Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Development of PCR-based markers specific to Solanum brevicaule by using the complete chloroplast genome sequences of Solanum species

엽록체 전장유전체 비교를 통한 PCR 기반의 Solanum brevicaule 특이적 분자마커 개발

  • Park, Tae-Ho (Department of Horticulture, Daegu University)
  • Received : 2022.03.07
  • Accepted : 2022.03.18
  • Published : 2022.03.31
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Abstract

Solanum brevicaule is one of the tuber-bearing wild Solanum species. Because of its resistance to several important pathogens infecting potatoes during cultivation, it can be used for potato breeding. However, the fact that S. brevicaule used in this study has an EBN value of two causes the sexual reproduction barriers between the species and cultivated potatoes. In this study, specific markers for discriminating S. brevicaule from other Solanum species were developed on the basis of the results of sequence alignments with the whole chloroplast genomes of S. brevicaule and seven other Solanum species. The chloroplast genome of S. brevicaule was completed by next-generation sequencing technology described in other recent studies. The total sequence length of the chloroplast genome of S. brevicaule is 155,531 bp. Its structure and gene composition are similar to those of other Solanum species. Phylogenetic analysis revealed that S. brevicaule was closely grouped with other Solanum species. BLASTN search showed that its genome sequence had 99.99% and 99.89% identity with those of S. spegazzinii (MH021562) and S. kurtzianum (MH021495), respectively. Sequence alignment identified 27 SNPs that were specific to S. brevicaule. Thus, three PCR-based CAPS markers specific to S. brevicaule were developed on the basis of these SNPs. This study will facilitate in further studies on evolutionary and breeding aspects in Solanum species.

Solanum brevicaule는 괴경을 형성하는 감자 야생종 중의 하나로 감자재배에서 문제가 되는 중요한 몇 가지 병에 대해 저항성 보여 감자의 신품종 육성을 위한 재료로 이용될 수 있다. 하지만, 본 연구에서 이용된 S. brevicaule의 EBN이 2인 사실로 인하여 재배종 감자와의 생식에 의한 종자생산에 장벽이 되고 있다. 본 연구에서는 차세대 유전체 기술에 의해 완성된 S. brevicaule의 엽록체 전장 유전체와 다른 7개 Solanum 종의 엽록체 전장 유전체를 비교하여 S. brevicaule를 다른 Solanum 종과 구별할 수 있는 Solanum 종 특이적인 분자마커를 개발하였다. S. brevicaule의 엽록체 전장 유전체의 총길이는 155,531 bp였으며, Blastn을 통해 S. spegazzinii 및 S. kurtzianum과 각각 99.99% 및 99.89%의 유사도를 확인할 수 있었다. 또한, 그 구조와 유전자의 구성이 다른 Solanum 종과 매우 유사하였으며, 계통수 분석에서도 다른 Solanum 종들과 매우 가까운 유연관계를 가지는 것으로 확인되었다. 엽록체 전장 유전체 다중 정렬에서는 총 27개의 S. brevicaule 특이적인 SNP 영역이 확인되었으며, 이들 중 세 개의 SNP 영역을 대상으로 최종적으로 S. brevicaule 특이적인 PCR 기반의 CAPS 분자마커를 개발하였다. 본 연구를 통해 얻은 S. brevicaule의 엽록체 전장 유전체와 S. brevicaule 특이적인 분자마커의 결과는 향후 Solanum 종을 대상으로 한 진화와 S. brevicaule를 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. Aversano R, Savarese S, De Nova JM, Frusciante L, Punzo M, Carputo D (2009) Genetic stability at nuclear and plastid DNA level in regenerated plants of Solanum species and hybrids. Euphytica 165:353-361 https://doi.org/10.1007/s10681-008-9797-z
  2. Bastia T, Carotenuto N, Basile B, Zoina A, Cardi T (2000) Induction of novel organelle DNA variation and transfer of resistance to frost and Verticillium wilt in Solanum tuberosum through somatic hybridization with 1EBN S. commersonii. Euphytica 116:1-10 https://doi.org/10.1023/A:1003943704037
  3. 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
  4. 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
  5. 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/gen-42-6-1111
  6. 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
  7. 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
  8. 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
  9. 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
  10. Cho K-S, Park T-H (2014) Potato breeding via protoplast fusion. J Plant Biotechnol 41:65-72 https://doi.org/10.5010/JPB.2014.41.2.65
  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 YS, Holmquist K, Spooner DM, Jansky SH (2011) A test of taxonomic and biogeographic predictivity: resistance to soft rot in wild relatives of cultivated potato. Ecol Epidemiol 101:205-212
  14. 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
  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. Hardigan MA, Bamberg J, Buell CR, Douches DS (2015) Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota. Plant Genome 8:1
  19. Hawkes JG (1990) The potato: Evolution, biodiversity and genetic resources. Belhaven Press, London, UK
  20. 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
  21. Jackson MT, Hawkes JG, Male-Kayiwa BS, Wanyera N (1988) The importance of the Bolivian wild potato species in breeding for Globodera pallida resistance. Plant Breed 101:261-268 https://doi.org/10.1111/j.1439-0523.1988.tb00298.x
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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 https://doi.org/10.1007/s11032-007-9111-0
  30. 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
  31. 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
  32. Miller JT, Spooner DM (1999) Collapse of species boundaries in the wild potato Solanum brevicaule complex (Solanaceae, S. sect. Petota): molecular data. Pl Syst Evol 214:103-130 https://doi.org/10.1007/BF00985734
  33. 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
  34. 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
  35. 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
  36. 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
  37. Park T-H (2019) Complete chloroplast genome of the wild diploid potato relative, Solanum brevicaule. Mitochondr DNA Part B 4:4159-4160 https://doi.org/10.1080/23802359.2019.1693292
  38. Park T-H (2021a) Complete chloroplast genome of the wild diploid potato relative, Solanum acaule. Mitochondr DNA Part B 6:1189-1191 https://doi.org/10.1080/23802359.2021.1902414
  39. 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
  40. 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
  41. Patel D, Power J, Anthony P, Badakshi F, Heslop-Harrison J, Davey M (2011) Somatic hybrid plants of Nicotiana x sanderae + N. debneyi with fungal resistance to Peronospora tabacina. Ann Bot 108:809-819 https://doi.org/10.1093/aob/mcr197
  42. 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
  43. Sarkar D, Tiwari J, Sharma S, Sharma Poonam S, Gopal J, Singh B, Luthra S, Pandey S, Pattanayak D (2011) Production and characterization of somatic hybrids between Solanum tuberosum L. and S. pinnatisectum Dun. Plant Cell Tiss Org Cult 107:427-440 https://doi.org/10.1007/s11240-011-9993-8
  44. 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
  45. 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
  46. Scotti N, Monti L, Cardi T (2003) Organelle DNA variation in parental Solanum spp. genotypes and nuclear-cytoplasmic interactions in Solanum tuberosum (+) S. commersonii somatic hybrid-backcross progeny. Theor Appl Genet 108:87-94 https://doi.org/10.1007/s00122-003-1406-x
  47. 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
  48. 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
  49. 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
  50. 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
  51. Thieme R, Rakosy-Tican E, Nachtigall M, Schubert J, Hammann T, Antonova O, Gavrilenko T, Heimbach U, Thieme T (2010) Characterization of the multiple resistance traits of somatic hybrids between Solanum cardiophyllum Lindl. and two commercial potato cultivars. Plant Cell Rep 29:1187-1201 https://doi.org/10.1007/s00299-010-0905-x
  52. 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
  53. Tiwari JK, Rawat S, Luthra SK, Zinta R, Sahu S, Varshney S, Kumar V, Dalamu D, Mandadi N, Kumar M, Chakrabarti SK, Rao AR, Rai A (2021) Genome sequence analysis provides insights on genomic variation and late blight resistance genes in potato somatic hybrid (parents and progeny). Mol Biol Rep 48:623-635 https://doi.org/10.1007/s11033-020-06106-x
  54. Tu W, Dong J, Zou Y, Zhao Q, Wang H, Ying J, Wu J, Du J, Cai X, Song B (2021) Interspecific potato somatic hybrids between Solanum malmeanum and S. tuberosum provide valuable resources for freezing-tolerance breeding. Plant Cell Tiss Organ Cult 147:73-83 https://doi.org/10.1007/s11240-021-02106-2
  55. 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
  56. 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 https://doi.org/10.1094/MPMI-18-0722
  57. 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
  58. 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
  59. 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
  60. 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
  61. Yu Y, Li Z, Wang P, Xiang F (2012) Genetic and biochemical characterization of somatic hybrids between Bupleurum scorzonerifolium and Gentianopsis paludosa. Protoplasma 249:1029-1035 https://doi.org/10.1007/s00709-011-0336-8
  62. Yurina NP, Odintsova MS (1998) Comparative structural organization of plant chloroplast and mitochondrial genomes. Russ J Genet 34:5-22