Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress

Yanqing Wu; Jiao Liu; Lu Zhao; Guisheng Zhou; Yuhan Tang

doi:10.1016/j.ygeno.2025.111000

Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress

Genomics. 2025 Jan 20:111000. doi: 10.1016/j.ygeno.2025.111000. Online ahead of print.

Authors

Yanqing Wu¹, Jiao Liu², Lu Zhao³, Guisheng Zhou⁴, Yuhan Tang⁵

Affiliations

¹ Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, Jiangsu, China; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, Jiangsu, China.
² Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, Jiangsu, China.
³ Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, Jiangsu, China; College for Overseas Education, Yangzhou University, Yangzhou 225000, China.
⁴ Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, Jiangsu, China; College for Overseas Education, Yangzhou University, Yangzhou 225000, China.
⁵ Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, Jiangsu, China; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, Jiangsu, China. Electronic address: [email protected].

PMID: 39842647
DOI: 10.1016/j.ygeno.2025.111000

Abstract

Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum ('Jitian 3') development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in "phenylpropanoid biosynthesis", "arginine and proline metabolism" and "tyrosine metabolism". Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.

Keywords: DNA methylation; Gene expression; Gibberellic acid (GA3); Salt stress; sorghum.