Plant Molecular Biology Reporter

, Volume 32, Issue 1, pp 290–302 | Cite as

A Novel Set of EST-Derived SSR Markers for Pear and Cross-Species Transferability in Rosaceae

  • Ming-yue Zhang
  • Lian Fan
  • Qing-zhong Liu
  • Yue Song
  • Shu-wei Wei
  • Shao-ling Zhang
  • Jun Wu
Brief Communication

Abstract

Pear is a fruit species with worldwide distribution belonging to the Rosaceae family. In this study, transcriptomes of 12 different tissues of pear were newly assembled, with a total of 17,353 SSR loci identified. Within these, repetitive sequences with dinucleotide and trinucleotide motifs were more abundant than other types. We developed 194 EST-SSR makers from the assembled sequences to test on seven pear varieties from different genetic backgrounds, on which 132 EST-SSR primers had amplicons. There were 108 primers with dinucleotide and trinucleotide motifs detecting a total of 311 alleles, with an average per primer of 2.88 and 2.86, respectively. These had better quality than primers with tetranucleotides, pentanucleotides, and hexanucleotides. Fifty polymorphic markers divided 36 pear genotypes into two groups with a similarity coefficient of 0.62. Results showed that Japanese pears had a comparatively close relationship with Chinese pears, indicating the great potential of the novel EST-SSR makers in future evaluations of pear germplasm. Furthermore, 54 EST-SSR markers were selected to test transferability to 96 other Rosaceae cultivars from eight species, including Japanese apricot, plum, apricot, peach, cherry, apple, strawberry, and loquat. Seventeen EST-SSR primers had PCR amplification products in at least one of the 96 accessions, with the highest transferability was from pear to apple at 29.63 %. Transferability from pear to Japanese apricot, plum, apricot, peach, cherry, strawberry, and loquat was 9.26, 14.81, 11.11, 12.96, 5.56, 3.7, and 12.96 %, respectively. Therefore, the newly developed EST-SSR markers can contribute to exploring the genetic relationship, evolution and comparative genomics, and gene introgressions in the Rosaceae family.

Keywords

Pear Expressed Sequence Tag - Simple Sequence Repeats (EST-SSRs) Transferability Rosaceae species 

Supplementary material

11105_2013_638_MOESM1_ESM.docx (713 kb)
ESM 1(DOCX 713 kb)

References

  1. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631PubMedCrossRefGoogle Scholar
  2. Bao L, Chen K, Zhang D, Cao Y, Yamamoto T, Teng Y (2007) Genetic diversity and similarity of pear (Pyrus L.) cultivars native to East Asia revealed by SSR (simple sequence repeat) markers. Genet Resour Crop Evol 54:959–971CrossRefGoogle Scholar
  3. Bassil N, Postman JD (2009) Identification of European and Asian pears using EST-SSRs from Pyrus. Genet Resour Crop Evol 57:357–370CrossRefGoogle Scholar
  4. Bombarely A, Merchante C, Csukasi F, Cruz-Rus E, Caballero JL, Medina-Escobar N, Blanco-Portales R, Botella Miguel A, Muñoz-Blanco J, Sánchez-Sevilla JF, Valpuesta V (2010) Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies. BMC Genomics 11:503PubMedCentralPubMedCrossRefGoogle Scholar
  5. Brant JB, Gustavo C-A, Peter MG (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83CrossRefGoogle Scholar
  6. Castillo A, Budak H, Varshney RK, Dorado G, Graner A, Hernandez P (2008) Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biol 8:97PubMedCentralPubMedCrossRefGoogle Scholar
  7. Cavagnaro PF, Chung S-M, Manin S, Yildiz M, Ali A, Alessandro MS, Iorizzo M, Senalik DA, Simon PW (2011) Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genomics 12:386Google Scholar
  8. Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio J-M, Ech C, Richardson T, Plomion C (2004) Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 29:1204–1214CrossRefGoogle Scholar
  9. Cho K-H, Shin IS, Kim SH, Kim J-H, Kim D-H, Shin YU, Hwang H-S (2012) Identification of Korean pear cultivars using combinations of SCAR markers. Hort Environ Biotechnol 53:228–236CrossRefGoogle Scholar
  10. Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591–608PubMedCrossRefGoogle Scholar
  11. Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922PubMedGoogle Scholar
  12. Dirlewanger E, Cosson P, Tavaud M, Aranzana M, Poizat C, Zanetto A, Arús P, Laigret F (2002) Development of microsatellite markers in peach (Prunus persica(L.) Batsch) and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theor Appl Genet 105:127–138PubMedCrossRefGoogle Scholar
  13. Ellis J, Burke J (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132PubMedCrossRefGoogle Scholar
  14. Erfani J, Ebadi A, Abdollahi H, Fatahi R (2012) Genetic diversity of some pear cultivars and genotypes using simple sequence repeat (SSR) markers. Plant Mol Biol Rep 30:1065–1072CrossRefGoogle Scholar
  15. Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407PubMedCrossRefGoogle Scholar
  16. Fan L, Zhang M-Y, Liu Q-Z, Li L-T, Song Y, Wang L-F, Zhang S-L, Wu J (2013) Transferability of newly developed pear ssr markers to other rosaceae species. Plant Mol Biol Rep. doi:07/s11105-013-0586-z.
  17. Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2008) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85–97CrossRefGoogle Scholar
  18. Ferreira dos Santos AR, Ramos-Cabrer AM, Díaz-Hernández MB, Pereira-Lorenzo S (2011) Genetic variability and diversification process in local pear cultivars from northwestern Spain using microsatellites. Tree Genet Genomes 7:1041–1056CrossRefGoogle 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 Breed 23:397–411CrossRefGoogle Scholar
  20. Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112:430–439PubMedCrossRefGoogle Scholar
  21. Hearnden PR, Eckermann PJ, McMichael GL, Hayden MJ, Eglinton JK, Chalmers KJ (2007) A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theor Appl Genet 115:383–391PubMedCrossRefGoogle Scholar
  22. Hu J, Wang L, Li J (2011) Comparison of genomic SSR and EST-SSR markers. Biol Plant 55:577–580CrossRefGoogle Scholar
  23. Kolpakov R (2003) mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31:3672–3678PubMedCentralPubMedCrossRefGoogle Scholar
  24. Li S, Jia J, Wei X, Zhang X, Li L, Chen H, Fan Y, Sun H, Zhao X, Lei T, Xu Y, Jiang F, Wang H, Li L (2007) A intervarietal genetic map and QTL analysis for yield traits in wheat. Mol Breed 20:167–178CrossRefGoogle Scholar
  25. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967PubMedCrossRefGoogle Scholar
  26. Liu D, He X, Li W, Chen C, Ge F (2012) Molecular cloning of a thaumatin-like protein gene from Pyrus pyrifolia and overexpression of this gene in tobacco increased resistance to pathogenic fungi. Plant Cell Tiss Organ Cult 111:29–39CrossRefGoogle Scholar
  27. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Zhu X, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:1–18CrossRefGoogle Scholar
  28. Ma Y-z, Zhang Y-x (2009) Classification position of Ku’erle aromatic pear identified by RAPD. Southwest China J Agric Sci 22:743–745Google Scholar
  29. Ma J-Q, Ma C-L, Yao M-Z, Jin J-Q, Wang Z-L, Wang X-C, Chen L (2012) Microsatellite markers from tea plant expressed sequence tags (ESTs) and their applicability for cross-species/genera amplification and genetic mapping. Sci Hortic 134:167–175CrossRefGoogle Scholar
  30. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46PubMedCrossRefGoogle Scholar
  31. Mnejja M, Garcia-Mas J, Audergon J-M, Arús P (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Genet Genomes 6:689–700CrossRefGoogle Scholar
  32. Moccia MD, Oger-Desfeux C, Marais GA, Widmer A (2009) A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping. BMC Genomics 10:243PubMedCentralPubMedCrossRefGoogle Scholar
  33. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200PubMedCrossRefGoogle Scholar
  34. Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800–805PubMedCrossRefGoogle Scholar
  35. Nishitani C, Terakami S, Sawamura Y, Takada N, Yamamoto T (2009) Development of novel EST-SSR markers derived from Japanese pear(Pyrus pyrifolia). Breed Sci 59:391–400CrossRefGoogle Scholar
  36. Parka YH, Ahna SG, Choia YM, Oha HJ, Ahnb DC, Kimb JG, Kanga JS, Choia YW, Jeongc BR (2010) Rose (Rosa hybrida L.) EST-derived microsatellite markers and their transferability to strawberry (Fragaria spp.). Sci Hortic 125:733–739CrossRefGoogle Scholar
  37. Pashley CH, Ellis JR, McCauley DE, Burke JM (2006) EST databases as a source for molecular markers: lessons from Helianthus. J Hered 97:381–388PubMedCrossRefGoogle Scholar
  38. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple-sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287PubMedCrossRefGoogle Scholar
  39. Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P (2006) SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus. Mol Genet Genomics 276:436–449PubMedCrossRefGoogle Scholar
  40. Potter D, Still SM, Grebenc T, Ballian D, Božič G, Franjiæ J, Kraigher H (2007) Phylogenetic relationships in tribe Spiraeeae (Rosaceae) inferred from nucleotide sequence data. Plant Syst Evol 266:105–118CrossRefGoogle Scholar
  41. Rohlf FJ (2002) NTSYS pc: numerical taxonomy system, version 2.1. Exeter, Setauket, NYGoogle Scholar
  42. Rozen S, Helen S (1999) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols. Humana Press, Totowa, pp 365–386Google Scholar
  43. Saha MC, Mian MAR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791PubMedCrossRefGoogle Scholar
  44. Shen X, Guo W, Zhu X, Yuan Y, Yu JZ, Kohel RJ, Zhang T (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed 15:169–181CrossRefGoogle Scholar
  45. Shiferaw E, Pè ME, Porceddu E, Ponnaiah M (2011) Exploring the genetic diversity of ethiopian grass pea (Lathyrus sativus L.) using EST-SSR markers. Mol Breed 30:789–797PubMedCentralPubMedCrossRefGoogle Scholar
  46. Silfverberg-Dilworth E, Matasci CL, Weg WE, Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2:202–224CrossRefGoogle Scholar
  47. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
  48. Teng Y, Tanabe K, Tamura F, Itai A (2002) Genetic relationships of Pyrus species and cultivars native to East Asia revealed by randomly amplified polymorphic DNA markers. J Am Soc Hortic Sci 127:262–270Google Scholar
  49. Tian Y-k, Wang C-h, Zhang J-c, Dai H-y, Chu Q-g (2003) A RAPD marker of apple columnar gene (Co). Acta Bot Boreali-occidentalia Sin 23:2176–2179Google Scholar
  50. Tian L, Gao Y, Cao Y, Liu F, Yang J (2012) Identification of Chinese white pear cultivars using SSR markers. Genet Resour Crop Evol 59:317–326CrossRefGoogle Scholar
  51. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55PubMedCrossRefGoogle Scholar
  52. Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W (2010) Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res Notes 3:42PubMedCentralPubMedCrossRefGoogle Scholar
  53. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408PubMedCrossRefGoogle Scholar
  54. 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 102:865–870CrossRefGoogle Scholar
  55. Yao L, Zheng X, Cai D, Gao Y, Wang K, Cao Y, Teng Y (2010) Exploitation of Malus EST-SSRs and the utility in evaluation of genetic diversity in Malus and Pyrus. Genet Resour Crop Evol 57:841–851CrossRefGoogle Scholar
  56. Yeh FC (1997) Population genetic analysis of codominant and dominant markers and quantitative traits. Belg J Bot 129:157Google Scholar
  57. Yeh FC, Yang RC, Boyle T, Ye ZH, Mao JX (1999) POPGENE, version 1.32: the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, EdmontonGoogle Scholar
  58. Yu JK, La Rota M, Kantety RV, Sorrells ME (2004) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742–751PubMedCrossRefGoogle Scholar
  59. Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687PubMedCrossRefGoogle Scholar
  60. Zhou Y, Li J, Korban SS, Han Y (2013) Apple SSRs present in coding and noncoding regions of expressed sequence tags show differences in transferability to other fruit species in Rosaceae. Can J Plant Sci 93:183–190CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Ming-yue Zhang
    • 1
  • Lian Fan
    • 1
  • Qing-zhong Liu
    • 2
  • Yue Song
    • 1
  • Shu-wei Wei
    • 1
  • Shao-ling Zhang
    • 1
  • Jun Wu
    • 1
  1. 1.Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingPeople’s Republic of China
  2. 2.Key Laboratory for Fruit Biotechnology Breeding of ShandongPomological Institute of ShandongTaianPeople’s Republic of China

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