Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

PCR-based markers to select plastid genotypes of Solanum acaule

Solanum acaule 색소체 유전자형 선발을 위한 특이적 분자마커 개발

  • Park, Tae-Ho (Department of Horticulture, Daegu University)
  • Received : 2022.09.13
  • Accepted : 2022.09.26
  • Published : 2022.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The tetraploid Solanum acaule is a wild potato species from Bolivia widely used for potato breeding because of its diverse attractive traits, including resistance to frost, late blight, potato virus X, potato virus Y, potato leafroll virus, potato spindle tuber viroid, and cyst nematode. However, the introgression of useful traits into cultivated potatoes via crossing has been limited by differences in endosperm balance number between species. Somatic fusion could be used to overcome sexual reproduction barriers and the development of molecular markers is essential to select proper fusion products. The chloroplast genome of S. acaule was sequenced using next-generation sequencing technology and specific markers for S. acaule were developed by comparing the obtained sequence with those of seven other Solanum species. The total length of the chloroplast genome is 155,570 bp, and 158 genes were annotated. Structure and gene content were very similar to other Solanum species and maximum likelihood phylogenetic analysis with 12 other species belonging to the Solanaceae family revealed that S. acaule is very closely related to other Solanum species. Sequence alignment with the chloroplast genome of seven other Solanum species revealed four InDels and 79 SNPs specific to S. acaule. Based on these InDel and SNP regions, one SCAR marker and one CAPS marker were developed to discriminate S. acaule from other Solanum species. These results will aid in exploring evolutionary aspects of Solanum species and accelerating potato breeding using S. acaule.

볼리비아 유래의 4배체 감자 야생종 중 하나인 Solanum acaule는 서리, 감자역병, 감자바이러스X, 감자바이러스Y, 감자잎말림바이러스, 감자걀쭉병, 선충 등에 대한 저항성과 같이 감자의 신품종 육성에 매우 유용한 형질들을 가지고 있어 감자 육종에 많이 이용되고 있다. 그러나 이러한 유용 형질들을 재배종 감자에 전통적인 교잡에 의해 도입하는 것은 야생종과 재배종 간의 서로 다른 EBN에 따라 매우 제한적이다. 따라서, 이러한 생리적 장벽을 극복하기 위해서는 체세포융합을 이용할 수 있는데, 육종에 활용할 적절한 체세포융합체를 선발하기 위해서는 적절한 분자마커의 개발이 필수적이다. 이에, 본 연구에서는 앞서 차세대 유전체 기술에 의해 완성되어 보고된 S. acaule의 엽록체 전장 유전체 정보를 기반으로 이를 다른 8개의 Solanum 종의 엽록체 전장 유전체 정보와 비교를 통해 S. acaule 특이적인 분자마커를 개발하였다. S. acaule의 엽록체 전장 유전체 총 길이는 155,570 bp였으며, 총 158개의 유전자로 구성되어 있었다. 전체적인 구조와 유전자의 구성은 다른 Solanum 종들과 매우 유사하였고 12종의 다른 가지과에 속해 있는 종과의 계통수 분석에서 다른 Solanum 종과 매우 가까운 유연관계를 가지는 것을 확인하였다. S. acaule의 엽록체 전장 유전체와 다른 7개 Solanum 종의 엽록체 전장 유전체 다중 정렬의 결과로 각각 4개와 79개의 S. acaule 특이적인 InDel 및 SNP 영역이 확인되었으며, 이 정보를 이용하여 각각 1개씩의 InDel 및 SNP 영역 유래의 PCR 기반의 분자마커를 개발하였다. 본 연구의 결과는 S. acaule의 진화적 측면에서의 연구와 S. acaule를 이용한 감자품종 육성 연구에 기여를 할 수 있을 것이다.

Keywords

Acknowledgement

이 성과는 정부(과학기술정보통신부)의 재원으로 한국연구재단의 지원을 받아 수행된 연구임(No. NRF-2021R1F1A1045981)

References

  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. Bitter G (1912) Solana nova vel minus cogita. Feddes Repert 11:1-393 https://doi.org/10.1002/fedr.19120110103
  5. 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
  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. Caranta C, Thabuis A, Palloix A (1999) Development of a CAPS marker for the Pvr4 locus: A tool for pyramiding potyvirus resistance genes in pepper. Genome 42:1111-1116 https://doi.org/10.1139/g99-069
  8. Chavez R, Brown CR, Iwanaga M (1988) Transfer of resistance to PLRV titer buildup from Solanum etuberosum to a tuberbearing Solanum gene pool. Theor Appl Genet 76:129-135 https://doi.org/10.1007/BF00288843
  9. Chen HH, Li PH (1980) Characteristics of cold acclimation and deacclimation in tuber-bearing Solanum species. Plant Physiol 65:1146-1148 https://doi.org/10.1104/pp.65.6.1146
  10. 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
  11. Chen P, Li PH, Cunningham P (1977) Ultrastructural differences in leaf cells of some Solanum species in relation to their frost resistance. Bot Gaz 138:276-285 https://doi.org/10.1086/336925
  12. 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
  13. 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
  14. Cho K-S, Cho J-H, Park Y-E, Park T-H (2019) Chloroplast genome sequence of Solanum demissum, a wild tuber-bearing species was completed. Mitochondr DNA Part B 4:1800-1802 https://doi.org/10.1080/23802359.2019.1612716
  15. 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
  16. 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
  17. 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
  18. 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
  19. Dvorak J (1983) Evidence for genetic suppression of heterogenetic chromosome pairing in polyploidy species of Solanum, sect. Petota. Can J Genet Cytol. 25:530-539 https://doi.org/10.1139/g83-080
  20. Estrada RN (1980) Frost resistance potato hybrids via Solanum acaule, Bitt. dipolid-tetraploid crosses. Amer Potato J 57: 609-619 https://doi.org/10.1007/BF02854131
  21. 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
  22. 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.
  23. Hawkes JG (1990) The potato: Evolution, biodiversity and genetic resources. Belhaven Press, London, UK
  24. 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
  25. 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
  26. 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
  27. 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
  28. Kim S, Park T-H (2019) PCR-based markers developed by comparison of complete chloroplast genome sequences discriminate Solanumchacoense from other Solanum species. J Plant Bioechnol 46:79-87 https://doi.org/10.5010/JPB.2019.46.2.079
  29. Kim S, Park T-H (2020a) Comparison of the complete chloroplast genome sequences of Solanum stoloniferum with other Solanum species generate PCR-based markers specific for Solanum stoloniferum. J Plant Bioechnol 47:131-140 https://doi.org/10.5010/JPB.2020.47.2.131
  30. Kim S, Park T-H (2020b) Development of Solanum hougasiispecific markers using the complete chloroplast genome sequences of Solanum species. J Plant Bioechnol 47: 141-149 https://doi.org/10.5010/JPB.2020.47.2.141
  31. 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
  32. 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
  33. Konovalov F, Toshchakova E, Gostimsky S (2005) A CAPS marker set for mapping in linkage group III of pea (Pisum sativum L.) Cell Mol Biol Lett 10:163-171
  34. Lee J, Yoon JB, Park HG (2008) A CAPS marker associated with the partial restoration of cytoplasmic male sterility in chili pepper (Capsicum annuum L.). Mol Breeding 21:95-104
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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.
  41. Park T-H (2017) The complete chloroplast genome of Solanum berthaultii, one of the potato wild relative species. Mitochondr DNA Part B 2:88-89 https://doi.org/10.1080/23802359.2017.1285213
  42. Park T-H (2021a) Complete chloroplast genome sequence of the wild diploid potato relative, Solanum acaule. Mitochondr DNA Part B 6:1189-1191 https://doi.org/10.1080/23802359.2021.1902414
  43. Park T-H (2021b) PCR-based markers for discriminating Solanum demissum were developed by comparison of complete chloroplast genome sequences of Solanum species. J Plant Biotechnol 48:18-25 https://doi.org/10.5010/JPB.2021.48.1.018
  44. Park T-H (2022) Development of PCR-based markers specific to Solanum brevicaule by using the complete chloroplast genome sequences of Solanum species. J Plant Biotechnol 49:30-38 https://doi.org/10.5010/JPB.2022.49.1.030
  45. Pettenkofer T, Finkeldey R, Muller M, Krutovsky KV, Vornam B, Leinemann L, Gailing O (2020) Development of novel Quercus rubra chloroplast genome CAPS markers for haplotype indentification. Silvae Genetica 69:78-85 https://doi.org/10.2478/sg-2020-0011
  46. 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
  47. Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants, pp.45-68. In: H. Henry (ed.) Diversity and evolution of plants: genotypic and phenotypic variation in higher plants. CABI Publishing, Wallingford, UK
  48. Rokka V-M, Tauriainen A, Pietila L, Pehu E (1998) Interspecific somatic hybrids between wild potato Solanum acaule Bitt. and anther-derived dihaploid potato (Solanum tuberosum L.). Plant Cell Rep 18:82-88 https://doi.org/10.1007/s002990050536
  49. Ross H (1986) Potato breeding-problems and perspectives. Verlag Paul Parey, Berlin and Hamburg, Germany
  50. 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
  51. 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
  52. 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
  53. Spooner DM, Ghislain M, Simon R, Jansky SH, Gavrilenko T (2014) Systematics, diversity, genetics, and evolution of wild and cultivated potatoes. Bot Rev 80:283-383 https://doi.org/10.1007/s12229-014-9146-y
  54. 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
  55. 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
  56. 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
  57. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. (2017) GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45: W6-W11. https://doi.org/10.1093/nar/gkx391
  58. 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
  59. van der Voort JR, Kanyuka K, van der Vossen E, Bendahmane A, Klein-Lankhorst R, Stiekema W, Baulcombe D, Bakker J (1999) Tight physical linkage of the nematode resistance gene Gpa2 and the virus resistance gene Rx on a single segment introgressed from the wild species Solanum tuberosum subsp. andigena CPC 1673 into cultivated potato. Mol Plant-Microb Interact 18:722-729
  60. Wang GX, Tang Y, Yan H, Sheng XG, Hao WW, Zhang L, Lu K, Liu F (2011) Production and characterization of interspecific somatic hybrids between Brassica oleracea var. botrytis and B. nigra and their progenies for the selection of advanced pre-breeding materials. Plant Cell Rep 30:1811-1821 https://doi.org/10.1007/s00299-011-1088-9
  61. Watanabe KN, Orrillo M, Vega S, Masuelli R, Ishiki K (1994) Potato germplasm enhancement with disomic tetraploid Solanum acaule. II. Assessment of breeding value of tetraploid F1 hybrids between tetrasomic tetraploid S. tuberosum and S. acaule. Theor Appl Genet 88:135-140 https://doi.org/10.1007/BF00225888
  62. 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
  63. Yamada T, Hosaka K, Nakagawa K, Kaide N, Misoo S, Kamijima O (1998) Nuclear genome constitution and other characteristics of somatic hybrids between dihaploid Solanum acaule and tetraploid S. tuberosum. Euphytica 102:239-246 https://doi.org/10.1023/A:1018325529119
  64. 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
  65. Yurina NP, Odintsova MS (1998) Comparative structural organization of plant chloroplast and mitochondrial genomes. Russ J Genet 34:5-22
  66. Zoteeva N, Chrzanowska M, Pakosinska E, Zimnoch-Guzowska E (2000) Resistance to Phytophthora infestans and potato virus X (PVX) in wild potato species Solanum acaule Bitt. from the collection of NI Vavilov Research Institute of plant industry. Plant Breed Seed Sci 44:81-86