Effects of ploidy variation on DNA methylation and gene expression in Pear (Pyrus communis L.)

Polyploid plants of fruit trees are generally characterized by dwarf growth, larger organs, and strong resistance to disease. They are therefore of great value in fruit breeding. Plant epigenetics generally has the forms of DNA methylation, RNA interference, and histone modification. The mechanisms of phenotypic variation and the physiological characteristics of plant polyploids are closely related to epigenetics. However, there have been few studies examining the relationship between DNA methylation and polyploidization in perennial woody plants. In this study, we compared the DNA methylation of unconverted diploids (q2x-1), tetraploids (4x-1, 4x-2) and diploid reference (2x-1) by methylation-sensitive amplification polymorphism (MSAP). The total methylation level of q2x-1, 4x-1, and 4x-2 was higher than that of 2x-1. The total methylation level of q2x-1 was higher than that of 4x-1 and 4x-2. Compared with 2x-1, the methylation pattern was mainly maintenance of methylation in q2x-1, 4x-1, and 4x-2, but the trend of demethylation of q2x-1, 4x-1, and 4x-2 was greater than that of methylation. Compared with q2x-1, the methylation pattern in 4x-1 and 4x-2 is also mainly maintaining methylation, but the trend of demethylation in 4x-1 and 4x-2 is less than that of methylation. The results of BLAST homology comparison and expression verification showed that the ploidy change of plants may affect the expression of genes related to adenosine triphosphate binding, RNA binding, arginine biosynthesis, and cell shape regulation, as well as promoting the polarization growth of leaf epidermis, auxin mediation, and RNA modification by causing a change of DNA methylation. This study provides a theoretical basis for studying the molecular mechanisms of plant ploidy change from the perspective of epigenetics.