Whole-genome DNA methylation analysis in cotton ( Gossypium hirsutum L.) under diferent salt stresses

Abstract

Salt stress, one of the most important abiotic stresses, is a serious constraint on cotton production. Cytosine methylationin nuclear DNA, an epigenetic modifcation found in plants, animals, and other organisms, imparts an impressive wealth of heritableinformation upon the DNA code. Although the cotton reference genome sequence is available to the public, the global DNA methylationdata under diferent salinity stresses are still not available. Here, Zhong07 and ZhongS9612, salt-tolerant and salt-sensitive cultivars,respectively, were selected and methylation-sensitive amplifcation polymorphism (MSAP) technology was adopted to evaluate DNAmethylation level alterations under diferent salt stresses in cotton. Te fndings indicated that diferent salt stresses exerted distinctefects on cotton seedling growth: specifcally, both the neutral salt NaCl and alkalescent salt NaHCO 3 showed relatively weak efects,while the alkaline salt Na2CO 3 resulted in overt harm to seedlings, signifcantly darkening their caudexes and roots. MSAP analysisshowed that afer NaCl, NaHCO3 , and Na 2CO 3 treatments, the DNA methylation levels of both leaves and roots decreased frst beforerising again. Te trend in the roots for both type B (methylation) and C (demethylation) was identical to that observed in leaves; however,methylation levels had a diferent trend with the varying pH values of the salt, showing that the variation of the methylation level andstatus were mainly induced by the varying PH values of the salt. Te analysis of transition type indicated that the main transition typewas from hemimethylation to complete methylation (type iii), accounting for 38.10% of the total transitions, showing that completemethylation played a vital function in the process of gene transcription and expression afer the salt treatments. Te methylation levelsof leaves difered from those of roots, indicating tissue specifcity. Target sequence analysis showed that DNA methylation level inducedby salt stress involves various kinds of metabolic pathways, whose synergistic efect helps cope with salt stresses.