Journal of Plant Biotechnology

  • Volume 50
  • /
  • Pages.34-44
  • /
  • 2023
  • /
  • 1229-2818(pISSN)
  • /
  • 2384-1397(eISSN)
The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Development of PCR-based markers for selecting plastid genotypes of Solanum hjertingii

Solanum hjertingii 색소체 유전자형 선발을 위한 PCR 기반 분자마커 개발

  • Tae-Ho Park (Department of Horticulture, Daegu University)
  • Received : 2023.03.31
  • Accepted : 2023.04.12
  • Published : 2023.04.26
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Abstract

The tetraploid Solanum hjertingii, a wild tuber-bearing species from Mexico is a relative of potato, S. tuberosum. The species has been identified as a potential source of resistance to blackening for potato breeding. It does not exhibit enzymatic browning nor blackspot which are physiological disorders. However, due to their sexual incompatibility, somatic hybridization between S. hjertingii and S. tuberosum must be used to introduce various traits from this wild species into potato. After somatic hybridization, molecular markers are essential for selecting fusion products. In this study, the chloroplast genome of S. hjertingii was sequenced by next-generation sequencing technology and compared with those of other Solanum species to develop specific markers for S. hjertingii. The chloroplast genome has a total sequence length of 155,545 bp, and its size, gene content, order and orientation are similar to those of the other Solanum species. Phylogenic analysis including 15 other Solanaceae species grouped S. hjertingii with S. demissum, S. hougasii, and S. stoloniferum. After detailed comparisons of the chloroplast genome sequence with eight other Solanum species, we identified one InDel and seven SNPs specific to S. hjertingii. Based on these, five PCR-based markers were developed for discriminating S. hjertingii from other Solanum species. The results obtained in this study will aid in exploring the evolutionary aspects of Solanum species and accelerating breeding using S. hjertingii.

멕시코 유래의 4배체 감자 근연야생종 중 하나인 Solanum hjertingii는 괴경에서 발생하는 흑변현상에 강한 것으로 알려져 감자의 신품종 육성에 유용한 형질로 이용이 가능하다. 이러한 저항성은 생리적 장해인 효소적 갈변과 흑반을 감소시킬 수 있다. 하지만, S. hjertingii와 S. tuberosum은 생리적 장벽에 기인한 교잡종 생산이 제한적인 관계로 직접적인 교배육종보다는 체세포잡종을 육성하는 방법을 활용할 수 있다. 체세포잡종 계통이 육성이 되면 분자표지를 이용한 적절한 잡종 계통을 선발하는 것이 필요하여, 본 연구에서는 S. hjertingii의 전체 엽록체 유전체 정보를 이용하여 S. hjertingii 특이적인 PCR 기반의 분자마커를 개발하였다. S. hjertingii의 전체 엽록체 유전체는 155,545 bp였으며, 다른 Solanum 종들과 구조 및 유전자 구성이 매우 유사하였고, 가지과의 다른 15개의 종들과 계통수 분석에서 근연야생종 S. demissum, S. hougasii, S. stoloniferum과 매우 가까운 유연관계를 나타냈다. 또한, S. hjertingii의 전체 엽록체 유전체와 8개의 다른 Solanum 종의 전체 엽록체 유전체의 다중 정렬 결과로 S. hjertingii 특이적인 1개의 InDel 영역과 7개의 SNP 영역을 확인하였고, 이를 이용하여 1개의 InDel 및 4개의 SNP 기반 PCR마커를 개발하였다. 본 연구의 결과는 S. hjertingii의 진화적 측면에서의 연구와 S. hjertingii를 이용한 감자의 신품종 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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. Collins A, Ke X (2012) Primer1: Primer design web service for tetra-primer ARMS-PCR. Open Bioinformatics J 6:55-58 https://doi.org/10.2174/1875036201206010055
  11. Culley DE, Dean BB, Brown CR (2002) Introgression of the low browning trait from the wild Mexican species Solanum hjertingii into cultivated potato (S. tuberosum L.) Euphytica 125:293-303
  12. 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
  13. 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
  14. 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
  15. Hara-Skrzypiec A, Jakuczun H (2013) Diploid potato hybrids as source of resistance to blackspot bruising. Am J Potato Res 90:451-459 https://doi.org/10.1007/s12230-013-9319-y
  16. Hawkes JG (1990) The potato: Evolution, biodiversity and genetic resources. Belhaven Press, London, UK
  17. Hermsen JGT (1966) Crossability, fertility and cytogenetic studies in Solanum acaule x Solanum bulbocastanum. Euphytica 15:149-155 https://doi.org/10.1007/BF00022317
  18. Hermsen JGT, Ramanna MS (1973) Double-bridge hybrids of Solanum bulbocastanum and cultivars of Solanum tuberosum. Euphytica 22:457-166
  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. Iwanaga M, Freyre R, Watanabe K (1991) Breaking the crossability barriers between disomic tetraploid Solanum acaule and tetrasomic tetraploid S. tuberosum. Euphytica 52:183-191 https://doi.org/10.1007/BF00029395
  21. 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
  22. 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
  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 Solanum chacoense from other Solanum species. J Plant Bioechnol 46:79-87
  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 hougasii-specific 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. Kou M, Xu J-I, Li Q, Liu Y-J, Wang X, Tang W, Yan H, Zhang Y-G, Ma D-F (2017) Development of SNP markers using RNA-seq technology and tetra-primer ARMS-PCR in sweetpotato. J Integr Agric 16:464-470 https://doi.org/10.1016/S2095-3119(16)61405-3
  28. Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C (2023) CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resourc 00:1-11
  29. 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
  30. Luthra SK, Tiwari JK, Kumar V, Lal M (2019) Evaluation of interspecific somatic hybrids of potato (Solanum tuberosum) and wild S. cardiophyllum for adaptability, tuber dry matter, keeping quality and late blight resistance. Agric Res 8:158-164 https://doi.org/10.1007/s40003-018-0369-8
  31. Mahmoudi S, Badali H, Rezaie S, Azarnezhad A, Barac A, Kord M, Ahmadikia K, Aala F, Askari FA, Meis JF, Khodavaisy S (2019) A simple and low cost tetra-primer ARMS-PCR method for detection triazole-resistant Aspergillus fumigatus. Mol Biol Rep 46:4537-4543 https://doi.org/10.1007/s11033-019-04909-1
  32. 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
  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 (2021) 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
  36. Park T-H (2022a) 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
  37. Park T-H (2022b) PCR-based markers to select plastid genotypes of Solanum acaule. J Plant Biotechnol 49:178-186 https://doi.org/10.5010/JPB.2022.49.3.178
  38. Park T-H (2022c) Complete chloroplast genome sequence of Solanum hjertingii, one of the wild potato relatives. Mitochondr DNA Part B 7:715-717 https://doi.org/10.1080/23802359.2022.2068983
  39. Park T-H, Vleeshouwers VG, Hutten RC, van Eck HJ, van der Vossen E, Jacobsen E, Visser RG (2005) High-resolution mapping and analysis of the resistance locus Rpi-abpt against Phytophthora infestans in potato. Mol Breeding 16:33-43 https://doi.org/10.1007/s11032-005-1925-z
  40. 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
  41. 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
  42. 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
  43. Sim SK, Ohmann SM, Tong CBS (1997) Comparison of polyphenol oxidase in tubers of Solanum tuberosum and the non-browning tubers of S. hjertingii. Am Potato J 74:1-13 https://doi.org/10.1007/BF02849167
  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. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. Ye S, Dhillon S, Ke X, Collins AR, Day INM (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res 29:e88
  52. Yurina NP, Odintsova MS (1998) Comparative structural organization of plant chloroplast and mitochondrial genomes. Russ J Genet 34:5-22
  53. Zou Z, Liu F, Fernando WGD (2018) Rapid detection of Leptosphaeria maculans avirulence gene AvrLm4-7 conferring the avirulence/virulence specificity on Brassica napus using a tetra-primer ARMS-PCR. Eur J Plant Pathol 152:515-520 https://doi.org/10.1007/s10658-018-1465-0