Journal of Plant Biotechnology

  • 제46권2호
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  • Pages.79-87
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  • 2019
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  • 1229-2818(pISSN)
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  • 2384-1397(eISSN)
한국식물생명공학회 (The Korean Society of Plant Biotechnology)
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PCR-based markers developed by comparison of complete chloroplast genome sequences discriminate Solanum chacoense from other Solanum species

  • Kim, Soojung (Department of Horticulture, Daegu University) ;
  • Park, Tae-Ho (Department of Horticulture, Daegu University)
  • 투고 : 2019.06.10
  • 심사 : 2019.06.15
  • 발행 : 2019.06.30
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초록

One of wild diploid Solanum species, Solanum chacoense, is one of the excellent resources for potato breeding because it is resistant to several important pathogens, but the species is not sexually compatible with potato (S. tuberosum) causing the limitation of sexual hybridization between S. tuberosum and S. chacoense. Therefore, diverse traits regarding resistance from the species can be introgressed into potato via somatic hybridization. After cell fusion, the identification of fusion products is crucial with molecular markers. In this study, S. chacoense specific markers were developed by comparing the chloroplast genome (cpDNA) sequence of S. chacoense obtained by NGS (next-generation sequencing) technology with those of five other Solanum species. A full length of the cpDNA sequence is 155,532 bp and its structure is similar to other Solanum species. Phylogenetic analysis resulted that S. chacoense is most closely located with S. commersonii. Sequence alignment with cpDNA sequences of six other Solanum species identified two InDels and 37 SNPs specific sequences in S. chacoense. Based on these InDels and SNPs regions, four markers for distingushing S. chacoense from other Solanum species were developed. These results obtained in this research could help breeders select breeding lines and facilitate breeding using S. chacoense in potato breeding.

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참고문헌

  1. Barsby TL, Shepard JF, Kemble RJ, Wong R (1984) Somatic hybridization in the genus Solanum: S. tuberosum and S. brevidens. Plant Cell Rep 3:165-167 https://doi.org/10.1007/BF00270215
  2. Bidani A, Nouri-Ellouz O, Lakhoua L, Shihachakr D, Cheniclet C, Mahjoub A, Drira N, Gargouri-Bouzid R (2007) Interspecific potato somatic hybrids between Solanum berthaultii and Solanum tubersoum L. showed recombinant plastome and improved tolerance to salinity. Plant Cell Tiss Organ Cult 91:179-189 https://doi.org/10.1007/s11240-007-9284-6
  3. Binding H, Jain SM, Finger J, Mordhorst G, Nehls R, Gressel J (1982) Somatic hybridization of an atrazine resistant biotype of Solanum nigrum with Solanum tuberosum. Theor Appl Genet 63:273-277 https://doi.org/10.1007/BF00304007
  4. Bohs L, Olmstead RG (1997) Phylogenetic relationships in Solanum (Solanaceae) based on ndhF sequences. Syst Bot 22:5-17 https://doi.org/10.2307/2419674
  5. Brown CR, Thomas PE (1993) Resistance to potato leafroll virus derived from Solanum chacoense: characterization and inheritance. Euphytica 74:51-57 https://doi.org/10.1007/BF00033767
  6. Calsa Junior T, Carraro DM, Benatti MR, Barbosa AC, Kitajima JP, Carrer H (2004) Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr Genet 46:366-373 https://doi.org/10.1007/s00294-004-0542-4
  7. Chen L, Guo X, Xie C, He L, Cai X, Tian L, Song B, Liu J (2013) Nuclear and cytoplasmic genome components of Solanum tuberosum + S. chacoense somatic hybrids and three SSR alleles related to bacterial wilt resistance. Theor Appl Genet 126:1861-1872 https://doi.org/10.1007/s00122-013-2098-5
  8. Cho KS, Cheon KS, Hong SY, Cho JH, Im JS, Mekapogu M, Yu YS, Park TH (2016) Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum. Plant Cell Rep 35:2113-2123 https://doi.org/10.1007/s00299-016-2022-y
  9. Cho K-S, Choi J-G, Cho J-H, Im J-S, Park Y-E, Hong S-Y, Park T-H (2017) Chloroplast genome of the wild tuber-bearing diploid potato relative Solanum chacoense. Mitochondr DNA Part B 2:915-917 https://doi.org/10.1080/23802359.2017.1413309
  10. Cho HM, Kim-Lee HY, Om YH, Kim JK (1997) Influence of endosperm balance number (EBN) in interploidal and interspecific crosses between Solanum tuberosum dihaploids and wild species. Korean J Breed 29:154-161
  11. Cho KS, Park TH (2016) Complete chloroplast genome sequence of Solanum nigrum and Development of markers for the discrimination of S. nigrum. Hort Environ Biotechnol 57: 69-78 https://doi.org/10.1007/s13580-016-0003-2
  12. Cho K-S, Yun B-K, Yoon Y-H, Hong S-Y, Mekapogu M, Kim K-H, Yang T-J (2015) Complete chloroplast genome sequence of tartary Buckwheat (Fagopyrum tataricum) and comparative analysis with common Buckwheat (F. esculentum). PloS One 10:e0125332 https://doi.org/10.1371/journal.pone.0125332
  13. Chung HJ, Jung JD, Park HW, Kim JH, Cha HW, Min SR, Jeong WJ, Liu JR (2006) The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp in cultivated potato chloroplast DNA sequence. Plant Cell Rep 25:1369-1379 https://doi.org/10.1007/s00299-006-0196-4
  14. Cooper SG, Douches DS, Zarka K, Grafius EJ (2009) Enhanced resistance to control potato tuberworm by combining engineered resistance, avidin, and natural resistance derived from, Solanum chacoense. Am J Potato Res 86:24-30 https://doi.org/10.1007/s12230-008-9057-8
  15. Daniell H, Lee S-B, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen PK (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112:1503-1518 https://doi.org/10.1007/s00122-006-0254-x
  16. Garcia-Lor A, Curk F, Snoussi-Trifa H, Morillon R, Ancillo G, Luro F, Navarro L and Ollitrault P (2013) A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species. Ann Bot 111:1-19 https://doi.org/10.1093/aob/mcs227
  17. Gargano D, Vezzi A, Scotti N, Gray JC, Valle G, Grillo S, Cardi T (2005) The complete nucleotide sequence genome of potato (Solanum tuberosum cv. Desiree) chloroplast DNA. In the abstract of the 2nd Solanaceae Genome Workshop, p. 107
  18. Guo WW, Cai XD, Grosser JW (2004) Somatic cell cybrids and hybrids in plant improvement, p. 635-659. In: H. Daniell, C. Chase (eds.) Molecular biology and biotechnology of plant organelles. Springer, Dordrecht, The Netherlands
  19. Hosaka K, Sanetomo R (2012) Development of a rapid identification method for potato cytoplasm and its use for evaluating Japanese collections. Theor Appl Genet 125:1237-1251 https://doi.org/10.1007/s00122-012-1909-4
  20. Jheng C-F, Chen T-C, Lin J-Y, Chen T-C, Wu W-L, Chang C-C (2012) The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Sci 190:62-73 https://doi.org/10.1016/j.plantsci.2012.04.001
  21. Kim KJ, Choi KS, Jansen RK (2005) Two chloroplast DNA inversion originated simultaneously during the early evolution of the sunflower family (Asteraceae). Mol Biol Evol 22: 1783-1792 https://doi.org/10.1093/molbev/msi174
  22. Kim S, Cho K-S, Park T-H (2018) Development of PCR-based markers for discriminating Solanum berthaultii using its complete chloroplast genome species. J Plant Biotechnol 45:207-216 https://doi.org/10.5010/JPB.2018.45.3.207
  23. Kim-Lee H, Moon JS, Hong YJ, Kim MS, Cho HM (2005) Bacterial wilt resistance in the progenies of the fusion hybrids between haploid of potato and Solanum commersonii. Amer J Potato Res 82:129-137 https://doi.org/10.1007/BF02853650
  24. Komori T, Nitta N (2005) Utilization of the CAPS/dCAPS method to convert rice SNPs into PCR-based markers. Breed Sci 55:93-98 https://doi.org/10.1270/jsbbs.55.93
  25. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403-410 https://doi.org/10.1046/j.1365-313X.1993.04020403.x
  26. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12 https://doi.org/10.1186/gb-2004-5-2-r12
  27. Lohse M, Drechsel O, Kahlau S, Bock R (2013) Organellar GenomeDRAW - a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41:W575-W581 https://doi.org/10.1093/nar/gkt289
  28. Lossl A, Gotz A, Braun A, Wenzel G (2000) Molecular markers for cytoplasm in potato: male sterility and contribution of different plastid-mitochondrial configurations to starch production. Euphytica 116:221-230 https://doi.org/10.1023/A:1004039320227
  29. Lynch DR, Kawchuk LM, Hachey J, Bains PS, Howard RJ (1997) Identification of a gene conferring high levels of resistance to Verticillium wilt in Solanum chacoense. Plant Dis 81:1011-1014 https://doi.org/10.1094/PDIS.1997.81.9.1011
  30. Micheletto S, Boland R, Huarte M (2000) Argentinian wild diploid Solanum species as sources of quantitative late blight resistance. Theor and Appl Genet 101:902-906 https://doi.org/10.1007/s001220051560
  31. Mohapatra T, Kirti PB, Dinesh Kumar V, Prakash S, Chopra VL (1998) Random chloroplast segregation and mitochondrial genome recombination in somatic hybrid plants of Diplotaxis catholica + Brassica juncea. Plant Cell Rep 17:814-818 https://doi.org/10.1007/s002990050489
  32. Nouri-Ellouz O, Triki MA, Jbir-Koubaa R, Louhichi A, Charfeddine S, Drira N, Gargouri-Bouzid R (2016) Somatic hybrids between potato and S. berthaultii show partial resistance to soil-borne fungi and potato virus Y. J Phythpathol 164:485-496 https://doi.org/10.1111/jph.12474
  33. Ortiz R, Ehlenfeldt MK (1992) The importance of endorsperm balance number in potato breeding and the evolution of tuber-bearing Solanum species. Euphytica 60:105-113 https://doi.org/10.1007/BF00029665
  34. Palmer JD (1991) Plastid chromosomes: structure and evolution, p. 5-53. In: L. Bogorad, K. Vasil (eds.) The molecular biology of plastids. Academic Press, San Diego, USA
  35. Park T-H, Gros J, Sikkema A, Vleeshouwers VGAA, Muskens M, Allefs S, Jacobsen E, Visser RGF, van der Vossen EAG (2005) The late blight resistance locus Rpi-blb3 from Solanum bulbocastanum belongs to a major late blight R gene cluster on chromosome 4 of potato. Mol Plant-Microb Interact 18:722-729 https://doi.org/10.1094/MPMI-18-0722
  36. Pavek JJ, Corsini DL (2001) Utilization of potato genetic resources in variety development. Amer J Potato Res 78:433-441 https://doi.org/10.1007/BF02896375
  37. Puite KJ, Roest S, Pijnacker LP (1986) Somatic hybrid potato plants after electrofusion of diploid Solanum tuberosum and Solanum phureja. Plant Cell Rep 5:262-265 https://doi.org/10.1007/BF00269817
  38. Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants, p. 45-68. In: H. Henry (ed.) Diversity and evolution of plants: genotypic and phenotypic variation in higher plants. CABI Publishing, Wallingford, UK
  39. Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, Jansen RK (2005) Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol Biol 59:309-322 https://doi.org/10.1007/s11103-005-8882-0
  40. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W (2003) Human-mouse alignments with BLASTZ. Genome Res 13:103-107 https://doi.org/10.1101/gr.809403
  41. Simko I, Jansky S, Stephenson S, Spooner D (2007) Genetics of resistance to pests and disease, p. 117-155. In: D. Vreugdenhil et al. (eds.) Potato biology and biotechnology. Elsevier, Oxford, UK
  42. Sinden SL, Sanford LL, Cantelo WW, Deahl KL (1986) Leptine Glycoalkaloids and resistance to the Colorado potato beetle (Coleoptera: Chrysomelidae) in Solanum chacoense. Environm Entomol 15:1057-1062 https://doi.org/10.1093/ee/15.5.1057
  43. Smilde WD, Brigneti G, Jagger L, Perkins S, Jones JDG (2005) Solanum mochiquense chromosome IX carries a novel late blight resistance gene Rpi-moc1. Theor Appl Genet 110:252-258 https://doi.org/10.1007/s00122-004-1820-8
  44. Sugiura M, Hirose T, Sugita M (1998) Evolution and mechanism of translation in chloroplast. Annu Rev Genet 32:437-459 https://doi.org/10.1146/annurev.genet.32.1.437
  45. Swofford DL (2001) Phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Sunderland
  46. Smyda-Dajmund P, Sliwka J, Wasilewicz-Flis I, Jakuczun H, Zimnoch-Guzowska E (2016) Genetic composition of interspecific potato somatic hybrids and autofused 4x plants evaluated by DArT and cytoplasmic DNA markers. Plant Cell Rep 35:1345-1358 https://doi.org/10.1007/s00299-016-1966-2
  47. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetic analysis version 6.0. Mol Biol Evol 30:2725-2729 https://doi.org/10.1093/molbev/mst197
  48. Uncu AT, Celik I, Devran Z, Ozkaynak E, Frary A, Frary A, Doganlar S (2015) Development of a SNP-based CAPS assay for the Me1 gene conferring resistance to root knot nematode in pepper. Euphytica 206:393-399 https://doi.org/10.1007/s10681-015-1489-x
  49. Uribe P, Jansky S, Halterman D (2014) Two CAPS markers predict Verticillium wilt resistance in wild Solanum species. Mol Breeding 33:465-476 https://doi.org/10.1007/s11032-013-9965-2
  50. Wang Y, Liu W, Xu L, Wang Y, Chen Y, Luo X, Tang M, Liu L (2017) Development of SNP markers based on transcriptome sequences and their application in germplasm identification in radish (Raphanus sativus L.). Mol Breeding 37:26 https://doi.org/10.1007/s11032-017-0632-x
  51. Wyman SK, Jansen RK, Boore JL (2004) Antomatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255 https://doi.org/10.1093/bioinformatics/bth352
  52. Xiang F, Xia G, Zhi D, Wang J, Nie H, Chen H (2004) Regeneration of somatic hybrids in relation to the nuclear and cytoplasmic genomes of wheat and Setaria italica. Genome 47:680-688 https://doi.org/10.1139/g04-023
  53. Yamaki S, Ohyangi H, Yamasaki M, Eiguchi M, Miyabayashi T, Kubo T, Kurata N and Nonomura K (2013) Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza. Breeding Sci 63:246-254 https://doi.org/10.1270/jsbbs.63.246
  54. Yurina NP, Odintsova MS (1998) Comparative structural organization of plant chloroplast and mitochondrial genomes. Russ J Genet 34:5-22