DNA methylation diversity analysis in the cashew germplasm accessions

Epigenetic diversity plays an important role in the phenotypic variations of plants, and an understanding of it can facilitate crop improvement. However, epigenetic variations in cashew have not been explored.

DNA methylation patterns were analysed in 24 cashew accessions using the amplified methylation polymorphism polymerase chain reaction (AMP-PCR), which captures methylation-sensitive CCGG-containing loci. Overall DNA methylation across the assayed loci was 47.85%, comprising 25.35% hemimethylation and 22.49% full methylation. Methylation sensitive markers were highly informative, with mean polymorphic information content (PIC), effective multiplex ratio (EMR), and discriminating power (D) of 0.35, 2.51 and 0.86, respectively. Methylation frequency varied from 13.59% to 48.37%, suggesting substantial epigenetic variability among the accessions. The mean epigenetic distance (0.76) among the accessions was considerably higher than the mean genetic distance (0.18). Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering based on the epigenetic distances differed from clustering based on genetic distances. Principal coordinate analysis explained 29.76% of the total epigenetic variation across the first three axes, and analysis of molecular variance (AMOVA) analysis showed that 89% of the variation was partitioned within populations. Epigenetic diversity showed a weakly positive correlation with phenotypic diversity of nine yield-related traits (r = 0.15), while it was weakly negative between genetic variations and phenotypic diversity (r = 0.12).

The study demonstrates that substantial epigenetic variation exists in the evaluated cashew germplasm and suggests that DNA methylation may contribute to phenotypic differentiation. These findings provide new insights into epigenetic diversity and highlight its potential utility in germplasm characterization and crop improvement.