Tree Genetics & Genomes

, 11:25 | Cite as

Evaluation of new IRAP markers of pear and their potential application in differentiating bud sports and other Rosaceae species

  • Jiangmei Sun
  • Hao Yin
  • Leiting Li
  • Yue Song
  • Lian Fan
  • Shaoling Zhang
  • Jun Wu
Original Paper


Inter-retrotransposon amplified polymorphisms (IRAP) are one of the main components of the retrotransposon-based molecular marker system, but currently have no applications in pear. In this context, new IRAP markers were developed and used to study the genetic polymorphism of pear cultivars and bud mutants. In total, eight polymorphic IRAP markers were selected in ten genotypes of pear with a wide variation in genetic backgrounds and for further genotypic identification of cultivars and bud sports. A total of 76 alleles with an average of 9.5 per locus were amplified and 96.05 % showed polymorphism. Through genetic structure analysis, 62 pear cultivars were divided into two groups, i.e., Oriental and Occidental pears, with a few samples showing a distinct admixed genetic background. When polymorphic IRAP markers were tested on a total of 33 bud sports and their corresponding parent cultivars, the genetic similarity coefficient ranged from 0.54 to 0.96. Each bud mutation was separated from its original variety, and 92.3 % of bud sports clustered perfectly with their original varieties. Furthermore, the transferability of pear IRAP to apples and other Rosaceae species was very high, ranging from 87.5 to 100 %. Our results demonstrate that IRAP markers are an excellent tool for the study of genetic relationships and comparative genomics analysis in pear and Rosaceae species.


Pear (Pyrus L.) Retrotransposons IRAP Bud sport Genetic polymorphism Transferability 



The work was financially supported by the Jiangsu Agriculture Science and Technology Innovation Fund (JASTIF) (CX (14) 2020), National Science Foundation of China (31372045), Ministry of Education Program for New Century Excellent Talents in University (NCET-13-0864).

Conflict of interests

The authors declare that they have no conflict of interests.

Data archiving statement

We followed standard Tree Genetics and Genomes policy. We archived the contigs in the FASTA format from the sequences which are available at our genome website

Supplementary material

11295_2015_849_MOESM1_ESM.doc (33 kb)
Fig. S1 (DOC 33 kb)
11295_2015_849_MOESM2_ESM.doc (92 kb)
Fig. S2 (DOC 91 kb)
11295_2015_849_MOESM3_ESM.doc (114 kb)
Table S1 (DOC 114 kb)


  1. Antonius-Klemola K, Kalendar R, Schulman AH (2006) TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theor Appl Genet 112(6):999–1008CrossRefPubMedGoogle Scholar
  2. Baránek M, Meszáros M, Sochorová J, Čechová J, Raddová J (2012) Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická. Sci Hortic 143:1–6CrossRefGoogle Scholar
  3. Bassam BJ, Caetano-Anollés G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196(1):80–83CrossRefPubMedGoogle Scholar
  4. Bassil N, Postman JD (2010) Identification of European and Asian pears using EST-SSRs from Pyrus. Genet Resour Crop Evol 57(3):357–370CrossRefGoogle Scholar
  5. Bonchev G, Parisod C (2013) Transposable elements and microevolutionary changes in natural populations. Mol Ecol Resour 13(5):765–75CrossRefPubMedGoogle Scholar
  6. Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell Online 24(3):1242–1255CrossRefGoogle Scholar
  7. Cai Y, Cao D, Zhao G (2007) Studies on genetic variation in cherry germplasm using RAPD analysis. Sci Hortic 111(3):248–254CrossRefGoogle Scholar
  8. Campbell BC, LeMare S, Piperidis G, Godwin ID (2011) IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol Breeding 27(2):193–206CrossRefGoogle Scholar
  9. Castro I, D’Onofrio C, Martín JP, Ortiz JM, De Lorenzis G, Ferreira V, Pinto-Carnide O (2012) Effectiveness of AFLPs and retrotransposon-based markers for the identification of Portuguese grapevine cultivars and clones. Mol Biotech 52(1):26–39CrossRefGoogle Scholar
  10. Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P (2014) The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLoS One 9(4):e92644CrossRefPubMedCentralPubMedGoogle Scholar
  11. del Mar Naval M, Zuriaga E, Pecchioli S, Llácer G, Giordani E, Badenes ML (2010) Analysis of genetic diversity among persimmon cultivars using microsatellite markers. Tree Genet Genomes 6(5):677–687CrossRefGoogle Scholar
  12. Dondini L, Sansavini S, Venturi S, De Franceschi P (2007) Retrotransposon based markers to discriminate sports in pear. XII EUCARPIA Symposium Fruit Breeding Genet 814:701–704Google Scholar
  13. Du J, Tian Z, Bowen NJ et al (2010) Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean. Plant Cell 22:48–61CrossRefPubMedCentralPubMedGoogle Scholar
  14. El Baidouri M, Carpentier M-C, Cooke R, Gao D, Lasserre E, Llauro C, Mirouze M, Picault N, Jackson SA, Panaud O (2014) Widespread and frequent horizontal transfers of transposable elements in plants. Genome Res 24(5):831–838CrossRefPubMedCentralPubMedGoogle Scholar
  15. Fan L, Zhang M, Liu Q, Li L, Song Y, Wang L, Zhang S, Wu J (2013) Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Mol Biol Rep 31(6):1271–1282CrossRefPubMedCentralPubMedGoogle Scholar
  16. Fedoroff NV (2012) Transposable elements, epigenetics, and genome evolution. Science 338(6108):758–767CrossRefPubMedGoogle Scholar
  17. Ferguson AA, Zhao DY, Jiang N (2013) Selective acquisition and retention of genomic sequences by pack-mutator-like elements based on guanine-cytosine content and the breadth of expression. Plant Physiol 163(3):1419–1432CrossRefPubMedCentralPubMedGoogle Scholar
  18. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3(5):329–341CrossRefPubMedGoogle Scholar
  19. Gasic K, Han Y, Kertbundit S, Shulaev V, Iezzoni AF, Stover EW, Bell RL, Wisniewski ME, Korban SS (2009) Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breeding 23(3):397–411CrossRefGoogle Scholar
  20. Goulao L, Cabrita L, Oliveira CM, Leitão JM (2001) Comparing RAPD and AFLPTM analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh.) cultivars. Euphytica 119(3):259–270CrossRefGoogle Scholar
  21. Han X, Wang L, Liu Z, Jan D, Shu Q (2008) Characterization of sequence-related amplified polymorphism markers analysis of tree peony bud sports. Sci Hortic 115(3):261–267CrossRefGoogle Scholar
  22. He P, Ma Y, Dai H, Li L, Liu Y, Li H, Zhao G, Zhang Z (2012) Development of Ty1-copia retrotransposon-based S-SAP markers in strawberry (Fragaria x ananassa Duch.). Sci Hortic 137:43–48CrossRefGoogle Scholar
  23. Jiang N, Bao Z et al (2002) Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161:1293–1305PubMedCentralPubMedGoogle Scholar
  24. Kalendar R, Schulman AH (2006) IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protocols 1(5):2478–2484CrossRefGoogle Scholar
  25. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98(5):704–711CrossRefGoogle Scholar
  26. Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH (2008) Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci U S A 105(15):5833–5838CrossRefPubMedCentralPubMedGoogle Scholar
  27. Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci 98(15):8714–8719CrossRefPubMedCentralPubMedGoogle Scholar
  28. Karlova R, Chapman N, David K, Angenent GC, Seymour GB, de Maagd RA (2014) Transcriptional control of fleshy fruit development and ripening. J Exp Bot 65(16):4527–4541CrossRefPubMedGoogle Scholar
  29. Kawakami T, Dhakal P, Katterhenry AN, Heatherington CA, Ungerer MC (2011) Transposable element proliferation and genome expansion are rare in contemporary sunflower hybrid populations despite widespread transcriptional activity of LTR retrotransposons. Genome Biol Evol 3:156–167CrossRefPubMedCentralPubMedGoogle Scholar
  30. Kim H, Yamamoto M, Hosaka F, Terakami S, Nishitani C, Sawamura Y, Yamane H, Wu J, Matsumoto T, Matsuyama T (2011) Molecular characterization of novel Ty1-copia-like retrotransposons in pear (Pyrus pyrifolia). Tree Genet Genomes 7(4):845–856CrossRefGoogle Scholar
  31. Kim H, Terakami S, Nishitani C, Kurita K, Kanamori H, Katayose Y, Sawamura Y, Saito T, Yamamoto T (2012) Development of cultivar-specific DNA markers based on retrotransposon-based insertional polymorphism in Japanese pear. Breeding Sci 62(1):53CrossRefGoogle Scholar
  32. Kimura T, Shi Y, Shoda M, Kotobuki K, Matsuta N, Hayashi T, Ban Y, Yamamoto T (2002) Identification of Asian pear varieties by SSR analysis. Breeding Sci 52(2):115–121CrossRefGoogle Scholar
  33. Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304(5673):982–982CrossRefPubMedGoogle Scholar
  34. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Ann Rev Genet 33(1):479–532CrossRefPubMedGoogle Scholar
  35. Liu MJ, Zhao J, Cai QL, Liu GC, Wang JR, Zhao ZH, Liu P, Dai L, Yan GJ, Wang WJ, Li XS, Chen Y, Sun YD, Liu ZG, Lin MJ, Xiao J, Chen YY, Li XF, Wu B, Ma Y, Jian JB, Yang W, Yuan Z, Sun XC, Wei YL, Yu LL, Zhang C, Liao SG, He RJ, Guang XM, Wang Z, Zhang YY, Luo LH (2014) The complex jujube genome provides insights into fruit tree biology. Nature Communications 5Google Scholar
  36. Lombard PB, Westwood MN (1987) Pear rootstocks, p. 145–183. In: Romand RC, Carlson RF (eds). Rootstocks for fruit crops. Wiley, New York. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101 (34):12404–12410Google Scholar
  37. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101(34):12404–12410CrossRefPubMedCentralPubMedGoogle Scholar
  38. Manninen O, Kalendar R, Robinson J, Schulman AH (2000) Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Mol Gen Genet 264(3):325–334CrossRefPubMedGoogle Scholar
  39. Mase N, Iketani H, Sato Y (2007) Analysis of bud sport cultivars of peach (Prunus persica (L.) Batsch) by simple sequence repeats (SSR) and restriction landmark genomic scanning (RLGS). J Jpn Soc Hortic Sci 76(1):20–27CrossRefGoogle Scholar
  40. McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19(3):362–367CrossRefPubMedGoogle Scholar
  41. Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel C-E (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 8(10):e77022CrossRefPubMedCentralPubMedGoogle Scholar
  42. Monte-Corvo L, Cabrita L, Oliveira C, Leitão J (2000) Assessment of genetic relationships among Pyrus species and cultivars using AFLP and RAPD markers. Genet Resour Crop Evol 47(3):257–265CrossRefGoogle Scholar
  43. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76(10):5269–5273CrossRefPubMedCentralPubMedGoogle Scholar
  44. NTSYS-pc RF (2000) Numerical taxonomy and multivariate analysis system, version2.1. Exeter Publishing, SetauketGoogle Scholar
  45. Oliveira CM, Mota M, Monte-Corvo L, Goulao L, Silva DM (1999) Molecular typing of Pyrus based on RAPD markers. Sci Hortic 79(3):163–174CrossRefGoogle Scholar
  46. Pan Z, Kawabata S, Sugiyama N, Sakiyama R, Cao Y (2001) Genetic diversity of cultivated resources of pear in north China. In: International Symposium on Asian Pears, Commemorating the 100th Anniversary of Nijisseiki Pear 587:187–194Google Scholar
  47. Petersen R (2014) Molecular genetic causes of columnar growth in apple (Malus x domestica). Mainz, Univ, DissGoogle Scholar
  48. Pierantoni L, Cho K, Shin I, Chiodini R, Tartarini S, Dondini L, Kang S, Sansavini S (2004) Characterisation and transferability of apple SSRs to two European pear F1 populations. Theor Appl Genet 109(7):1519–1524CrossRefPubMedGoogle Scholar
  49. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedCentralPubMedGoogle Scholar
  50. Rigal M, Mathieu O (2011) A “mille-feuille” of silencing: epigenetic control of transposable elements. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1809(8):452–458CrossRefGoogle Scholar
  51. Schulman AH (2007) Molecular markers to assess genetic diversity. Euphytica 158(3):313–321CrossRefGoogle Scholar
  52. Shi Y, Yamamoto T, Hayashi T (2002) Characterization of copia-like retrotransposons in pear [Pyrus serotina]. J Jpn Soc Hortic Sci 71:723–729CrossRefGoogle Scholar
  53. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8(4):272–285CrossRefPubMedGoogle Scholar
  54. Smýkal P (2006) Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. J Appl Genet 47(3):221–230CrossRefPubMedGoogle Scholar
  55. Tanskanen JA, Sabot F, Vicient C, Schulman AH (2007) Lifewithout GAG: the BARE-2 retrotransposon as a parasite’s parasite. Gene 390:166–174CrossRefPubMedGoogle Scholar
  56. Tignon M, Kettmann R, Watillon B (1998) AFLP: use for the identification of apple cultivars and mutants. In: XXV International Horticultural Congress, part 11. Appl Biotechnol Mol Biol Breeding-Gene 521:219–226Google Scholar
  57. Vanneste K, Baele G, Maere S, Van de Peer Y (2014) Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary. Genome Res 24(8):1334–1347CrossRefPubMedCentralPubMedGoogle Scholar
  58. Voytas DF, Cummings MP, Koniczny A, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci U S A 89(15):7124–7128CrossRefPubMedCentralPubMedGoogle Scholar
  59. Wang S, Schnell RA, Lefebvre PA (1998) Isolation and characterization of a new transposable element in Chlamydomonas reinhardtii. Plant Mol Biol 38(5):681–687CrossRefPubMedGoogle Scholar
  60. Wessler SR (2006) Eukaryotic transposable elements: teaching old genomes new tricks. The implicit genome 138–165Google Scholar
  61. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8(12):973–982CrossRefPubMedGoogle Scholar
  62. Wolters PJ, Schouten HJ, Velasco R, Si-Ammour A, Baldi P (2013) Evidence for regulation of columnar habit in apple by a putative 2OG-Fe(II) oxygenase. New Phytol 200(4):993–999CrossRefPubMedGoogle Scholar
  63. Woodrow P, Pontecorvo G, Ciarmiello LF (2012) Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker. Mol Biol Rep 39(4):3409–3418CrossRefPubMedGoogle Scholar
  64. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23(2):396–408CrossRefPubMedCentralPubMedGoogle Scholar
  65. Yamamoto T, Kimura T, Sawamura Y, Kotobuki K, Ban Y, Hayashi T, Matsuta N (2001) SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor Appl Genet 102(6–7):865–870CrossRefGoogle Scholar
  66. Yang C, Wei Z, Jiang J (2006) DNA extraction of birch leaves by improved CTAB method and optimization of its ISSR system. J Forestry Res 17(4):298–300CrossRefGoogle Scholar
  67. Yao J, Dong Y, Morris BA (2001) Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor. Proc Natl Acad Sci 98(3):1306–1311CrossRefPubMedCentralPubMedGoogle Scholar
  68. Yeh FC, Yang R, Boyle T, Ye Z, Mao JX (1999) POPGENE, version 1.32: the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, AB, CanadaGoogle Scholar
  69. Yin H, Liu J, Xu Y, Liu X, Zhang S, Ma J, Du J (2013) TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato. PLoS One 8(7):e68587CrossRefPubMedCentralPubMedGoogle Scholar
  70. Yin H, Du J, Li L, Jin C, Fan L, Li M, Wu J, Zhang S (2014) Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.). Genome Biol Evol 6(6):1423–1436CrossRefPubMedCentralPubMedGoogle Scholar
  71. Zhang M, Fan L, Liu Q, Song Y, Wei S, Zhang S, Wu J (2013) A novel set of EST-derived SSR markers for pear and cross-species transferability in Rosaceae. Plant Mol Biol Rep 32(1):290–302CrossRefGoogle Scholar
  72. Zhao G, Dai H, Chang L, Ma Y, Sun H, He P, Zhang Z (2010) Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji. Tree Genet Genomes 6(1):149–159Google Scholar
  73. Zhao Y, Lin H, Guo Y, Liu Z, Guo X, Li K (2013) Genetic linkage maps of pear based on srap markers. Pak J Botany 45(4):1265–1271Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Jiangmei Sun
    • 1
  • Hao Yin
    • 1
  • Leiting Li
    • 1
  • Yue Song
    • 1
  • Lian Fan
    • 1
  • Shaoling Zhang
    • 1
  • Jun Wu
    • 1
  1. 1.Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina

Personalised recommendations