Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu1,
- Xiangguo Zeng2,
- Yuguo Liu1,3,
- Yongping Li4,
- Minghao Qu5,
- Wen-Biao Jiao1,3,
- Yongchao Han2 and
- Chunying Kang1,3
- 1National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China;
- 2Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Industrial Crops, Hubei Academy of Agricultural Sciences, Wuhan 430063, China;
- 3Hubei Hongshan Laboratory, Wuhan 430070, China;
- 4School of Breeding and Multiplication, Hainan University, Sanya 572025, China;
- 5Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Plant Germplasm Research Center, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
Abstract
Somatic mutations arise and accumulate during tissue culture and vegetative propagation, potentially affecting various traits in horticultural crops, but their characteristics are still unclear. Here, somatic mutations in regenerated woodland strawberry derived from tissue culture of shoot tips under different conditions and 12 cultivated strawberry individuals are analyzed by whole genome sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 × 10−8–3.0 × 10−6 mutations per site. CG methylation shows a stable reduction (0.71%–8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved genome is assembled for the strawberry cultivar “Beni hoppe.” The 12 “Beni hoppe” individuals randomly selected from different locations show 4731–6005 mutations relative to the reference genome, and the mutation frequency varies among the subgenomes. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale and nucleotide resolution in plants.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279378.124.
- Received March 19, 2024.
- Accepted September 16, 2024.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
