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. 2024 Jun 17;25(1):158.
doi: 10.1186/s13059-024-03310-x.

DNA methylation variations underlie lettuce domestication and divergence

Shuai Cao  1 , Nunchanoke Sawettalake  1 , Ping Li  1 , Sheng Fan  1 , Lisha Shen  2   3
Affiliations

DNA methylation variations underlie lettuce domestication and divergence

Shuai Cao et al. Genome Biol. .

Abstract

Background: Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morphologically distinct vegetable types: leafy lettuce and stem lettuce. However, the role of epigenetic variation in lettuce domestication and divergence remains largely unknown.

Results: To understand the genetic and epigenetic basis underlying lettuce domestication and divergence, we generate single-base resolution DNA methylomes from 52 Lactuca accessions, including major lettuce cultivars and wild relatives. We find a significant increase of DNA methylation during lettuce domestication and uncover abundant epigenetic variations associated with lettuce domestication and divergence. Interestingly, DNA methylation variations specifically associated with leafy and stem lettuce are related to regulation and metabolic processes, respectively, while those associated with both types are enriched in stress responses. Moreover, we reveal that domestication-induced DNA methylation changes could influence expression levels of nearby and distal genes possibly through affecting chromatin accessibility and chromatin loop.

Conclusion: Our study provides population epigenomic insights into crop domestication and divergence and valuable resources for further domestication for diversity and epigenetic breeding to boost crop improvement.

Keywords: DNA methylation; Divergence; Domestication; Epigenetic variation; Lettuce.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Increased CG methylation diversity during lettuce domestication. a Seedling morphology of the wild relative species (L. serriola, L. virosa, L. indica, and L. saligna) and cultivated lettuce including cos, butterhead, crisp, and stem lettuce at 2 weeks after planting. Different types of cultivated lettuce are believed to originate from a single domestication event from L. serriola at approximately 4000 BC [5, 6]. Scale bar, 10 cm. b A neighbor-joining phylogenetic tree of 52 Lactuca accessions based on the methylation levels of all CG loci. c Principal component analysis (PCA) of all Lactuca accessions based on CG methylation levels. d Diversity of CG methylation (mCG) and SNP variations of the wild lettuce (L. serriola) and cultivated lettuce (L. sativa). Different letters above the violins indicate significant differences (P < 0.01, two-sided Wilcoxon signed-rank test) in a pairwise comparison
Fig. 2
Fig. 2
Elevated CG methylation levels during lettuce domestication. a Increased CG methylation levels in cultivated lettuces compared to the wild lettuce L. serriola (wild). Asterisks indicate significant differences of CG methylation levels (mCG) in cos, butterhead (butter), crisp, and stem lettuce as compared with the wild lettuce L. serriola (**P < 0.01, two-tailed paired Student’s t-test). b Heatmap of methylation level changes along chromosome 1 (Chr1) during lettuce domestication. Methylation level changes (ΔmCG) in butterhead vs. L. serriola (butter), cos vs. L. serriola (cos), crisp vs. L. serriola (crisp), and stem vs. L. serriola (stem) were calculated for each 100-kb window. Distribution of genes and TEs along Chr 1 is shown above. c Average CG methylation levels around genes (left) and TEs (right). TSS indicates transcription start site, TTS indicates transcription termination site. Asterisks indicate significant differences (**P < 0.01, Wilcoxon signed-rank test) of CG methylation levels in cultivars as compared with the wild lettuce L. serriola (wild). Cultivars include cos, butterhead, crisp and stem lettuce. See Additional file 2: Fig. S1, c and d, for the comparison of each cultivar with the wild lettuce L. serriola. d Distribution of DMRs in different genomic regions divided into gene body, +2 kb flanking region (2 kb upstream of TSS), − 2 kb flanking region (2 kb downstream of TTS), TEs, and intergenic regions excluding TEs. The average distributions of different genomic regions across the whole genome are shown as references
Fig. 3
Fig. 3
High correlation of DNA methylation changes among leafy lettuce cultivars. a Correction of CG methylation changes among lettuce cultivars, relative to the wild lettuce L. serriola. b, c Shared and unique hyper- (b) and hypo- (c) DMRs in different types of lettuce cultivars, relative to the wild lettuce L. serriola. d Heatmap showing methylation levels of type-specific hyper- and hypo-DMRs found in leafy lettuce. Leafy lettuces include cos, butterhead (butter), and crisp lettuce. Grey blocks indicate DMRs showing significant differential methylation levels between leafy lettuce and stem lettuce, representing high-fidelity leafy-specific DMRs. The left panel shows examples for a high-fidelity leafy-specific hyper-DMR across LsAMY1 (Lsat_1_v5_gn_6_112060) and a high-fidelity leafy-specific hypo-DMR across LsIQD31 (Lsat_1_v5_gn_3_102080). Shown above the methylation profiles are the gene structures of LsAMY1 and LsIQD31, in which blue and yellow boxes indicate exons and untranslated regions, respectively, and purple lines indicate introns and other genomic regions. e Gene Ontology (GO) enrichment of genes associated with these high-fidelity leafy-specific DMRs
Fig. 4
Fig. 4
Independently altered DNA methylation in stem lettuce. a Heatmap showing methylation levels of the stem lettuce specific hyper- and hypo-DMRs, relative to the wild lettuce L. serriola. DMRs in the grey blocks show significant differences between leafy type and stem lettuce, representing high-fidelity stem-specific DMRs. b Methylation levels of the high-fidelity stem-specific DMRs in the wild lettuce L. saligna. Asterisks and ns indicate significant difference (**P < 0.01, Wilcoxon signed-rank test) and no statistical difference (P ≥ 0.01, Wilcoxon signed-rank test), respectively. c Enrichment of regions with the same SNPs in L. saligna and stem lettuce observed in high-fidelity stem-specific DMRs. Blue bars indicate fractions of regions with the same SNPs in stem lettuce and L. saligna, but different from other Lactuca species, including cos, butter, and crisp lettuce, L. serriola, L. virosa, and L. indica. d GO enrichment of genes associated with the high-fidelity stem-specific DMRs
Fig. 5
Fig. 5
Shared domestication-induced DMRs of lettuce cultivars. a Heatmap showing methylation levels of shared hyper- and hypo-DMRs of lettuce cultivars. b, c GO enrichment of genes associated with shared hyper- (b) and hypo-DMRs (c). The plots show 10 top-scoring biological processes. d DNA motifs enriched in the shared domestication-induced DMRs (upper panels) are similar to the motifs of binding sites of 3XHMG-BOX1 and ERF48 in published dataset (lower panels). E-value (e) indicates an estimate of the expected number of motifs by the MEME, while Q-value (q) indicates the probability that a random motif has an optimal alignment as the target motif. e Density of shared DMRs within 10 kb of ERF48 binding motif. The grey line indicates random genomic regions. Asterisk indicates significant difference (**P < 0.01, Wilcoxon signed-rank test). f Density of ERF48 binding motif within 10 kb of genes. The grey line indicates random genomic regions. Asterisk indicates significant difference (**P < 0.01, Wilcoxon signed-rank test)
Fig. 6
Fig. 6
Domestication-induced DNA methylation changes contribute to gene expression changes through cis- or trans-acting effects. a Metaplots showing chromatin accessibility in the shared domestication-induced DMRs of lettuce cultivars, located near the genes (left panel) and far from genes (right panel). Asterisks indicate significant differences (**P < 0.01, Wilcoxon signed-rank test) of the chromatin accessibility in DMRs compared with the whole genome. b Increased gene expression changes (absolute values) between stem lettuce and the wild lettuce L. serriola in DMR-associated proximal genes (DPGs) and distal genes (DDGs) compared with all genes. Asterisks indicate significant differences (**P < 0.01, Wilcoxon signed-rank test). c An example showing methylation changes (Chr1: 59,076,400–59,077,800; upper panel and middle box plot in the lower panel) related to the proximal gene (DPG: Lsat_1_v5_gn_1_50480; right box plot in the lower panel) and the distal gene (DDG: Lsat_1_v5_gn_1_50600; left box plot in the lower panel) that are in one chromatin loop with more than 64 kb physical distance. The middle panel shows the gene structures of these genes, in which blue and yellow boxes indicate exons and untranslated regions, respectively, and purple lines indicate introns and other genomic regions. Different letters on the boxes indicate significant differences (P < 0.01, Wilcoxon signed-rank test) in a pairwise comparison
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References

    1. Shatilov MV, Razin AF, Ivanova MI. Analysis of the world lettuce market. IOP Conference Series. 2019;395:012053.
    1. Lebeda A, Ryder EJ, Grube R, Dolezˇalova´ I, Krˇ´ıstkova E. Lettuce (Asteraceae; Lactuca spp.). Genetic Resources, Chromosome Engineering, and Crop Improvement Vol 3 (ed Singh, R J). 2006:377-472.
    1. de Vries IM. Origin and domestication of Lactuca sativa L. Genet Resour Crop Ev. 1997;44:165–174. doi: 10.1023/A:1008611200727. - DOI
    1. Lindqvist K. On the origin of cultivated lettuce. Hereditas. 1960;46:319–350. doi: 10.1111/j.1601-5223.1960.tb03091.x. - DOI
    1. Zhang L, Su W, Tao R, Zhang W, Chen J, Wu P, Yan C, Jia Y, Larkin RM, Lavelle D, et al. RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. Nat Commun. 2017;8:2264. doi: 10.1038/s41467-017-02445-9. - DOI - PMC - PubMed

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