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Zhang H, Ali A, Hou F, Wu T, Guo D, Zeng X, Wang F, Zhao H, Chen X, Xu P, Wu X. Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2018; 18:314. [PMID: 30497392 PMCID: PMC6267922 DOI: 10.1186/s12870-018-1553-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. RESULTS In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing). CONCLUSIONS We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.
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Affiliation(s)
- Hongyu Zhang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Asif Ali
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Feixue Hou
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Tingkai Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Daiming Guo
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiufeng Zeng
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Fangfang Wang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Huixia Zhao
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiaoqiong Chen
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Peizhou Xu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xianjun Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
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Liu C, Wang M, Wang L, Guo Q, Liang G. Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids. Genome 2018; 61:437-447. [PMID: 29687741 DOI: 10.1139/gen-2017-0232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.
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Affiliation(s)
- Chao Liu
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Mingbo Wang
- b CSIRO Agriculture and Food, Clunies Ross Street, Canberra ACT 2061, Australia
| | - Lingli Wang
- c Technical Advice Station of Economic Crop, Yubei district, Chongqing, P.R. China
| | - Qigao Guo
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Guolu Liang
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
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Analysis of DNA methylation in different maize tissues. J Genet Genomics 2009; 35:41-8. [PMID: 18222408 DOI: 10.1016/s1673-8527(08)60006-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Revised: 07/20/2007] [Accepted: 07/21/2007] [Indexed: 11/22/2022]
Abstract
DNA methylation plays an important role in gene expression regulation during biological development and tissue differentiation in plants. This study adopted methylation-sensitive Amplified fragment length polymorphism (AFLP) to compare the levels of DNA cytosine methylation at CCGG sites in tassel, bracteal leaf, and ear leaf from maize inbred lines, 18 White and 18 Red, respectively, and also examined specific methylation patterns of the three tissues. Significant differences in cytosine methylation level among the three tissues and the same changing tendency in two inbred lines were detected. Both MSAP (methylation sensitive amplification polymorphism) ratio and full methylation level were the highest in bracteal leaf, and the lowest in tassel. Meanwhile, different methylation levels were observed in the same tissue from the inbred lines, 18 White and 18 Red. Full methylation of internal cytosine was the dominant type in the maize genome. The differential methylation patterns in the three tissues were observed. In addition, sequencing of nine differentially methylated fragments and the subsequent blast search revealed that the cytosine methylated 5' -CCGG-3' sequences were distributed in repeating sequences, in the coding and noncoding regions. Southern hybridization was used to verify the methylation polymorphism. These results clearly demonstrated the power of the MSAP technique for large-scale DNA methylation detection in the maize genome, and the complexity of DNA methylation change during plant growth and development. The different methylation levels may be related to specific gene expression in various tissues.
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Zhang H, Peng H, Li P, Deng Q, Xu P, Li Y, Wang X, Wu X. The microarray analysis for gene expression in haploids and diploids derived from twin-seedling rice. ACTA ACUST UNITED AC 2008; 51:503-12. [DOI: 10.1007/s11427-008-0061-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 01/21/2008] [Indexed: 01/23/2023]
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Peng H, Zhang J, Wu X. The ploidy effects in plant gene expression: progress, problems and prospects. ACTA ACUST UNITED AC 2008; 51:295-301. [PMID: 18368306 DOI: 10.1007/s11427-008-0039-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 12/18/2007] [Indexed: 12/26/2022]
Abstract
Polyploidy and haploid are widely employed in the studies of genetics and evolution, and great progress has been made in these fields, inspiring the enthusiasm of scientists to explore the ploidy effects in gene expression. In this paper, we review the gene expression and its regulation in polyploids, especially in autopolyploids. We summarize some limitations in previous reports on polyploidy gene expression and its regulation, especially the limitations in the research materials. We propose an idea to create homologous ploidy series with twin-seedlings and to employ high-throughput techniques to investigate the polyploidy transcriptome and its regulation.
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Affiliation(s)
- Hai Peng
- Laboratory of Germplasm and Genetics, College of Life Science, Jianghan University, Wuhan 430056, China
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