ARTICLE ADDENDUM Plant Signaling & Behavior 10:9, e1057368; September 2015; © 2015 Taylor and Francis Group, LLC

Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana Rik Kooke1,2,3 and Joost J B Keurentjes1,3,* 1

Laboratory of Genetics; Wageningen University; Wageningen, The Netherlands; 2Laboratory of Plant Physiology; Wageningen University; Wageningen,

The Netherlands; 3Centre for Biosystems Genomics; Wageningen, The Netherlands

E

Keywords: adaptation, arabidopsis, dnamethylation, epigenetic regulation, morphology, phenotypic plasticity, pleiotropy Abbreviations: Epi-RIL, epigenetic Recombinant Inbred Line; ddm1, decrease in DNA methylation 1; Epi-QTL, epigenetic Quantitative Trait Locus; DMR, Differentially Methylated Region; TE, Transposable Element. *Correspondence to: Joost J B Keurentjes; Email: [email protected] Submitted: 05/08/2015

pigenetic variation is frequently observed in plants and direct relationships between differences in DNA methylation and phenotypic responses to changing environments have often been described. The identification of contributing genetic loci, however, was until recently hampered by the lack of suitable genome wide mapping resources that specifically segregate for epigenetic marks. The development of epi-RIL populations in the model species Arabidopsis thaliana has alleviated this obstacle, enabling the accurate genetic analysis of epigenetic variation. Comprehensive morphological phenotyping of a ddm1 derived epi-RIL population in different environments and subsequent epi-QTL mapping revealed a high number of epiQTLs and pleiotropic effects of several DMRs on numerous traits. For a number of these epi-QTLs epistatic interactions could be observed, further adding to the complexity of epigenetic regulation. Moreover, linkage to epigenetic marks indicated a specific role for DNA-methylation variation, rather than TE transposition, in plastic responses to changing environments. These findings provide supportive evidence for a role of epigenetic regulation in evolutionary and adaptive processes.

Revised: 05/28/2015 Accepted: 05/28/2015 http://dx.doi.org/10.1080/15592324.2015.1057368 Addendum to: Kooke R, Johannes F, Wardenaar R, Becker F, Etcheverry M, Colot V, Vreugdenhil D, Keurentjes JJB. Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. Plant Cell 2015; 27:337-48.

www.tandfonline.com

For many properties of plants variation can be observed between natural accessions. Genetic analyses using mapping populations have identified many QTLs involved in these traits but often fail to explain all observed variation.1-3 One explanation might be the contribution of Plant Signaling & Behavior

epigenetic variation, which is difficult to discriminate from sequence variation in conventional RIL populations. The development of epi-RIL populations, however, specifically allows analyzing the effect of DNA-methylation differences.4 Recent work in Arabidopsis shows that the phenotypic variation between epi-RILs, introduced by DNA-methylation differences, is highly heritable and differs between environments.5 Epigenetic modifications might, therefore, serve as an important resource for adaptation to changing environments.6 In support of the original paper 5 we summarize the major findings and reanalyzed the data for further clarification. Specifically, we quantified the amount of observed variation in trait values in the epi-RIL population and estimated the partition of variation into epigenetic and other factors. Moreover, we assessed the contribution of DMRs and TEs to the percentage explained variance using linear mixed models. Epi-RILs derived from ddm1 exhibit substantial reduction in DNA-methylation, an increase in TE transcription, and occasional transposition of TEs.7 A population of 99 epi-RILs was grown under optimal and saline conditions and phenotyped for a number of morphological traits, such as leaf area, flowering time, branching, and plant height. Substantial levels of variation were observed among epi-RILs in both growing conditions, although considerable dissimilarities occurred between traits. Illustratively, leaf area was much more variable than flowering time in both optimal and saline conditions (Table 1 e1057368-1

Table 1. Partition of variation in morphological traits detected among epi-RILs.PH, plant height in optimal conditions; MSB, main stem pffiffiffiffiffiffiffi ffi branching in optimal conditions; FT, flowering time in saline conditions; LA, leaf area in optimal conditions; CV, coefficient of variation calculated as Var/X *100%, where Var is the total observed variation in the population and X is the population mean; VG, % genetic variation; VE, % random error variation; QTLs, % variation explained by detected epi-QTLs; Res., % unexplained genetic variation; Variant, DMR marker (MM*) or TE (AT*) representing detected epi-QTLs; Position, position of DMR or TE (chr:bp); % expl., total explained variation accounted for by significant DMRs or TEs Trait

CV

VG

VE

QTLs

Res.

Variant

Position

% expl.

PH

23.3

37.0

63.0

12.3

24.7

MSB

29.8

58.0

42.0

47.1

10.9

FT

12.4

43.0

57.0

19.4

23.6

LA

39.0

46.0

54.0

33.8

12.2

MM11 MM698 ATCOPIA78.2 MM123 MM661 MM726 ATENSPM3.1 MM123 MM854 ATENSPM3.1 MM11 MM160 MM382 MM686 MM859 ATENSPM3/HELITRON2 ATENSPM3.2 ATENSPM3/ATLA

1:9574179 4:11363449 4:10736583 1:17258838 4:5588246 5:9561317 1:16837097 1:17258838 5:16674280 1:16837097 1:9574179 1:24459659 2:10540595 4:8313708 5:17613965 1:20152775 2:12762111 2:10510170

12.9 14.7 1.0 39.6 24.0 14.5 1.5 13.4 12.2 1.3 32.8 21.3 12.5 12.7 12.9 0.0 0.5 11.6

and Fig. 1). In general, plants suffered under saline conditions with smaller rosette sizes and reduced reproductive success. Leaf area after 20 days, for instance, decreased with approximately 18% under saline conditions and total plant length was reduced by 15%. However, the epi-RILs were much more affected by the saline conditions than the wild-type Col-0, suggesting increased sensitivity of hypomethylated plants to environmental perturbations. In addition, trait variation was increased under saline conditions, indicating a reduction in developmental stability.8 The variation in flowering time, for example, was increased by 17% and variation in main stem branching increased by 11% under saline conditions. Again, wild-type plants were more robust against environmental perturbation than epi-RILs, implying increased phenotypic plasticity of hypomethylated plants. To identify the epigenetic causes underlying the observed variation in morphological traits and plasticity an epi-QTL analysis was performed. For most traits significant epi-QTLs could be detected and a number of epi-QTLs were detected for multiple traits and

e1057368-2

environments, indicating pleiotropic effects of these loci. For example, a pleiotropic epi-QTL was detected at chromosome 1 for average internode length in optimal conditions, phenotypic plasticity of average internode length and rosette branching, and main stem branching in optimal and saline conditions. Most epi-QTLs displayed positive effect signs although a fair amount represented negative effects. This contrast demonstrates that demethylation can affect genetic regulation in both directions, which might have consequences for evolutionary adaptation to changing environments. Particularly, the plasticity epi-QTLs displayed negative effect signs, illustrating once more that DNA demethylation can increase plant sensitivity to environmental variation. For a number of traits multiple epiQTLs with opposite effect signs could be detected, which implies that the direction of genetic regulation depends on the property of the locus rather than on the targeted trait. Moreover, the regulation of complex traits might depend on the methylation status at multiple loci, as significant epistatic interactions were detected between epi-QTLs on different chromosomes. Significant

Plant Signaling & Behavior

epistasis was detected for the level of variation in total plant height in optimal conditions and leaf area in saline conditions. Although the major differences between epi-RILs consist of DNA-methylation changes, incidental transposition of TEs could also contribute to the observed variation.9 The detected epi-QTLs were, therefore, analyzed for the presence of DMRs and de novo TE insertions. In cases where de novo TE insertions coincided with DMRs in the epi-QTL support interval the contributing effect of each of the genetic factors was estimated by linear modeling. In contrast to DMRs, de novo TE insertions could account only for a very small amount of the observed variation for a very limited number of epiQTLs (Table 1 and Fig. 1). These results strongly suggest that the observed variation in morphological traits and phenotypic plasticity between epi-RILs is regulated by epigenetic factors such as DNA (de)methylation. It further supports the evidence for pleiotropic regulation of morphology and plasticity by epigenetic mechanisms. Together, these results imply an important role for epigenetic mechanisms in evolution, adaptation and species formation.

Volume 10 Issue 9

Figure 1. Variation in morphological traits detected among epi-RILs. (A) Level of observed variation in four different traits. (B) Division of variation explained by genetic factors and random error. (C) Division of genetic variation explained by detected epi-QTLs and residual unexplained genetic variation. (D) Division of explained variation by contribution of DMRs and TEs. PH, plant height in optimal conditions; MSB, main stem pffiffiffiffiffiffiffiffibranching in optimal conditions; FT, flowering time in saline conditions; LA, leaf area in optimal conditions; CV, coefficient of variation calculated as Var/X *100%, where Var is the total observed variation in the population and X is the population mean; VG, genetic variation; VE, random error variation; epi-QTLs, variation explained by detected epi-QTLs; Residual, unexplained genetic variation; DMR#, explained variation accounted for by significant DMRs; TE#, explained variation accounted for by significant TEs. DMR and TE numbering follow the order listed in Table 1.

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Funding

This research was supported by the Centre for Biosystems Genomics, The Netherlands.

References 1. Kooke R, Keurentjes JJB. Multi-dimensional regulation of metabolic networks shaping plant development and performance. J Exp Bot 2012; 63:3353-65; PMID:22140247; http://dx.doi.org/10.1093/jxb/err373

www.tandfonline.com

2. Molenaar JA, Keurentjes JJB. Exploiting natural variation in Arabidopsis. Methods Mol Biol 2014; 1062:139-53; PMID:24057363; http://dx.doi.org/10.1007/978-162703-580-4_6 3. Wijnen CL, Keurentjes JJB. Genetic resources for quantitative trait analysis: novelty and efficiency in design from an Arabidopsis perspective. Curr Opin Plant Biol 2014; 18:103-9; PMID:24657834; http://dx.doi.org/ 10.1016/j.pbi.2014.02.011 4. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, et al. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 2009; 5:e1000530; PMID:19557164; http://dx.doi.org/ 10.1371/journal.pgen.1000530 5. Kooke R, Johannes F, Wardenaar R, Becker F, Etcheverry M, Colot V, Vreugdenhil D, Keurentjes JJB. Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. Plant Cell 2015; 27:337-48; PMID:25670769; http://dx.doi.org/ 10.1105/tpc.114.133025

Plant Signaling & Behavior

6. Mirouze M, Paszkowski J. Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 2011; 14:267-74; PMID:21450514; http://dx.doi.org/ 10.1016/j.pbi.2011.03.004 7. Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T. Bursts of retrotransposition reproduced in Arabidopsis. Nature 2009; 461:423-6; PMID:19734880; http://dx.doi.org/10.1038/ nature08351 8. Sangster TA, Salathia N, Undurraga S, Milo R, Schellenberg K, Lindquist S, Queitsch C. HSP90 affects the expression of genetic variation and developmental stability in quantitative traits. Proc Natl Acad Sci U S A 2008; 105:2963-8; PMID:18287065; http://dx.doi.org/ 10.1073/pnas.0712200105 9. Cortijo S, Wardenaar R, Colome-Tatche M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, et al. Mapping the epigenetic basis of complex traits. Science 2014; 343:1145-8; PMID:24505129; http://dx.doi.org/10.1126/ science.1248127

e1057368-3

Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana.

Epigenetic variation is frequently observed in plants and direct relationships between differences in DNA methylation and phenotypic responses to chan...
NAN Sizes 1 Downloads 12 Views