDM1), which affects DNA methylation in all sequence contexts, is required for a wild-type level of heterosis, whereas the alterations in gene expression produced by transchromosomal methylation via the RNA-directed DNA methylation (RdDM) pathway do not appear to contribute to hybrid vigor (28,29).…”

Section: Discussionmentioning

confidence: 99%

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

Wang

Greaves

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

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...

show abstract

Section: Discussionmentioning

confidence: 99%

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

Wang

Greaves

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The accumulation of 24‐nt small RNAs was reported to decrease in F 1 hybrids of Arabidopsis , rice or maize (He et al ; Groszmann et al ; Barber et al ), which indicates the potential role of siRNAs in heterosis. However, RNA polymerase IV, a key enzyme for generating 24‐nt siRNAs, was shown to be not involved in heterosis of Arabidopsis (Kawanabe et al ). In addition, miRNA expression and histone modification also changes in F 1 hybrids (Ni et al ; Chen et al ; He et al ).…”

Section: Epigenetic Regulation In Heterosismentioning

confidence: 99%

Exploring the molecular basis of heterosis for plant breeding

Liu

Zhang

et al. 2019

JIPB

View full text Add to dashboard Cite

Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

show abstract

“…Extensive studies of both DNA methylation and histone modifications have been conducted in plants, primarily in the dicot model plant Arabidopsis thaliana (Zhang et al, 2006(Zhang et al, , 2007b(Zhang et al, , 2016cCokus et al, 2008;Lister et al, 2008;Banaei Moghaddam et al, 2010;Moghaddam et al, 2011;Dowen et al, 2012;Greaves et al, 2012Greaves et al, , 2014Stroud et al, 2013;Pikaard and Mittelsten Scheid, 2014;Kawanabe et al, 2016;Lauss et al, 2018) and the monocot model plant Oryza sativa (rice) (Li et al, 2008(Li et al, , 2012He et al, 2010;Chodavarapu et al, 2012;Hu et al, 2014;Liu et al, 2015;Tan et al, 2016). This is primarily because both plant species have relatively small genome sizes, welldefined evolutionary histories and phylogenetic framework, and possess high-quality reference genomes and mutant resources, and in the case of rice represents a staple food crop.…”

Section: Introductionmentioning

confidence: 99%

Extensive allele‐level remodeling of histone methylation modification in reciprocal F₁ hybrids of rice subspecies

Zhang

et al. 2018

The Plant Journal

View full text Add to dashboard Cite

Summary Epigenetic mechanisms play a major role in heterosis, partly as a result of the remodeling of epigenetic modifications in F1 hybrids. Based on chromatin immunoprecipitation‐sequencing (ChIP‐Seq) analyses, we show that at the allele level extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F1 hybrids of Oryza sativa (rice) cultivars Nipponbare and 93‐11, representing the two subspecies japonica and indica. Globally, the allele modification‐altered loci in leaf or root of the reciprocal F1 hybrids involved ˜12–43% or more of the genomic regions carrying either of two typical histone methylation markers, H3K4me3 (>21 000 genomic regions) and H3K27me3 (>11 000 genomic regions). Nevertheless, at the total modification level, the majority (from ˜43 to >90%) of the modification‐altered alleles lay within the range of parental additivity in the hybrids because of concerted alteration in opposite directions, consistent with an overall attenuation of allelic differences in the modifications. Importantly, of the genomic regions that did show non‐additivity in total modification level by either marker in the two tissues of hybrids, >80% manifested transgressivity, which involved genes enriched in specific functional categories. Extensive allele‐level alteration of H3K4me3 alone was positively correlated with genome‐wide changes in allele‐level gene expression, whereas at the total level, both H3K4me3 and H3K27me3 remodeling, although affecting just a small number of genes, contributes to the overall non‐additive gene expression to variable extents, depending on tissue/marker combinations. Our results emphasize the importance of allele‐level analysis in hybrids to assess the remodeling of epigenetic modifications and their relation to changes in gene expression.

show abstract

Role of DNA methylation in hybrid vigor in Arabidopsis thaliana

Cited by 72 publications

References 37 publications

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

Exploring the molecular basis of heterosis for plant breeding

Extensive allele‐level remodeling of histone methylation modification in reciprocal F₁ hybrids of rice subspecies

Contact Info

Product

Resources

About

Role of DNA methylation in hybrid vigor in Arabidopsis thaliana

Cited by 72 publications

References 37 publications

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

Exploring the molecular basis of heterosis for plant breeding

Extensive allele‐level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies

Contact Info

Product

Resources

About

Extensive allele‐level remodeling of histone methylation modification in reciprocal F₁ hybrids of rice subspecies