The creation of autotetraploid provides insights into critical features of DNA methylome changes after genome doubling in water spinach ( Ipomoea aquatica Forsk)

Water spinach ( Forsk) is an essential green leafy vegetable in Asia. In this study, we induced autotetraploid water spinach by colchicine. Furthermore, DNA methylation and transcriptome of tetraploid and diploid were compared using Whole Genome Bisulfite Sequencing (WGBS) and RNA-sequencing techniq...

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Published inFrontiers in plant science Vol. 14; p. 1155531
Main Authors Hao, Yuanyuan, Su, Xiao, Li, Wen, Li, Lin, Zhang, Yu, Mumtaz, Muhammad Ali, Shu, Huangying, Cheng, Shanhan, Zhu, Guopeng, Wang, Zhiwei
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 14.04.2023
Subjects
autotetraploid
differentially methylated region
DNA Methylation
phenotypic variation
Plant Science
water spinach
DNA Methylation
differentially methylated region
water spinach
autotetraploid
phenotypic variation
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Summary:Water spinach ( Forsk) is an essential green leafy vegetable in Asia. In this study, we induced autotetraploid water spinach by colchicine. Furthermore, DNA methylation and transcriptome of tetraploid and diploid were compared using Whole Genome Bisulfite Sequencing (WGBS) and RNA-sequencing techniques. Autotetraploid water spinach was created for the first time. Compared with the diploid parent, autotetraploid water spinach had wider leaves, thicker petioles and stems, thicker and shorter adventitious roots, longer stomas, and larger parenchyma cells. The whole genome methylation level of the autotetraploid was slightly higher than that of the diploid. Compared with the diploid, 12281 Differentially Methylated Regions (DMRs)were found in the autotetraploid, including 2356 hypermethylated and 1310 hypomethylated genes, mainly enriched in 'Arginine and Proline metabolism', 'beta - Alanine metabolism', 'Plant homone signal translation', 'Ribome', and 'Plant - pathgen interaction' pathways. Correlation analysis of transcriptome and DNA methylation data showed that 121 differentially expressed genes undergone differential methylation, related to four pathways 'Other types of O-glycan biosynthesis', 'Terpenoid backbone biosynthesis', 'Biosynthesis of secondary metabolites', and 'Metabolic paths'. This work obtained important autotetraploid resources of water spinach and revealed the genomic DNA methylation changes after genome doubling, being helpful for further studying the molecular mechanism of variations caused by polyploids of the genus.
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This article was submitted to Plant Bioinformatics, a section of the journal Frontiers in Plant Science
Reviewed by: Riaz Ahmad, Dera Ismail Khan, Pakistan; Taimoor Hassan Farooq, Bangor College China, a joint unit of Bangor University and Central South University of Forestry and Technology, China; Sami Abou Fayssal, University of Forestry, Bulgaria
Edited by: Muhammad Abdullah, Shanghai Jiao Tong University, China
ISSN:1664-462X
1664-462X
DOI:10.3389/fpls.2023.1155531