Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development

Abstract

Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.

Systematic Analysis of the DNA Methylase and Demethylase Gene Families in Rapeseed (Brassica napus L.) and Their Expression Variations After Salt and Heat stresses

“…Epigenetics is the study of heritable phenotypic changes that do not involve changes in the DNA sequence. Mounting evidence has implied DNA methylation, as one kind of epigenetic regulatory pathways, in various aspects of plant growth and development via a number of key processes including genomic imprinting and repression of transposable elements [1][2][3][4][5][6][7]. DNA methylation mainly occurs as modifications of cytosine into 5-methylcytosine (5-meC), in sequence targets such as CG, CHG, CHH (where H stands for A, C or T), and as conversion of purines into N6-methyladenine (N6-mA) and 7-methylguanine (7-mG) [8,9].…”

Light‐ and temperature‐entrainable circadian clock in soybean development

“…. In plants, time-keeping pacemakers adjust the period and phase of endogenous circadian rhythms in response to external and internal cues, conferring improved fitness (Yanovsky & Kay, 2003;Dodd et al, 2005; de Montaigu et al, 2010; Wang et al, 2011;Sun et al, 2016;Sun et al, 2018;Wang et al, 2019). In recent years, orthologs of many Arabidopsis clock-associated components have been identified in multiple agricultural crops and have been shown to function in the regulation of agronomic traits (Campoli et al, 2012;Bendix et al, 2013;Liu et al, 2015;Xie et al, 2015;Muller et al, 2016;Liew et al, 2017;Lu et al, 2017).…”

Prospects for Molecular Breeding in Cotton,Gossypiumspp

“…Many studies have been carried out to identify genes that are differentially expressed, however paucity of the causes of the differential expression, hints us towards epigenetic regulations and transcription factors as the probable cause. Very few methylation studies have been carried out in cotton for fiber quality [79], male sterility [80], cold stress [81], salt tolerance [82], fruiting branch development [83]. Thus, there is huge scope for studies like differential methylation, studies on transcription factor, and correlating them with the differential expression patterns.…”