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

Salt stress, one of the most important abiotic stresses, is a serious constraint on cotton production. Cytosine methylation in nuclear DNA, an epigenetic modification found in plants, animals, and other organisms, imparts an impressive wealth of heritable information upon the DNA code. Although the cotton reference genome sequence is available to the public, the global DNA methylation data under different salinity stresses are still not available. Here, Zhong07 and ZhongS9612, salt-tolerant and salt-sensitive cultivars, respectively, were selected and methylation-sensitive amplification polymorphism (MSAP) technology was adopted to evaluate DNA methylation level alterations under different salt stresses in cotton. The findings indicated that different salt stresses exerted distinct effects on cotton seedling growth: specifically, both the neutral salt NaCl and alkalescent salt NaHCO3 showed relatively weak effects, while the alkaline salt Na2CO3 resulted in overt harm to seedlings, significantly darkening their caudexes and roots. MSAP analysis showed that after NaCl, NaHCO3, and Na2CO3 treatments, the DNA methylation levels of both leaves and roots decreased first before rising again. The trend in the roots for both type B (methylation) and C (demethylation) was identical to that observed in leaves; however, methylation levels had a different trend with the varying pH values of the salt, showing that the variation of the methylation level and status were mainly induced by the varying PH values of the salt. The analysis of transition type indicated that the main transition type was from hemimethylation to complete methylation (type iii), accounting for 38.10% of the total transitions, showing that complete methylation played a vital function in the process of gene transcription and expression after the salt treatments. The methylation levels of leaves differed from those of roots, indicating tissue specificity. Target sequence analysis showed that DNA methylation level induced by salt stress involves various kinds of metabolic pathways, whose synergistic effect helps cope with salt stresses.