본문 바로가기
KERD
논문KCI 등재

PCR-based markers developed by comparison of complete chloroplast genome sequences discriminate Solanum chacoense from other Solanum species

2

조회

0

다운로드

10

인용

0

참고문헌

키워드

주제분류농학

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.

Abstract

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.

참고문헌 (54)

  1. Barsby TL, "Somatic hybridization in the genus Solanum: S. tuberosum and S. brevidens", Plant Cell Rep, 3, pp.165~167 (1984)
  2. Bidani A, "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, pp.179~189 (2007)
  3. Binding H, "Somatic hybridization of an atrazine resistant biotype of Solanum nigrum with Solanum tuberosum", Theor Appl Genet, 63, pp.273~277 (1982)
  4. Bohs L, "Phylogenetic relationships in Solanum (Solanaceae) based on ndhF sequences", Syst Bot, 22, pp.5~17 (1997)
  5. Brown CR, "Resistance to potato leafroll virus derived from Solanum chacoense : characterization and inheritance", Euphytica, 74, pp.51~57 (1993)
  6. Calsa Junior T, "Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome", Curr Genet, 46, pp.366~373 (2004)
  7. Chen L, "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, pp.1861~1872 (2013)
  8. Cho KS, "Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum", Plant Cell Rep, 35, pp.2113~2123 (2016)
  9. Cho K-S, "Chloroplast genome of the wild tuber-bearing diploid potato relative Solanum chacoense", Mitochondr DNA Part B, 2, pp.915~917 (2017)
  10. Cho HM, "Influence of endosperm balance number (EBN) in interploidal and interspecific crosses between Solanum tuberosum dihaploids and wild species", Korean J Breed, 29, pp.154~161 (1997)
  11. 조광수, "Complete Chloroplast Genome Sequence of Solanum nigrum and Development of Markers for the Discrimination of S. nigrum", Horticulture, Environment, and Biotechnology, 57(1), pp.69~78 (2016), 한국원예학회
  12. Cho K-S, "Complete chloroplast genome sequence of tartary Buckwheat (Fagopyrum tataricum) and comparative analysis with common Buckwheat (F. esculentum)", PloS One, 10, pp.e0125332~ (2015)
  13. Chung HJ, "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, pp.1369~1379 (2006)
  14. Cooper SG, "Enhanced resistance to control potato tuberworm by combining engineered resistance, avidin, and natural resistance derived from, Solanum chacoense", Am J Potato Res, 86, pp.24~30 (2009)
  15. Daniell H, "Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes", Theor Appl Genet, 112, pp.1503~1518 (2006)
  16. Garcia-Lor A, "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, pp.1~19 (2013)
  17. Gargano D, "The complete nucleotide sequence genome of potato (Solanum tuberosum cv. Desiree) chloroplast DNA", The abstract of the 2nd Solanaceae Genome Workshop, pp.107~ (2005)
  18. Guo WW, "Molecular biology and biotechnology of plant organelles", pp.635~659 (2004), Springer
  19. Hosaka K, "Development of a rapid identification method for potato cytoplasm and its use for evaluating Japanese collections", Theor Appl Genet, 125, pp.1237~1251 (2012)
  20. Jheng C-F, "The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids", Plant Sci, 190, pp.62~73 (2012)
  21. Kim KJ, "Two chloroplast DNA inversion originated simultaneously during the early evolution of the sunflower family (Asteraceae)", Mol Biol Evol, 22, pp.1783~1792 (2005)
  22. 김수정, "Development of PCR-based markers for discriminating Solanum berthaultii using its complete chloroplast genome sequence", Journal of Plant Biotechnology, 45(3), pp.207~216 (2018), 한국식물생명공학회
  23. Kim-Lee H, "Bacterial wilt resistance in the progenies of the fusion hybrids between haploid of potato and Solanum commersonii", Amer J Potato Res, 82, pp.129~137 (2005)
  24. Komori T, "Utilization of the CAPS", dCAPS method to convert rice SNPs into PCR-based markers, 2005, pp.55, 93~98
  25. Konieczny A, "A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers", Plant J, 4, pp.403~410 (1993)
  26. Kurtz S, "Versatile and open software for comparing large genomes", Genome Biol, 5, pp.R12~ (2004)
  27. Lohse M, "Organellar GenomeDRAW – a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets", Nucleic Acids Res, 41, pp.W575~W581 (2013)
  28. Lössl A, "Molecular markers for cytoplasm in potato: male sterility and contribution of different plastid-mitochondrial configurations to starch production", Euphytica, 116, pp.221~230 (2000)
  29. Lynch DR, "Identification of a gene conferring high levels of resistance to Verticillium wilt in Solanum chacoense", Plant Dis, 81, pp.1011~1014 (1997)
  30. Micheletto S, "Argentinian wild diploid Solanum species as sources of quantitative late blight resistance", Theor and Appl Genet, 101, pp.902~906 (2000)
  31. Mohapatra T, "Random chloroplast segregation and mitochondrial genome recombination in somatic hybrid plants of Diplotaxis catholica + Brassica juncea", Plant Cell Rep, 17, pp.814~818 (1998)
  32. Nouri-Ellouz O, "Somatic hybrids between potato and S. berthaultii show partial resistance to soil-borne fungi and potato virus Y", J Phythpathol, 164, pp.485~496 (2016)
  33. Ortiz R, "The importance of endorsperm balance number in potato breeding and the evolution of tuber-bearing Solanum species", Euphytica, 60, pp.105~113 (1992)
  34. Palmer JD, "The molecular biology of plastids", pp.5~53 (1991), Academic Press
  35. Park T-H, "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, pp.722~729 (2005)
  36. Pavek JJ, "Utilization of potato genetic resources in variety development", Amer J Potato Res, 78, pp.433~441 (2001)
  37. Puite KJ, "Somatic hybrid potato plants after electrofusion of diploid Solanum tuberosum and Solanum phureja", Plant Cell Rep, 5, pp.262~265 (1986)
  38. Raubeson LA, "Diversity and evolution of plants:genotypic and phenotypic variation in higher plants", pp.45~68 (2005), CABI Publishing
  39. Saski C, "Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes", Plant Mol Biol, 59, pp.309~322 (2005)
  40. Schwartz S, "Human-mouse alignments with BLASTZ", Genome Res, 13, pp.103~107 (2003)
  41. Simko I, "Potato biology and biotechnology", pp.117~155 (2007), Elsevier
  42. Sinden SL, "Leptine Glycoalkaloids and resistance to the Colorado potato beetle (Coleoptera: Chrysomelidae) in Solanum chacoense", Environm Entomol, 15, pp.1057~1062 (1986)
  43. Smilde WD, "Solanum mochiquense chromosome IX carries a novel late blight resistance gene Rpi-moc1", Theor Appl Genet, 110, pp.252~258 (2005)
  44. Sugiura M, "Evolution and mechanism of translation in chloroplast", Annu Rev Genet, 32, pp.437~459 (1998)
  45. Swofford DL., "analysis using parsimony (* and other methods)" (2001), Sinauer Associates
  46. Smyda-Dajmund P, "Genetic composition of interspecific potato somatic hybrids and autofused 4x plants evaluated by DArT and cytoplasmic DNA markers", Plant Cell Rep, 35, pp.1345~1358 (2016)
  47. Tamura K, "MEGA6: molecular evolutionary genetic analysis version 6.0", Mol Biol Evol, 30, pp.2725~2729 (2013)
  48. Uncu AT, "Development of a SNP-based CAPS assay for the Me1 gene conferring resistance to root knot nematode in pepper", Euphytica, 206, pp.393~399 (2015)
  49. Uribe P, "Two CAPS markers predict Verticillium wilt resistance in wild Solanum species", Mol Breeding, 33, pp.465~476 (2014)
  50. Wang Y, "Development of SNP markers based on transcriptome sequences and their application in germplasm identification in radish(Raphanus sativus L.)", Mol Breeding, 37, pp.26~ (2017)
  51. Wyman SK, "Antomatic annotation of organellar genomes with DOGMA", Bioinformatics, 20, pp.3252~3255 (2004)
  52. Xiang F, "Regeneration of somatic hybrids in relation to the nuclear and cytoplasmic genomes of wheat and Setaria italica", Genome, 47, pp.680~688 (2004)
  53. Yamaki S, "Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza", Breeding Sci, 63, pp.246~254 (2013)
  54. Yurina NP, "Comparative structural organization of plant chloroplast and mitochondrial genomes", Russ J Genet, 34, pp.5~22 (1998)

관련 논문AI추천

이 간행물의 다른 논문 (8건)