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Volume 12
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10.3390/agronomy12051039
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Article

Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.)

by
Wenqiu Lin
1,2,3,
Xi’ou Xiao
1,2,3,*,
Weisheng Sun
1,2,3,
Shenghui Liu
1,2,3,
Qingsong Wu
1,2,3,
Yanli Yao
1,2,
Hongna Zhang
4 and
Xiumei Zhang
1,2,3,*
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
3
Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
4
Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou 570228, China
*
Authors to whom correspondence should be addressed.
Agronomy 2022, 12(5), 1039; https://doi.org/10.3390/agronomy12051039
Submission received: 14 March 2022 / Revised: 19 April 2022 / Accepted: 24 April 2022 / Published: 27 April 2022
(This article belongs to the Special Issue Horticultural Genetics and Biotechnology)
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Abstract

DNA methylation plays an important role in somaclonal variation. Cytosine-5 DNA methyltransferases (C5-MTases) are crucial enzymes for maintaining the de novo genome DNA methylation status, and the gene family has been identified and characterized in several species. However, limited information is available about the role of C5-MTases in the somaclonal variation of pineapple. Herein, the characteristic of DNA methylation in the leaf variants of pineapple showed that the methylation rate of variants decreased and the demethylation was mainly. Six AcC5-MTases were identified from pineapple genome. Phylogenetic analysis indicated that the six members could be classified into four subgroups, namely, AcMET, AcCMT, AcDRM, and AcDNMT, demonstrating evolutionary conservation in the C5-MTases across pineapple and other plant species. Cis-elements were presented in AcC5-MTase promoters, including light-responsive, phytohormone-responsive, and plant growth and development elements. Furthermore, we investigated the expression profiles of AcC5-MTases in different tissues and their transcript abundance in the leaves of somaclonal variation. Interestingly, most AcC5-MTase genes were highly expressed in leaf and carpopodium. AcMET, AcCMT2, and AcDRM2 were upregulated in pineapple somaclonal variants, indicating that AcC5-MTases might play an important role in the somaclonal variation of pineapple. Our results will aid in understanding the complex roles of methylation in plants and provide a basis for analyzing the role of methylation modification in the somaclonal variation of pineapple.
Keywords: DNA methylation; AcC5-MTase; expression profiles; somaclonal variation; pineapple DNA methylation; AcC5-MTase; expression profiles; somaclonal variation; pineapple

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MDPI and ACS Style

Lin, W.; Xiao, X.; Sun, W.; Liu, S.; Wu, Q.; Yao, Y.; Zhang, H.; Zhang, X. Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.). Agronomy 2022, 12, 1039. https://doi.org/10.3390/agronomy12051039

AMA Style

Lin W, Xiao X, Sun W, Liu S, Wu Q, Yao Y, Zhang H, Zhang X. Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.). Agronomy. 2022; 12(5):1039. https://doi.org/10.3390/agronomy12051039

Chicago/Turabian Style

Lin, Wenqiu, Xi’ou Xiao, Weisheng Sun, Shenghui Liu, Qingsong Wu, Yanli Yao, Hongna Zhang, and Xiumei Zhang. 2022. "Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.)" Agronomy 12, no. 5: 1039. https://doi.org/10.3390/agronomy12051039

APA Style

Lin, W., Xiao, X., Sun, W., Liu, S., Wu, Q., Yao, Y., Zhang, H., & Zhang, X. (2022). Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.). Agronomy, 12(5), 1039. https://doi.org/10.3390/agronomy12051039

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