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Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)

1
South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
2
Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(11), 877; https://doi.org/10.3390/genes10110877
Received: 13 August 2019 / Revised: 26 October 2019 / Accepted: 29 October 2019 / Published: 1 November 2019
(This article belongs to the Section Plant Genetics and Genomics)
DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants. In general, SV plants exhibited methylation patterns analogous to those of cutting seedlings (CK). A total of 27.98% of the genomic cytosines of CK were methylcytosines, which was higher than that of 5 SV plants. Moreover, mCG and mCHG was hypermethylated, whereas mCHH was hypomethylated among the 5 SV plants genomic when compared with the CK. Most of the variation of DNA methylation was distributed in gene bodies, thus suggesting that phenotypic differences are probably perturbed by genes methylated from callus culture. In addition, the methylated genes were highly enriched for the Gene Ontology (GO) categories of binding and catalytic activity, cell part and organelle, cellular process, abiotic stimulus, and DNA modification. These results suggest that methylation mediates these pathways in the callus culture of pineapple. The results also suggested that the callus culture induced DNA methylation may result in the SV. View Full-Text
Keywords: pineapple; DNA methylation; somaclonal variation; bisulfite sequencing; callus culture pineapple; DNA methylation; somaclonal variation; bisulfite sequencing; callus culture
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Lin, W.; Xiao, X.; Zhang, H.; Li, Y.; Liu, S.; Sun, W.; Zhang, X.; Wu, Q. Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.). Genes 2019, 10, 877.

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