Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers

Abstract

Polyploid plants typically display advantages on some agronomically important traits over their diploid counterparts. Extensive studies have shown genetic, transcriptomic, and epigenetic dynamics upon polyploidization in multiple plant species. However, few studies have unveiled those alternations imposed only by ploidy level, without any interference from heterozygosity. Cultivated potato is highly heterozygous. Thus, in this study, we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid potato. We confirmed their ploidy levels using chloroplast counting and karyotyping. Oligo-FISH and genome re-sequencing validated that these potato lines are nearly homozygous. We investigated variations in phenotypes, transcription, and histone modifications between two ploidies. Both autotetraploid lines produced larger but fewer tubers than the diploid line. Interestingly, each autotetraploid line displayed ploidy-related differential expression for various genes. We also discovered a genome-wide enrichment of H3K27ac in genic regions upon whole-genome doubling (WGD). However, such enrichment was not associated with the differential gene expression between two ploidies. The tetraploid lines may exhibit better resistance to cold-induced sweetening (CIS) than the diploid line in tubers, potentially regulated through the expression of CIS-related key genes, which seems to be associated with the levels of H3K4me3 in cold-stored tubers. These findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes, transcription, and histone modifications, as well as on CIS-related genes in response to cold storage.

Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31900386 to Z.Z.), Sichuan Science and Technology Program (2021YFH0025 to Z.Z. and 2021YFYZ0019 to B.Z. and Z.Z.), State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China at Sichuan Agricultural University (SKL-KF202205 to B.Z.), State Key Laboratory of Crop Biology Open Fund (2020KF01 to B.Z.). All data were visualized using R program (https://www.r-project.org). Circos plots were drawn using OmicCircos package (https://bioconductor.org/packages/OmicCircos/).

Author contributions

Z.Z. and B.Z. designed and supervised the study. Z.Z. and B.Z. developed the plant materials. H.G. and M.Z. performed the data analysis. G.Z., L.H., C.Y., M.W. and D.Z. performed the experiments. H.G., M.Z., G.Z., J.H., W.H. and Z.Z. prepared the manuscript. All of the authors read and approved the manuscript.

Data availability

Raw reads generated from potato in this study are available from National Center for Biotechnology Information (NCBI) under project number PRJNA873910.

Conflict of interest statement

The authors declare that they have no competing interests.

References

[1] Corneillie S, De Storme N, Van Acker R et al. Polyploidy affects plant growth and alters cell wall composition. Plant Physiol. 2019; 179: 74-87.

[2] Fasano C, Diretto G, Aversano R et al. Transcriptome and metabolome of synthetic solanum autotetraploids reveal key genomic stress events following polyploidization. New Phytol. 2016; 210: 1382-94.

[3] Van de Peer Y, Mizrachi E, Marchal K . The evolutionary significance of polyploidy. Nat Rev Genet. 2017; 18: 411-24.

[4] Fawcett JA, Maere S, Van De Peer Y . Plants with double genomes might have had a better chance to survive the cretaceous-tertiary extinction event. Proc Natl Acad Sci. 2009; 106: 5737-42.

[5] Chen R, Feng Z, Zhang X et al. A new way of rice breeding: Polyploid rice breeding. Plan Theory. 2021; 10: 422.

[6] Jansky SH, Spooner DM . The evolution of potato breeding. Plant Breed Rev. 2018; 41: 169-214.

[7] Jansky SH, Charkowski AO, Douches DS et al. Reinventing potato as a diploid inbred line-based crop. Crop Sci. 2016; 56: 1412-22.

[8] Parisod C, Holderegger R, Brochmann C . Evolutionary consequences of autopolyploidy. New Phytol. 2010; 186: 5-17.

[9] Zhang H, Zhu B, Qi B et al. Evolution of the BBAA component of bread wheat during its history at the allohexaploid level. Plant Cell. 2014; 26: 2761-76.

[10] Yang J, Liu D, Wang X et al. The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet. 2016; 48: 1225-32.

[11] Edger PP, Poorten TJ, VanBuren R et al. Origin and evolution of the octoploid strawberry genome. Nat Genet. 2019; 51: 541-7.

[12] Chen ZJ, Sreedasyam A, Ando A et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet. 2020; 52: 525-33.

[13] Li YP, Liu TJ, Luo HF et al. The transcriptional landscape of cultivated strawberry (Fragaria×ananassa) and its diploid ancestor (Fragaria vesca) during fruit development. J Integr Agric. 2021; 20: 1540-53.

[14] Auger DL, Gray AD, Ream TS et al. Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics. 2005; 169: 389-97.

[15] Song MJ, Potter BI, Doyle JJ et al. Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana. Plant Cell. 2020; 32: 1434-48.

[16] Chen P, Chen J, Sun M et al. Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress. Biotechnol Biofuels. 2020; 13: 170.

[17] Wang L, Cao S, Wang P et al. DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance. Proc Natl Acad Sci. 2021; 118: e2023981118.

[18] Stupar RM, Bhaskar PB, Yandell BS et al. Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics. 2007; 176: 2055-67.

[19] Dai F, Wang Z, Luo G et al. Phenotypic and transcriptomic analyses of autotetraploid and diploid mulberry (Morus alba L.). Int J Mol Sci. 2015; 16: 22938-56.

[20] Zhang X, Bernatavichute YV, Cokus S et al. Genome-wide analysis of mono-, di-and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009; 10: R62-14.

[21] Charron J-BF, He H, Elling AA et al. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell. 2009; 21: 3732-48.

[22] Zhang X, Clarenz O, Cokus S et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007; 5: e129.

[23] Sowokinos JR . Biochemical and molecular control of cold-induced sweetening in potatoes. Am J Potato Res. 2001; 78: 221-36.

[24] Bhaskar PB, Wu L, Busse JS et al. Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato. Plant Physiol. 2010; 154: 939-48.

[25] Bethke PC, Bussan AJ . Acrylamide in processed potato products. Am J Potato Res. 2013; 90: 403-24.

[26] Zhu X, Gong H, He Q et al. Silencing of vacuolar invertase and asparagine synthetase genes and its impact on acrylamide formation of fried potato products. Plant Biotechnol J. 2016; 14: 709-18.

[27] Clasen BM, Stoddard TJ, Luo S et al. Improving cold storage and processing traits in potato through targeted gene knockout. Plant Biotechnol J. 2016; 14: 169-76.

[28] Hameed A, Mehmood MA, Shahid M et al. Prospects for potato genome editing to engineer resistance against viruses and cold-induced sweetening. GM Crops Food. 2020; 11: 185-205.

[29] Van Harsselaar JK, Lorenz J, Senning M et al. Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.). BMC Genomics. 2017; 18: 37.

[30] Liu J, Li J, Fu C . Comparative physiology and transcriptome analysis reveals the regulatory mechanism of genome duplication enhancing cold resistance in Fragaria nilgerrensis. Environ Exp Bot. 2021; 188: 104509.

[31] Hardigan MA, Crisovan E, Hamilton JP et al. Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. Plant Cell. 2016; 28: 388-405.

[32] Potato Genome Sequencing Consortium . Genome sequence and analysis of the tuber crop potato. Nature. 2011; 475: 189-95.

[33] Karp A, Risiott R, Jones MG et al. Chromosome doubling in monohaploid and dihaploid potatoes by regeneration from cultured leaf explants. Plant Cell Tissue Organ Cult. 1984; 3: 363-73.

[34] de Alencar LD, Azevedo P, Latado RR . Mothers’ command: phenotypes changes resulting from reciprocal interploidy crosses. Euphytica. 2020; 216: 21.

[35] Miller M, Zhang C, Chen ZJ . Ploidy and hybridity effects on growth vigor and gene expression in Arabidopsis thaliana hybrids and their parents. G3. 2012; 2: 505-13.

[36] Saminathan T, Nimmakayala P, Manohar S et al. Differential gene expression and alternative splicing between diploid and tetraploid watermelon. J Exp Bot. 2015; 66: 1369-85.

[37] Hutten R, Schippers M, Hermsen J et al. Comparative performance of diploid and tetraploid progenies from 2x.2x crosses in potato. Euphytica. 1995; 81: 187-92.

[38] Maris B . Comparison of diploid and tetraploid potato families derived from Solanum phureja x dihaploid S. tuberosum hybrids and their vegetatively doubled counterparts. Euphytica. 1990; 46: 15-33.

[39] Ordoñez B. Assessment of ploidy by chloroplast count in stomatal guard cells. 2014. Lima (Peru). International Potato Center (CIP). 4 p.

[40] Braz GT, He L, Zhao H et al. Comparative oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics. 2018; 208: 513-23.

[41] Hardigan MA, Laimbeer FPE, Newton L et al. Genome diversity of tuber-bearing solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. Proc Natl Acad Sci. 2017; 114: E9999-10008.

[42] Gong Z, Wu Y, Koblížková A et al. Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell. 2012; 24: 3559-74.

[43] Gong L, Zhang H, Gan X et al. Transcriptome profiling of the potato (Solanum tuberosum L.) plant under drought stress and water-stimulus conditions. PLoS One. 2015; 10: e0128041.

[44] Li Q, Qin Y, Hu X et al. Transcriptome analysis uncovers the gene expression profile of salt-stressed potato (Solanum tuberosum L.). Sci Rep. 2020; 10: 5411.

[45] Hancock RD, Morris WL, Ducreux LJ et al. Physiological, biochemical and molecular responses of the potato (Solanum tuberosum L.) plant to moderately elevated temperature. Plant Cell Environ. 2014; 37: 439-50.

[46] Mu H-Z, Liu Z-J, Lin L et al. Transcriptomic analysis of phenotypic changes in birch (Betula platyphylla) autotetraploids. Int J Mol Sci. 2012; 13: 13012-29.

[47] Ruiz M, Oustric J, Santini J et al. Synthetic polyploidy in grafted crops. Front Plant Sci. 2020; 11: 1586.

[48] Liu Z, Jia Y, Ding Y et al. Plasma membrane CRPK1-mediated phosphorylation of 14-3-3 proteins induces their nuclear import to fine-tune CBF signaling during cold response. Mol Cell. 2017; 66: 117-128.e5.

[49] Kriegel A, Andrés Z, Medzihradszky A et al. Job sharing in the endomembrane system: vacuolar acidification requires the combined activity of V-ATPase and V-PPase. Plant Cell. 2015; 27: 3383-96.

[50] Wang J, Lv J, Liu Z et al. Integration of transcriptomics and metabolomics for pepper (Capsicum annuum L.) in response to heat stress. Int J Mol Sci. 2019; 20: 5042.

[51] Yang X, Zhu W, Zhang H et al. Heat shock factors in tomatoes: genome-wide identification, phylogenetic analysis and expression profiling under development and heat stress. PeerJ. 2016; 4: e1961.

[52] Trapero-Mozos A, Morris WL, Ducreux LJ et al. Engineering heat tolerance in potato by temperature-dependent expression of a specific allele of HEAT-SHOCK COGNATE 70. Plant Biotechnol J. 2018; 16: 197-207.

[53] Bian XH, Li W, Niu CF et al. A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis. New Phytol. 2020; 225: 268-83.

[54] Stewart JJ, Demmig-Adams B, Cohu CM et al. Growth temperature impact on leaf form and function in Arabidopsis thaliana ecotypes from northern and southern Europe. Plant Cell Environ. 2016; 39: 1549-58.

[55] Karimi R, Ershadi A, Rezaei Nejad A et al. Abscisic acid alleviates the deleterious effects of cold stress on ‘Sultana’grapevine (Vitis vinifera L.) plants by improving the anti-oxidant activity and photosynthetic capacity of leaves. J Hortic Sci Biotechnol. 2016; 91: 386-95.

[56] Oliveira G, Peñuelas J . Effects of winter cold stress on photosynthesis and photochemical efficiency of PSII of the Mediterranean Cistus albidus L. and Quercus ilex L. Plant Ecol. 2005; 175: 179-91.

[57] Basu P, Sharma A, Garg I et al. Tuber sink modifies photosynthetic response in potato under water stress. Environ Exp Bot. 1999; 42: 25-39.

[58] Zierer W, Rüscher D, Sonnewald U et al. Tuber and tuberous root development. Annu Rev Plant Biol. 2021; 72: 551-80.

[59] Müller-Röber BT, Koßmann J, Hannah LC et al. One of two different ADP-glucose pyrophosphorylase genes from potato responds strongly to elevated levels of sucrose. Mol Gen Genet MGG. 1990; 224: 136-46.

[60] Salanoubat M, Belliard G . The steady-state level of potato sucrose synthase mRNA is dependent on wounding, anaerobiosis and sucrose concentration. Gene. 1989; 84: 181-5.

[61] Liu X, Zhang C, Ou Y et al. Systematic analysis of potato acid invertase genes reveals that a cold-responsive member, StvacINV1, regulates cold-induced sweetening of tubers. Mol Gen Genomics. 2011; 286: 109-18.

[62] Zhang C, Yang Z, Tang D et al. Genome design of hybrid potato. Cell. 2021; 184: 3873-3883.e12.

[63] Podwyszyńska M, Markiewicz M, Broniarek-Niemiec A et al. Apple autotetraploids with enhanced resistance to apple scab (Venturia inaequalis) due to genome duplication-phenotypic and genetic evaluation. Int J Mol Sci. 2021; 22: 527.

[64] Zeng Z, Zhang T, Li G et al. Phenotypic and epigenetic changes occurred during the autopolyploidization of Aegilops tauschii. Cereal Res Commun. 2012; 40: 476-85.

[65] Xia J, Ma YJ, Wang Y et al. Deciphering transcriptome profiles of tetraploid Artemisia annua plants with high artemisinin content. Plant Physiol Biochem. 2018; 130: 112-26.

[66] Yu Z, Haberer G, Matthes M et al. Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc Natl Acad Sci. 2010; 107: 17809-14.

[67] Onufriev AV, Schiessel H . The nucleosome: from structure to function through physics. Curr Opin Struct Biol. 2019; 56: 119-30.

[68] Allis CD, Jenuwein T . The molecular hallmarks of epigenetic control. Nat Rev Genet. 2016; 17: 487-500.

[69] Yan W, Chen D, Schumacher J et al. Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis. Nat Commun. 2019; 10: 1705.

[70] Ricci WA, Lu Z, Ji L et al. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants. 2019; 5: 1237-49.

[71] Kato A, Lamb JC, Birchler JA . Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci. 2004; 101: 13554-9.

[72] Han Y, Zhang T, Thammapichai P et al. Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics. 2015; 200: 771-9.

[73] He L, Zhao H, He J et al. Extraordinarily conserved chromosomal synteny of citrus species revealed by chromosome-specific painting. Plant J. 2020; 103: 2225-35.

[74] Ye J, Shakya R, Shrestha P et al. Tuber-specific silencing of the acid invertase gene substantially lowers the acrylamide-forming potential of potato. J Agric Food Chem. 2010; 58: 12162-7.

[75] Zeng Z, Zhang W, Marand AP et al. Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biol. 2019; 20: 123.

[76] Chen S, Zhou Y, Chen Y et al. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34: i884-90.

[77] Kim D, Paggi JM, Park C et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37: 907-15.

[78] Pertea M, Pertea GM, Antonescu CM et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33: 290-5.

[79] Love MI, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15: 550.

[80] Trapnell C, Williams BA, Pertea G et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28: 511-5.

[81] Li H, Durbin R . Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009; 25: 1754-60.

[82] Zhang Y, Liu T, Meyer CA et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9: R137.

[83] Tian T, Liu Y, Yan H et al. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 2017; 45: W122-9.

[84] Li H . A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27: 2987-93.

[85] Rausch T, Zichner T, Schlattl A et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012; 28: i333-9.