Epigenetic diversity of Saccharum spp. accessions assessed by methylation-sensitive amplification polymorphism (MSAP)

Abstract

The epigenetic diversity of six genotype groups (commercial cultivars, S. officinarum, S. spontaneum, S. robustum, S. barberi, and Erianthus sp.) was assessed through methylation-sensitive amplification polymorphism (MSAP). A total of 1341 MSAP loci were analyzed, of which 1117 (83.29%) were susceptible to cytosine methylation and responsible for a higher proportion of overall diversity among genotypes. The MSAP selective primer combinations captured different proportions of internal and external cytosine methylation loci across genotype groups, while the average external cytosine frequency was higher for all genotype groups. The genotypes were divided into two subpopulations with a high differentiation index (φst = 0.086) based on epigenetic loci. The genotypes were clustered in three subgroups for both methylated and unmethylated loci, considering dissimilarity values. Four methylated fragments (MFs) were randomly selected and subsequently sequenced and compared with sugarcane public databases using BLASTN. MF alignments suggest that cytosine methylation occurs in sugarcane near CpG islands and tandem repeats within transcribed regions and putative cis-regulatory sequences, which assigned functions are associated with stress adaptation. These results provide the first insights about the distribution of this epigenetic mark in sugarcane genome, and suggest a biological relevance of methylated loci.

Keywords: Cytosine methylation; Epigenome diversity; Saccharum spp.; Wild accessions.

Fig. 1

Average percentages of unmethylation, external cytosine methylation, and internal cytosine methylation for the six sugarcane genotype groups (commercial, S. robustum, S. barberi, S. spontaneum, S. officinarum, and Erianthus sp.)

Fig. 2

Population epigenetic structure of the 60 sugarcane genotypes using the binary matrix of relative total methylation, transformed from the MSAP data set. a Inference of the optimal number of subpopulations (k) using the delta K variation (Δk), with k varying from 1 to 9. b Bar plot with each column representing the estimated membership coefficients, in K = 2, for each genotype, which are represented with numbers from 1 to 60 and grouped as follows: commercial (1–10), S. robustum (11–15), S. barberi (17–20), S. spontaneum (16, 21–43), S. officinarum (44–55), and Erianthus sp. (56–60). Subpopulation 1 and subpopulation 2 are represented by orange and green colors, respectively

Fig. 3

Dendrogram of 60 sugarcane genotypes (commercial, S. robustum, S. barberi, S. spontaneum, S. officinarum, and Erianthus sp.) obtained via Neighbor Joining for methylation-susceptible loci (MSL) based on dissimilarity values (Jaccard complement). Bootstrap values are shown in the nodes

Fig. 4

Dendrogram of the 60 sugarcane genotypes (commercial, S. robustum, S. barberi, S. spontaneum, S. officinarum, and Erianthus sp.) obtained via Neighbor Joining for non-methylated loci (NML) based on dissimilarity values (Jaccard complement). Bootstrap values are shown in the nodes