Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication

Abstract

A colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding, including self-pruning, was identified. This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine. We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips. The genes showing increases in the autotetraploid were mainly related to stress response pathways, whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis. Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines. Comparison between the methylomes revealed that they were conserved in CG and CHG contexts. In the autotetraploid grapevine, hypodifferentially methylated regions (DMRs) and hyper-DMRs in the gene body increased or decreased gene expression, respectively. Our results indicated that a hypo-DMR in the ACO1 gene body increased its expression and might promote self-pruning. This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication. Overall, our results provide valuable information for understanding the relationships between DNA methylation, gene expression, and autotetraploid breeding in grape.

References

[1] Feldman, M. & Levy, A. A. Allopolyploidy - A shaping force in the evolution of wheat genomes. Cytogenet. Genome Res. 109, 250-258 (2005).

[2] Jiao, Y. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97-100 (2011).

[3] Wang, X., Shi, X., Hao, B., Ge, S. & Luo, J. Duplication and DNA segmental loss in the rice genome: Implications for diploidization. N. Phytol. 165, 937-946 (2005).

[4] Salse, J. In silico archeogenomics unveils modern plant genome organisation, regulation and evolution. Curr. Opin. Plant Biol. 15, 122-130 (2012).

[5] Lou, P. et al. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell 24, 2415-2426 (2012).

[6] Barker, M. S. et al. Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25, 2445-2455 (2008).

[7] Ramsey, J. & Schemske, D. W. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29, 467-501 (1998).

[8] Soltis, P. S. & Soltis, D. E. The role of genetic and genomic attributes in the success of polyploids. PNAS 97, 7051-7057 (2000).

[9] Sattler, M. C., Carvalho, C. R. & Clarindo, W. R. The polyploidy and its key role in plant breeding. Planta 243, 281-296 (2015).

[10] Valenti, R. J. Induced polyploidy in Tilapia aurea (Steindachner) by means of temperature shock treatment. J. Fish. Biol. 7, 519-528 (1975).

[11] Peachey, B. L. & Allen, S. K. Evaluation of cytochalasin B and 6-dimethylaminopurine for tetraploidy induction in the Eastern oyster, Crassostrea virginica. Aquaculture 450, 199-205 (2016).

[12] Javadian, N., Karimzadeh, G., Sharifi, M., Moieni, A. & Behmanesh, M. In vitro polyploidy induction: changes in morphology, podophyllotoxin biosynthesis, and expression of the related genes in Linum album (Linaceae). Planta 245, 1165-1178 (2017).

[13] Lavania, U. C. & Srivastava, S. Enhanced productivity of tropane alkaloids and fertility in artificial autotetraploids of Hyoscyamus niger L. Euphytica 52, 73-77 (1991).

[14] Zager, J. J., Lange, I., Srividya, N., Smith, A. & Lange BM . Gene networks underlying cannabinoid and terpenoid accumulation in cannabis. Plant Physiol. pp. 01506.2018 (2019).

[15] Dai, F., Wang, Z., Luo, G. & Tang, C. Phenotypic and transcriptomic analyses of autotetraploid and diploid mulberry (Morus alba L.). Int. J. Mol. Sci. 16, 22938-22956 (2015).

[16] Sartor, M. E., Quarin, C. L. & Espinoza, F. Mode of reproduction of colchicine-induced paspalum plicatulum tetraploids. Crop Sci. 49, 1270-1276 (2009).

[17] Mu, H. et al. Transcriptomic analysis of phenotypic changes in birch (Betula platyphylla) Autotetraploids. Int. J. Mol. Sci. 13, 13012-13029 (2012).

[18] Plummer, J. A., Mullins, M. G. & Vine, J. H. Seasonal changes in endogenous ABA and IAA and the influence of applied ABA and auxin in relation to shoot growth and abscission in Valencia Orange (Citrus sinensis (L.) Osbeck). Plant Growth Regul. 10, 139-151 (1991).

[19] Jiang, C. Z., Lu, F., Imsabai, W., Meir, S. & Reid, M. S. Silencing polygalacturonase expression inhibits tomato petiole abscission. J. Exp. Bot. 59, 973-979 (2008).

[20] Zhang, J.-Z., Zhao, K., Ai, X.-Y. & Hu, C.-G. Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis). BMC Genomics 15, 892 (2014).

[21] Agustí, J., Merelo, P., Cercós, M., Tadeo, F. R. & Talón, M. Ethylene-induced differential gene expression during abscission of citrus leaves. J. Exp. Bot. 59, 2717-2733 (2008).

[22] Pattison, R. J. & Catalá, C. Evaluating auxin distribution in tomato (Solanum lycopersicum) through an analysis of the PIN and AUX/LAX gene families. Plant J. 70, 585-598 (2012).

[23] Mishra, A., Khare, S., Trivedi, P. K. & Nath, P. Effect of ethylene, 1-MCP, ABA and IAA on break strength, cellulase and polygalacturonase activities during cotton leaf abscission. South Afr. J. Bot. 74, 282-287 (2008).

[24] Huberman, M., Riov, J., Aloni, B. & Goren, R. Role of ethylene biosynthesis and auxin content and transport in high temperature-induced abscission of pepper reproductive organs. J. Plant Growth Regul. 16, 129-135 (1997).

[25] Bell, A. C. & Felsenfeld, G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482-485 (2000).

[26] Tate, P. H. & Bird, A. P. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev. 3, 226-231 (1993).

[27] Lou, S. et al. Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol. 15, 408 (2014).

[28] Song, Q. & Chen, Z. J. Epigenetic and developmental regulation in plant polyploids. Curr. Opin. Plant Biol. 24, 101-109 (2015).

[29] Shinshi, H., Usami, I. & Ohme-Takagi, M. Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene. Plant Mol. Biol. 27, 923-932 (1995).

[30] Bertini, L. et al. Pathogen-responsive wheat PR4 genes are induced by activators of systemic acquired resistance and wounding. Plant Sci. 164, 1067-1078 (2003).

[31] Belle, J. M. et al. The lithium tolerance of the Arabidopsis cat2 mutant reveals a cross-talk between oxidative stress and ethylene. Plant J. 52, 1052-1065 (2007).

[32] Kwon, S. J. et al. GDSL lipase-like 1 regulates systemic resistance associated with ethylene signaling in Arabidopsis. Plant J. 2, 235-245 (2009).

[33] Yang, S. H. & Choi, D. Characterization of genes encoding ABA 8′-hydroxylase in ethylene-induced stem growth of deepwater rice (Oryza sativa L.). Biochem. Biophys. Res. Commun. 350, 685-690 (2006).

[34] Ivanova, I., Bulgarian, V., Todorova, D. & Academy, B. Influence of ethylene releasing agent ethrel on cytokinin oxidase/dehydrogenase activity in tissues of pisum sativum. Biol. Physiol. Des. Plantes. 59, 301-304 (2006).

[35] Kou, H. P. et al. Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.). J. Plant Physiol. 168, 1685-1693 (2011).

[36] Verhoeven, K. J. F., Jansen, J. J., van Dijk, P. J. & Biere, A. Stress-induced DNA methylation changes and their heritability in asexual dandelions. N. Phytol. 185, 1108-1118 (2010).

[37] Ganguly. D., Crisp, P. A., Eichten, S. R. & Pogson, B. J. The Arabidopsis DNA methylome is stable under transgenerational drought stress. Plant Pysiol. 175, 1893-1912 (2017).

[38] Lavania, U. C. et al. Autopolyploidy differentially influences body size in plants, but facilitates enhanced accumulation of secondary metabolites, causing increased cytosine methylation. Plant J. 71, 539-549 (2012).

[39] Martelotto, L. G. et al. Genome rearrangements derived from autopolyploidization in Paspalum sp. Plant Sci. 172, 970-977 (2007).

[40] Wang, C. G. et al. Marker-based analysis of genome structure and DNA methylation in a watermelon (Citrullus lanatus) ploidy series. Bot. Stud. 50, 389-402 (2009).

[41] Williams, B. P. & Gehring, M. Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit. Nat. Commun. 8 https://doi.org/10.1038/s41467-017-02219-3 (2017)

[42] Wang, G. Q. et al. The transcription factor AtDOF4.7 is involved in ethylene- and IDA-mediated organ abscission in Arabidopsis. Front. Plant Sci. 7, 863 (2016).

[43] Xu, Y., Zhang, W., Chen, G. & Wang, J. DNA methylation alteration is a major consequence of genome doubling in autotetraploid Brassica rapa. Arch. Biol. Sci. 69, 689-697 (2017).

[44] Zhang, J. et al. Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression. PNAS 112, E7022-E7029 (2015).

[45] Keyte, A. L., Percifield, R., Liu, B. & Jonathan, F. WENDEL. Infraspecific DNA Methylation Polymorphism in Cotton (Gossypium hirsutum L.). J. Hered. 97, 444-450 (2006).

[46] Zhu, H. et al. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 17, 551-565 (2016).

[47] Aihong, M., Peige, F., Jianshe, S. & Shaohua, L. Study on induction of tetraploid grapes. Sci. Agric. Sin. 38, 1645-1651 (2005).

[48] Gao, R. et al. Morphological, genome and gene expression changes in newly induced autopolyploid chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino. Int. J. Mol. Sci. 17, 1690 (2016).

[49] Speirs, J., Binney, A., Collins, M., Edwards, E. & Loveys, B . Expression of ABA synthesis and metabolism genes under different irrigation strategies and atmospheric VPDs is associated with stomatal conductance in grapevine (Vitis vinifera L. cv Cabernet Sauvignon). J. Exp. Bot. 64, 1907-1916 (2013).

[50] Kruskal, W. H. & Wallis, W. A. Use of ranks in one-criterion variance analysis. J. Am. Stat. Assoc. 47, 583-621 (1952).