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The Wild Side of Potato: Insights into the Genome Sequence of the Stress-Tolerant S. commersonii

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The Potato Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Solanum commersonii is a potato species native to Central and South America. Despite being genetically isolated from cultivated potato, in the past few years it has garnered significant research interest because it exhibits high tolerance to both biotic and abiotic stresses. Among the abiotic stresses, particularly interesting are its freezing tolerance and capacity to cold acclimatize. Little is understood of the genetic determinants and mechanisms beyond its resistance traits. This is partially due to the lack of genomic resources for potato germplasm. The group at the University of Naples has recently decoded, for the first time, the genome of S. commersonii, ushering in a new era of whole-genome sequencing of wild potato relatives. After illustrating the genome structure and organization of this species and its intriguing evolutionary roots, this chapter describes findings relative to the identification of the candidate genes for cold stress tolerance. The genome sequence of S. commersonii will pave the way to an understanding of the molecular dynamics that have given this species so many adaptive characteristics.

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References

  • Aversano R, Caruso I, Aronne G, De Micco V, Scognamiglio N, Carputo D (2013) Stochastic changes affect Solanum wild species following autopolyploidization. J Exp Bot 64(2):625–635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aversano R, Contaldi F, Ercolano MR, Grosso V, Iorizzo M, Tatino F et al (2015a) The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives. Plant Cell 27(4):954–968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aversano R, Scarano MT, Aronne G, Caruso I, D’Amelia V, De Micco V, Fasano C, Termolino P, Carputo D (2015b) Genotype-specific changes associated to early synthesis of autotetraploids in wild potato species. Euphytica 202(2):307–316

    Article  Google Scholar 

  • Aversano R, Contaldi F, Adelfi MG, D’Amelia V, Diretto G, De Tommasi N, Vaccaro C, Vassallo A, Carputo D (2017) Comparative metabolite and genome analysis of tuber-bearing potato species. Phytochemistry. doi:10.1016/j.phytochem.2017.02.011

    PubMed  Google Scholar 

  • Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frickey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK (2008) A gene expression atlas of the model legume Medicago truncatula. Plant J 55(3):504–513

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42(1):251–269

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen JL, Coleman C, Liu JMR, Ramakrishna W (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7:732–736

    Article  CAS  PubMed  Google Scholar 

  • Boulesteix M, Weiss M, BiĂ©mont C (2006) Differences in genome size between closely related species: the Drosophila melanogaster species subgroup. Mol Biol Evol 23(1):162–167

    Article  CAS  PubMed  Google Scholar 

  • Bradshaw JE, Bryan GJ, Ramsay G (2006) Genetic resources (including wild and cultivated Solanum species) and progress in their utilisation in potato breeding. Potato Res 49:49–65

    Article  Google Scholar 

  • Cai B, Li CH, Yao QH, Zhou J, Tao JM, Zhang Z (2009) Analysis of SSR in grape genome and development of SSR database. J Nanjing Agric Univ 32(4):501–510

    Google Scholar 

  • Carputo D, Barone A, Cardi T, Sebastiano A, Frusciante L, Peloquin SJ (1997) Endosperm balance number manipulation for direct in vivo germplasm introgression to potato from a sexually isolated relative (Solanum commersonii Dun.). Proc Natl Acad Sci USA 94:12013–12017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caruso I, Lepore L, De Tommasi N, Dal Piaz F, Frusciante L, Aversano R, Garramone R, Carputo D (2011) Secondary metabolite profile in induced tetraploids of wild Solanum commersonii Dun. Chem Biodivers 8(12):2226–2237

    Article  CAS  PubMed  Google Scholar 

  • Carvallo MA, Pino MT, Jeknic Z, Zou C, Doherty CJ, Shiu S-H, Chen THH, Thomashow MF (2011) A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana. J Exp Bot 62:3807–3819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chinnusamy V, Zhu J, Zhu JK (2006) Gene regulation during cold acclimation in plants. Physiol Plant 26:52–61

    Article  Google Scholar 

  • D’Amelia V, Aversano R, Ruggiero A, Batelli G, Appelhagen I, Dinacci C, Hill L, Martin C, Carputo D (2017) Subfunctionalization of duplicate MYB genes in Solanum commersonii generated the cold-induced ScAN2 and the anthocyanin regulator ScAN1. Plant Cell Environ (Accepted with minor revision)

    Google Scholar 

  • Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics 6:202–211

    Article  CAS  PubMed  Google Scholar 

  • Fasano C, Diretto G, Aversano R, D’Agostino N, Di Matteo A, Frusciante L, Giuliano G, Carputo D (2016) Transcriptome and metabolome of synthetic Solanum autotetraploids reveal key genomic stress events following polyploidization. New Phytol 210(4):1382–1394

    Article  CAS  PubMed  Google Scholar 

  • Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF (1998) Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J 16(4):433–442

    Article  CAS  PubMed  Google Scholar 

  • Gilmour SJ, Fowler SG, Thomashow MF (2004) Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant Mol Biol 54:767–781

    Article  CAS  PubMed  Google Scholar 

  • Guang L, Zhang Z, Wang XW, Xue HB, Liu YH, Wang SH, Qiao Y-S (2012) Evaluation and application of the SSR loci in apple genome. Sci Agric Sinica 44(21):4415–4428

    Google Scholar 

  • Hawkes JG (1990) The potato: evolution, biodiversity and genetic resources. Belhaven Press, Washington, USA

    Google Scholar 

  • Hirsch CN, Hirsch CD, Felcher K, Coombs J, Zarka D, Van Deynze A, De Jong W, Veilleux RE, Jansky SH, BethkeP, Douches DS, Buell CR (2013) Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries. G3 (Bethesda) 3(6):1003–1013

    Google Scholar 

  • Jackson SA, Hanneman RE (1999) Crossability between cultivated and wild tuber-and non-tuber-bearing Solanum. Euphytica 109:51–67

    Article  Google Scholar 

  • Jiao Y, Tausta SL, Gandotra N, Sun N, Liu N, Clay NK (2009) A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41:258–263

    Article  CAS  PubMed  Google Scholar 

  • Johnston SA, den Nijs TPM, Peloquin SJ, Hanneman RE Jr (1980) The significance of genic balance to endosperm development in interspecific crosses. Theor Appl Genet 57:5–9

    Article  CAS  PubMed  Google Scholar 

  • Jurka J (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16(9):418–420

    Google Scholar 

  • Lakhotia N, Joshi G, Bhardwaj AR, Katiyar-Agarwal S, Agarwal M, Jagannath A, Goel S, Kumar A (2014) Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing. BMC Plant Biol 14:6

    Article  PubMed  PubMed Central  Google Scholar 

  • Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J 63(1):86–99

    CAS  PubMed  Google Scholar 

  • Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459–473

    CAS  PubMed  PubMed Central  Google Scholar 

  • Machida-Hirano R (2015) Diversity of potato genetic resources. Breed Sci 65(1):26–40

    Article  PubMed  PubMed Central  Google Scholar 

  • Massa AN, Childs KL, Lin H, Bryan GJ, Giuliano G, Buell CR (2011) The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. PLoS ONE. 6(10):e26801

    Google Scholar 

  • Michael TP, Jackson S (2013) The First 50 Plant Genomes. Plant Genome 6:7

    Article  Google Scholar 

  • Micheletto S, Boland R, Huarte M (2000) Argentinian wild diploid Solanum species as sources of quantitative late blight resistance. Theor Appl Genet 101(5):902–909

    Article  Google Scholar 

  • Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proc Natl Acad Sci USA 101:3985–3990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Palta JP, Simon G (1993) Breeding potential for improvement of freezing stress resistance: genetic separation of freezing tolerance, freezing avoidance, and capacity to cold acclimate. In: Li PH (ed) Advances in plant cold hardiness. CRC Press, Boca Raton, Florida, USA, pp 299–310

    Google Scholar 

  • Pennycooke JC, Cheng H, Roberts SM, Yang Q, Rhee SY, Stockinger EJ (2008) The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions, and rearrangements. Plant Mol Biol 67:483–497

    Article  CAS  PubMed  Google Scholar 

  • Piegu B, Guyot R, Picault N, Roulin A, Sanyal A, Kim H, Collura K, Brar DS, Jackson SA, Wing RA, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition- driven genomic expansions in Oryza australiensis, a wild relative of rice. Genet Res 16:1262–1269

    Article  CAS  Google Scholar 

  • Pino MT, Skinner JS, Jeknić Z, Hayes PM, Soeldner AH, Thomashow MF, Chen TH (2008) Ectopic AtCBF1 over-expression enhances freezing tolerance and induces cold acclimation-associated physiological modifications in potato. Plant, Cell Environ 31(4):393–406

    Article  CAS  Google Scholar 

  • Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop. Nature 475:189–195

    Article  Google Scholar 

  • RodrĂ­guez F, Spooner DM (2009) Nitrate reductase phylogeny of potato (Solatium sect. Petota) genomes with emphasis on the origins of the polyploid species. Syst botany 34:207–219

    Article  Google Scholar 

  • Sattler MC, Carvalho CR, Clarindo WR (2016) The polyploidy and its key role in plant breeding. Planta 243(2):281–296

    Article  CAS  PubMed  Google Scholar 

  • Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501–506

    Article  CAS  PubMed  Google Scholar 

  • Sekhon RS, Lin H, Childs LK, Hansey CN, Buell CR, de Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription during maize development. Plant J 66(4):553–563

    Article  CAS  PubMed  Google Scholar 

  • Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS ONE 8(4):e61005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shakoor N, Nair R, Crasta O, Morris G, Feltus A, Kresovich S (2014) A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. BMC Plant Biol 14(1):35

    Article  PubMed  PubMed Central  Google Scholar 

  • Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Article  Google Scholar 

  • Van Buskirk HA, Thomashow MF (2006) Arabidopsis transcription factors regulating cold acclimation. Physiol Plant 126:72–80

    Article  Google Scholar 

  • Verdier J, Torres-Jerez I, Wang M, Andriankaja A, Allen SN, He J, Tang Y, Murray JD, Udvardi MK (2013) Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation. Plant J 74(2):351–362

    Article  CAS  PubMed  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57(1):781–803

    Google Scholar 

  • Zhao C, Lang Z, Zhu JK (2015) Cold responsive gene transcription becomes more complex. Trends Plant Sci 20(8):466–468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Agricultural Sciences, University of Naples Federico II, Via UniversitĂ  100, Portici, Italy

    Salvatore Esposito, Vincenzo D’Amelia, Clizia Villano, Felice Contaldi, Domenico Carputo & Riccardo Aversano

Authors
  1. Salvatore Esposito
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  2. Vincenzo D’Amelia
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  3. Clizia Villano
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  4. Felice Contaldi
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  5. Domenico Carputo
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  6. Riccardo Aversano
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Corresponding author

Correspondence to Domenico Carputo .

Editor information

Editors and Affiliations

  1. ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India

    Swarup Kumar Chakrabarti

  2. Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China

    Conghua Xie

  3. ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India

    Jagesh Kumar Tiwari

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Esposito, S., D’Amelia, V., Villano, C., Contaldi, F., Carputo, D., Aversano, R. (2017). The Wild Side of Potato: Insights into the Genome Sequence of the Stress-Tolerant S. commersonii . In: Kumar Chakrabarti, S., Xie, C., Kumar Tiwari, J. (eds) The Potato Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-66135-3_7

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