Changes of cytosine methylation in pecan tissues of different stages by quantitative methylation-sensitive amplified polymorphism

Abstract

Cytosine methylation plays an important role in plant development by regulating gene expressions. However, few studies have investigated methylation changes during the tissue differentiation and development of perennial plants. Here, the fluorescence-labeled methylation-sensitive amplified polymorphism method was used with eight primer combinations to detect methylation in leaves and xylem obtained at the stages of inflorescence emergence (IE), ovary start growth, and fruit maturity (FM) in two pecan (Carya illinoinensis) cvs. Pawnee and Stuart. The results show that the total methylation in the xylem was generally higher than in the leaves at each stage. Substantial methylation variations were observed at the amplified sites in pecan tissues at the various stages. The methylation patterns changed between the leaf and xylem, with frequencies from 44.97 to 67.01 % over the three stages in the two cultivars, among which the variation frequency between the tissues at the FM stage was the highest for each cultivar. The frequencies of methylation variation between the leaf samples at any two stages ranged from 31.86 to 45.88 %, with higher variation frequencies between the xylem samples (40.90 -59.44 %) for each cultivar, which is consistent with the comparative results of polymorphism rates between the leaf and xylem over the three stages. Cluster analysis and principal coordinate analysis suggest that the xylem at the IE and FM stages had relatively distant epigenetic relationships with other tissue samples as a whole. This study reveals the patterns of methylation variation and methylation relationships among pecan tissues undergoing different developmental processes, implying the important roles of methylation in tissue differentiation and development of trees. These results lay a theoretical foundation for elucidating the regulatory mechanisms of methylation involved in tree development.

Grafting with Different Rootstocks Induced DNA Methylation Alterations in Pecan [Carya illinoinensis (Wangenh.) K. Koch]

“…We previously used the MSAP method to successfully detect methylation in different pecan cultivars and tissues at different stages [20,21]. However, unlike MSAP technology, which covers preselected CCGG sites using a limited number of primer pairs (G= guanine), WGBS allows DNA methylation to be detected on a genome-wide scale with single-base resolution and is considered the "gold standard" [22].…”