Advertisement

Euphytica

, Volume 177, Issue 3, pp 309–334 | Cite as

Microsatellite markers: an overview of the recent progress in plants

  • Rajwant K. Kalia
  • Manoj K. Rai
  • Sanjay Kalia
  • Rohtas Singh
  • A. K. Dhawan
Review

Abstract

In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4–5 years) made in plant genetics using SSR markers.

Keywords

Cross-species transferability Expressed sequence tags Molecular markers Population genetics Transcription slippage 

References

  1. Achtak H, Oukabli A, Ater M, Santoni S, Kjellberg F, Khadari B (2009) Microsatellite markers as reliable tools for fig cultivar identification. J Am Soc Hort Sci 134:624–631Google Scholar
  2. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372PubMedCrossRefGoogle Scholar
  3. Ai HL, Wang H, Li DZ, Yang JB (2009) Isolation and characterization of 13 microsatellite loci from Incarvillea mairei (Bignoniaceae), an endemic species to the Himalaya–Hengduan mountains region. Conser Genet 10:1613–1615CrossRefGoogle Scholar
  4. Alba V, Montemurro C, Antonella WS, Pasqualone AB (2009) SSR-based identification key of cultivars of Olea europaea L. diffused in Southern-Italy. Sci Hort 123:1–16CrossRefGoogle Scholar
  5. Ali ML, Rajewski JF, Baenziger PS, Gill KS, Eskridge KM, Dweikat I (2008) Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers. Mol Breed 21:497–509CrossRefGoogle Scholar
  6. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  7. Armour JA, Neumann R, Gobert S, Jeffreys AJ (1994) Isolation of human simple repeat loci by hybridization selection. Hum Mol Genet 3:599–605PubMedCrossRefGoogle Scholar
  8. Arya L, Verma M, Gupta VK, Karihaloo JL (2009) Development of EST–SSRs in finger millet (Eleusine coracana ssp coracana) and their transferability to pearl millet (Pennisetum glaucum). J Plant Biochem Biotechnol 18:97–100Google Scholar
  9. Asp T, Frei UK, Didion T, Nielsen KK, Lübberstedt T (2007) Frequency, type, and distribution of EST–SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa. BMC Plant Biol 7:36PubMedCrossRefGoogle Scholar
  10. Astarini IA, Plummer JA, Lancaster RA, Yan G (2008) Identification of ‘Sib’ plants in hybrid cauliflowers using microsatellite markers. Euphytica 164:309–316CrossRefGoogle Scholar
  11. Bao JS, Corke H, Sun M (2002) Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.). Theor Appl Genet 105:898–905PubMedCrossRefGoogle Scholar
  12. Barkley NA, Newman ML, Wang ML, Hotchkiss MW, Pederson GA (2005) Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST–SSR markers. Genome 48:731–737PubMedCrossRefGoogle Scholar
  13. Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing geneticdiversity and population structure in a Citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531PubMedCrossRefGoogle Scholar
  14. Barkley NA, Dean RE, Pittman RN, Wang ML, Holbrook CC, Pederson GA (2007) Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing. Genet Res 89:93–106PubMedCrossRefGoogle Scholar
  15. Barreneche T, Casasoli M, Russell K, Akkak A, Meddour H, Plomion C, Villani F, Kremer A (2004) Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs). Theor Appl Genet 108:558–566PubMedCrossRefGoogle Scholar
  16. Becker J, Huen M (1995) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27:835–845PubMedCrossRefGoogle Scholar
  17. Beckmann JS, Soller M (1990) Towards a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellite sites. Nat Biotechnol 8:930–932CrossRefGoogle Scholar
  18. Bennetzen JL (2000) Transposable element contributions to plant genome evolution. Plant Mol Biol 42:251–269PubMedCrossRefGoogle Scholar
  19. Bhat PR, Kumar KV, Hendre PS, Kumar RP, Varshney RK, Aggarwal RK (2005) Identification and characterization of expressed sequence tags-derived simple sequence repeats, markers from robusta coffee variety ‘C × R’ (an interspecific hybrid of Coffea canephora × Coffea congensis). Mol Ecol Notes 5:80–83CrossRefGoogle Scholar
  20. Bhattramakki D, Dong J, Chhabra K, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988–1002PubMedCrossRefGoogle Scholar
  21. Bohn M, Utz HF, Melchinger AE (1999) Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance. Crop Sci 39:228–237CrossRefGoogle Scholar
  22. Born C, Vignes H, Muloko N, Wickings EJ, Hossaert-Mckey M, Chevallier MH (2006) Isolation and characterization of polymorphic microsatellite loci from Aucoumea klaineana Pierre (Burseraceae), a tropical rainforest tree of Central Africa. Mol Ecol Notes 6:1054–1056CrossRefGoogle Scholar
  23. Boys J, Cherry M, Dayanandan S (2005) Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae). Am J Bot 92:833–841CrossRefGoogle Scholar
  24. Breseghello F, Sorrells ME (2006a) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177PubMedCrossRefGoogle Scholar
  25. Breseghello F, Sorrells ME (2006b) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330CrossRefGoogle Scholar
  26. Caruso M, Federici CT, Roose ML (2008) EST–SSR markers for asparagus genetic diversity evaluation and cultivar identification. Mol Breed 21:195–204CrossRefGoogle Scholar
  27. 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 8:97PubMedCrossRefGoogle Scholar
  28. Chagne D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio JM, Echt C, Richardson T, Plomion C (2004) Cross-species transferability and mapping of genomic and cDNASSRs in pines. Theor Appl Genet 109:1204–1214PubMedCrossRefGoogle Scholar
  29. Chang CL, Marra G, Chauhan DP, Ha HT, Chang DK, Ricciardiello L, Randolph A, Carethers JM, Boland CR (2002) Oxidative stress inactivates the human DNA mismatch repair system. Am J Physiol Cell Physiol 283:148–154Google Scholar
  30. Chapman MA, Hvala J, Strever J, Matvienko M, Kozik A, Michelmore RW, Tang S, Knapp SJ, Burke JM (2009) Development, polymorphism and cross-taxon utility of EST–SSR markers from saflower (Carthamus tinctorius L.). Theor Appl Genet 120:85–91PubMedCrossRefGoogle Scholar
  31. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567CrossRefGoogle Scholar
  32. Chen T, Zhou R, Ge XJ, Shi S (2008) Development and characterization of microsatellite markers for a mangrove tree species Sonneratia caseolaris (L.) Engler (Lythraceae sensu lato). Conserv Genet 9:957–959CrossRefGoogle Scholar
  33. Chen J, Wang H, Shen H, Chai M, Li J, Qi M, Yang W (2009) Genetic variation in tomato populations from four breeding programs revealed by single nucleotide polymorphism and simple sequence repeat markers. Sci Hort 122:6–16CrossRefGoogle Scholar
  34. 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
  35. Chuanchai P, Xuelin T, Silapapun A, Suthipong P, Wei L, Messmer R (2010) Early hybrid testing in tropical maize: are molecular markers useful for selecting the parental component? Kasetsart J Nat Sci 44:70–78Google Scholar
  36. Chung AM, Staub JE, Chen JF (2006) Molecular phylogeny of Cucumis species as revealed by consensus chloroplast SSR marker length and sequence variation. Genome 49:219–229PubMedCrossRefGoogle Scholar
  37. Cifarelli RA, Gallitelli M, Cellini F (1995) Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones. Nucleic Acids Res 23:3802–3803PubMedCrossRefGoogle Scholar
  38. Cooper S, Bull CM, Gardner MG (1997) Characterization of microsatellite loci from the socially monogamous lizard Tiliqua rugosa using a PCR-based isolation technique. Mol Ecol 6:793–795PubMedCrossRefGoogle Scholar
  39. Cordeiro GM, Maguire TL, Edwards KJ, Henry RJ (1999) Optimization of a microsatellite enrichment technique in Saccharum spp. Plant Mol Biol Rep 17:225–229CrossRefGoogle Scholar
  40. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs across transferable to Erianthus and Sorghum. Plant Sci 160:1115–1123PubMedCrossRefGoogle Scholar
  41. Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 8:55PubMedCrossRefGoogle Scholar
  42. Decroocq V, Fave 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
  43. Delseny M, Laroche M, Penon P (1983) Detection of sequences with Z-DNA forming potential in higher plants. Biochem Biophys Res Commun 116:113–120PubMedCrossRefGoogle Scholar
  44. Dresselhaus T, Cordts S, Heuer S, Sauter M, Lorz H, Kranz E (1999) Novel ribosomal genes from maize are differentially expressed in the zygotic and somatic cell cycles. Mol Gen Genet 261:416–427PubMedCrossRefGoogle Scholar
  45. Edwards A, Civitello A, Hammond HA, Caskey CT (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet 49:746–756PubMedGoogle Scholar
  46. Ek M, Eklund M, Von Post R, Dayteg C, Henriksson T, Weibull P, Ceplitis A, Isaac P, Tuvesson S (2005) Microsatellite markers for powdery mildew resistance in pea (Pisum sativum L.). Hereditas 142:86–91PubMedCrossRefGoogle Scholar
  47. Ellegren H (2002) Microsatellite evolution: a battle between replication slippage and point mutation. Trends Genet 18:70CrossRefGoogle Scholar
  48. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445PubMedCrossRefGoogle Scholar
  49. Ellis JR, Burke JM (2007) EST–SSRs as a resource for population genetic analyses. Heredity 99:125–132PubMedCrossRefGoogle Scholar
  50. Ender A, Schwenk K, Stdler T, Streit B, Schierwater B (1996) RAPD identification of microsatellites in Daphnia. Mol Ecol 5:437–441PubMedGoogle Scholar
  51. Erre P, Chessa I, Mun˜oz-Diez C, Belaj A, Rallo L, Trujillo I (2010) Genetic diversity and relationships between wild and cultivated olives (Olea europaea L.) in Sardinia as assessed by SSR markers. Genet Resour Crop Evol 57:41–54CrossRefGoogle Scholar
  52. Feingold S, Lloyd J, Norero N, Bonierbale M, Lorenzen J (2005) Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor Appl Genet 111:456–466PubMedCrossRefGoogle Scholar
  53. Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST–SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85–97CrossRefGoogle Scholar
  54. Fisher PJ, Gardner RC, Richardson TE (1996) Single locus microsatellites isolated using 5¢-anchored PCR. Nucleic Acids Res 24:4369–4371PubMedCrossRefGoogle Scholar
  55. Fraser LG, Tsang GK, Datson PM, De Silva HN, Harvey CF, Gill GP, Crowhurst RN, McNeilage MA (2009) A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes. BMC Genomics 10:102PubMedCrossRefGoogle Scholar
  56. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Kenichi M, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554:17–22PubMedCrossRefGoogle Scholar
  57. Gasic K, Han Y, Kertbundit S, Shulaev V, Iezzoni AF, Stover EW, Richard L, Michael B, Wisniewski E, Korban SS (2009) Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breed 23:397–411CrossRefGoogle Scholar
  58. Gil-Ariza DJ, Amaya I, López-Aranda JM, Sánchez-Sevilla JF, Botella MÁ, Valpuesta V (2009) Impact of plant breeding on the genetic diversity of cultivated strawberry as revealed by expressed sequence tag-derived simple sequence repeat markers. J Am Soc Hort Sci 134:337–347Google Scholar
  59. Gimenes MA, Hoshino AA, Barbosa AV, Palmieri DA, Lopes CR (2007) Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea). BMC Plant Biol 7:9PubMedCrossRefGoogle Scholar
  60. Gomez SM, Denwar NN, Ramasubramanian T, Simpson CE, Burow G, Burke JJ, Puppala N, Burow MD (2008) Identification of peanut hybrids using microsatellite markers and horizontal polyacrylamide gel electrophoresis. Peanut Sci 35:123–129CrossRefGoogle Scholar
  61. Gong L, Stift G, Kofler R, Pachner M, Lelley T (2008) Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Theor Appl Genet 117:37–48PubMedCrossRefGoogle Scholar
  62. Graham J, Woodhead M, Smith K, Russell J, Marshall B, Ramsay G, Squire G (2009) New insight into wild red raspberry populations using simple sequence repeat markers. J Am Soc Hort Sci 134:109–119Google Scholar
  63. Guan R, Chang R, Li Y, Wang L, Liu Z, Qiu L (2010) Genetic diversity comparison between Chinese and Japanese soybeans (Glycine max (L.) Merr.) revealed by nuclear SSRs. Genet Resour Crop Evol 57:229–242CrossRefGoogle Scholar
  64. Guo W, Wang W, Zhou B, Zhang T (2006) Cross-species transferability of G. arboreum-derived EST–SSRs in the diploid species of Gossypium. Theor Appl Genet 112:1573–1581PubMedCrossRefGoogle Scholar
  65. Gupta S, Prasad M (2009) Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome 52:761–771PubMedCrossRefGoogle Scholar
  66. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–165CrossRefGoogle Scholar
  67. Gupta M, Chyi YS, Romero-Severson J, Owen JL (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 89:998–1006CrossRefGoogle Scholar
  68. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST–SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323PubMedCrossRefGoogle Scholar
  69. Hamada HM, Petrino MG, Kakunaga T (1982) A novel repeated element with Z-DNAforming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79:6465–6469PubMedCrossRefGoogle Scholar
  70. Hamilton MB, Pincus EL, Di-Fiore A, Fleischer RC (1999) Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27:500–507PubMedGoogle Scholar
  71. Hashemi SH, Mirmohammadi-Maibody SAM, Nematzadeh GA, Arzani A (2009) Identification of rice hybrids using microsatellite and RAPD markers. Afr J Biol 8:2094–2101Google Scholar
  72. He XY, Zhang YL, He ZH, Wu YP, Xiao YG, Ma CX, Xia XC (2008) Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker. Theor Appl Genet 116:213–221PubMedCrossRefGoogle Scholar
  73. Hiebert CW, Thomas JB, Somers DJ, McCallum BD, Fox SL (2007) Microsatellite mapping of adult-plant leaf rust resistance gene Lr22a in wheat. Theor Appl Genet 115:877–884PubMedCrossRefGoogle Scholar
  74. Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 14:271–281PubMedCrossRefGoogle Scholar
  75. Ince AG, Karaca M, Onus AN (2010) Polymorphic microsatellite markers transferable across capsicum species. Plant Mol Biol Rep 28:285–291CrossRefGoogle Scholar
  76. Inoue E, Ning L, Hara H, Ruan S, Anzai H (2009) Development of simple sequence repeat markers in chinese chestnut and their characterization in diverse chestnut cultivars. J Am Soc Hort Sci 134:610–617Google Scholar
  77. IRGSP (2005) The map based sequence of rice genome. Nature 436:793–800CrossRefGoogle Scholar
  78. Jackson AL, Chen R, Loeb LA (1998) Induction of microsatellite instability by oxidative DNA damage. Proc Natl Acad Sci USA 95:12468–12473PubMedCrossRefGoogle Scholar
  79. Jacob HJ, Lindpaintnesr K, Kusumir EL, Bunkery K, Mao IP, Gantenv D, Dzau J, Lander ES (1991) Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensive rat. Cell 67:213–224PubMedCrossRefGoogle Scholar
  80. Jakse J, Stajner N, Kozjak P, Cerenak A, Javornik B (2008) Trinucleotide microsatellite repeat is tightly linked to male sex in hop (Humulus lupulus L.). Mol Breed 21:139–148CrossRefGoogle Scholar
  81. Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11:424–429CrossRefPubMedGoogle Scholar
  82. Jia X, Zhang Z, Liu Y, Zhang C, Shi Y, Song Y, Wang T, Li Y (2009) Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theor Appl Genet 118:821–829PubMedCrossRefGoogle Scholar
  83. Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240Google Scholar
  84. Juhász AG, Stágel A, Ács S, Zatykó L (2006) Microsatellite markers and automated fragment analysis techniques for efficient and precise hybrid identification and genetic purity testing in pepper (Capsicum annuum L.). Acta Agr Hungarica 54:141–146CrossRefGoogle Scholar
  85. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711CrossRefGoogle Scholar
  86. Kandpal RP, Kandpal G, Weissman SM (1994) Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers. Proc Natl Acad Sci USA 91:88–92PubMedCrossRefGoogle Scholar
  87. Kang M, Pan L, Yao X, Huang H (2006) Development and characterization of polymorphic microsatellite loci in endangered fern Adiantum reniforme var. sinense. Conserv Genet 7:807–810CrossRefGoogle Scholar
  88. Kantety RV, Rota ML, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510PubMedCrossRefGoogle Scholar
  89. Karagyozov L, Kalcheva ID, Chapman VM (1993) Construction of random small-insert genomic libraries highly enriched for simple sequence repeats. Nucleic Acids Res 21:3911–3912PubMedCrossRefGoogle Scholar
  90. Khattak JZK, Torp AM, Andersen SB (2006) A genetic linkage map of Spinacia oleracea and localization of a sex determination locus. Euphytica 148:311–318CrossRefGoogle Scholar
  91. Khattak JZK, Christiansen JL, Torp AM, Andersen SB (2007)  Genic microsatellite markers for discrimination of spinach cultivars. Plant Breed 126:454–456CrossRefGoogle Scholar
  92. Kijas JM, Fowler JC, Garbett CA, Thomas MR (1994) Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. Biotechniques 16:656–662PubMedGoogle Scholar
  93. Korpelainen H, Bisang I, Hedena LS, Kolehmainen J (2008) The first sex-specific molecular marker discovered in the moss Pseudocalliergon trifarium. J Hered 99:581–587PubMedCrossRefGoogle Scholar
  94. Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutation. Proc Natl Acad Sci USA 95:10774–10778PubMedCrossRefGoogle Scholar
  95. Lacis G, Rashal I, Ruisa S, Trajkovski V, Iezzoni AF (2009) Assessment of genetic diversity of Latvian and Swedish sweet cherry (Prunus avium L.) genetic resources collections by using SSR (microsatellite) markers. Sci Hort 121:451–457CrossRefGoogle Scholar
  96. Lagat M, Danson J, Kimani M, Kuria A (2008) A quantitative trait loci for resistance to maize streak virus disease in maize genotypes used in hybrid development. Afr J Biotechnol 7:2573–2577Google Scholar
  97. Lawson MJ, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7:R14PubMedCrossRefGoogle Scholar
  98. Lench NJ, Norris A, Bailey A, Booth A, Markham AF (1996) Vectorette PCR isolation of microsatellites repeat sequences using anchored dinucleotide repeat primers. Nucleic Acids Res 24:2190–2191PubMedCrossRefGoogle Scholar
  99. Li YC, Fahima T, Korol AB, Peng J, Roder MS, Kirzhner V, Beiles A, Nevo E (2000) Microsatellite diversity correlated with ecological-edaphic and genetic factors in three microsites of wild emmer wheat in North Israel. Mol Biol Evol 17:851–862PubMedGoogle Scholar
  100. Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465PubMedCrossRefGoogle Scholar
  101. Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007PubMedCrossRefGoogle Scholar
  102. Li TH, Li YX, Li ZC, Zhang HL, Qi YW, Wang T (2008) Simple sequence repeat analysis of genetic diversity in primary core collection of peach (Prunus persica). J Integr Plant Biol 50:102–110PubMedCrossRefGoogle Scholar
  103. Li M, Yuyama N, Luo L, Hirata M, Cai H (2009) In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum. Mol Breed 24:41–47CrossRefGoogle Scholar
  104. Li R, Han Z, Xincheng Z, Yanan G, Fengxia Y, Guoan S, Jiancheng W, Chunqing Z (2010) Genetic diversity in Chinese sorghum landraces revealed by chloroplast simple sequence repeats. Genet Resour Crop Evol 57:1–15CrossRefGoogle Scholar
  105. Liang X, Chen X, Hong Y, Liu H, Zhou G, Li S, Guo B (2009) Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol 9:35PubMedCrossRefGoogle Scholar
  106. Liewlaksaneeyanawin C, Ritland CE, El-Kassaby YA, Ritland K (2004) Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 109:361–369PubMedCrossRefGoogle Scholar
  107. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401PubMedGoogle Scholar
  108. Liu LW, Wang Y, Gong YQ, Zhao TM, Liu G, Li XY, Yu FM (2007) Assessment of genetic purity of tomato (Lycopersicon esculentum L.) hybrid using molecular markers. Sci Hort 115:7–12CrossRefGoogle Scholar
  109. Lunt DH, Hutchinson WF, Carvalho GR (1999) An efficient method for PCR-based identification of microsatellite arrays (PIMA). Mol Ecol 8:893–894Google Scholar
  110. Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R (2008) Transferability of the EST–SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287PubMedCrossRefGoogle Scholar
  111. Mallory MA, Hall RV, McNabb AR, Pratt DB, Jellen EN, Maughan PJ (2008) Development and characterization of microsatellite markers for the grain amaranths. Crop Sci 48:1098–1106CrossRefGoogle Scholar
  112. Martí ÀF, Alonso JM, Espiau MT, Rubio-Cabetas MJ, Company RS (2009) Genetic diversity in Spanish and foreign almond germplasm assessed by molecular characterization with simple sequence repeats. J Am Soc Hort Sci 134:535–542Google Scholar
  113. McCallum J, Thomson S, Pither-Joyce M, Kenel F (2008) Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. J Am Soc Hort Sci 133:810–818Google Scholar
  114. Meyer W, Michell TG, Freedman EZ, Vilgalys R (1993) Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J Clin Biol 31:2274–2280Google Scholar
  115. Min WK, Han JH, Kang WH, Lee HR, Kim BD (2008) Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3′ end of simple sequence repeats in the pepper genome. Mol Cells 26:250–257PubMedGoogle Scholar
  116. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200PubMedCrossRefGoogle Scholar
  117. Nadir E, Margalit H, Gallily T, Ben-Sasson SA (1996) Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications. Proc Natl Acad Sci USA 93:6470–6475PubMedCrossRefGoogle Scholar
  118. Naresh V, Yamini KN, Rajendrakumar P, Kumar VD (2009) EST–SSR marker-based assay for the genetic purity assessment of safflower hybrids. Euphytica 170:347–353CrossRefGoogle Scholar
  119. Nasiri J, Haghnazari A, Saba J (2009) Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on SSR markers. Afr J Biotechnol 8:3405–3417Google Scholar
  120. Nazareno AG, Pereira RAS, Feres JM, Mestriner MA, Alzate-Marin AL (2009) Transferability and characterization of microsatellite markers in two Neotropical Ficus species. Genet Mol Biol 32:568–571CrossRefGoogle Scholar
  121. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BC, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776PubMedCrossRefGoogle Scholar
  122. Nishikawa T, Vaughan DA, Kadowaki K (2005) Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor Appl Genet 110:696–705PubMedCrossRefGoogle Scholar
  123. Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, Ohyama A, Fukuoka H (2009) Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet 119:1143–1153PubMedCrossRefGoogle Scholar
  124. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155PubMedCrossRefGoogle Scholar
  125. Ohyama A, Asamizu E, Negoro S, Miyatake K, Yamaguchi H, Tabata S, Fukuoka H (2009) Characterization of tomato SSR markers developed using BAC-end and cDNA sequences from genome databases. Mol Breed 23:685–691CrossRefGoogle Scholar
  126. Orr HT, Zoghbi HY (2007) Trinucleotide repeat disorders. Annu Rev Neurosci 30:575–621PubMedCrossRefGoogle Scholar
  127. Ostrander EA, Jong PM, Rine J, Duyk G (1992) Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci USA 89:3419–3423PubMedCrossRefGoogle Scholar
  128. Paetkau D (1999) Microsatellites obtained using strand extension: an enrichment protocol. Biotechniques 26:690–697PubMedGoogle Scholar
  129. Pan L, Xia Q, Quan Z, Liu H, Ke W, Ding Y (2010) Development of novel EST-SSRs from sacred lotus (Nelumbo nucifera gaertn) and their utilization for the genetic diversity analysis of N. nucifera. J Hered 101:71–82PubMedCrossRefGoogle Scholar
  130. Parasnis AS, Ramakrishna W, Chowdari KV, Gupta VS, Ranjekar PK (1999) Microsatellite (GATA)n reveals sex-specific differences in papaya. Theor Appl Genet 99:1047–1052CrossRefGoogle Scholar
  131. Parida SK, Kumar ARK, Dalal V, Singh NK, Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theor Appl Genet 112:808–817PubMedCrossRefGoogle Scholar
  132. Parida SK, Kalia SK, Sunita K, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338PubMedCrossRefGoogle Scholar
  133. 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
  134. Pearson CE, Edamura NK, Cleary JD (2005) Repeat instability: mechanisms of dynamic mutations. Nat Rev Genet 6:729–742PubMedCrossRefGoogle Scholar
  135. Pestsova E, Ganal MW, Roder MS (2000) Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43:689–697PubMedCrossRefGoogle Scholar
  136. Pollegioni P, Woeste K, Mugnozza GS, Malvolti ME (2009) Retrospective identification of hybridogenic walnut plants by SSR fingerprinting and parentage analysis. Mol Breed 24:321–335CrossRefGoogle Scholar
  137. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222Google Scholar
  138. Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142–147PubMedCrossRefGoogle Scholar
  139. Rabello E, Souza AN, Saito D, Tsai SM (2005) In silico characterization of microsatellites in Eucalyptus spp.: abundance, length variation and transposon associations. Genet Mol Biol 28:582–588CrossRefGoogle Scholar
  140. Rajendrakumar P, Biswal AK, Balachandran SM, Srinivasarao K, Sundaram RM (2007) Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics 23:1–4PubMedCrossRefGoogle Scholar
  141. Rallo P, Tenzer I, Gessler C, Baldoni L, Dorado G, Martin A (2003) Transferability of olive microsatellite loci across the genus Olea. Theor Appl Genet 107:940–946PubMedCrossRefGoogle Scholar
  142. Ramsay L, Macaulay M, degli Ivanissevichb S, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005PubMedGoogle Scholar
  143. Richardson T, Cato S, Ramser J, Kahl G, Weising K (1995) Hybridization of microsatellites to RAPD: a new source of polymorphic markers. Nucleic Acids Res 23:3798–3799PubMedCrossRefGoogle Scholar
  144. Risterucci AM, Duval MF, Rohde W, Billotte N (2005) Isolation and characterization of microsatellite loci from Psidium guajava L. Mol Ecol Notes 5:745–748CrossRefGoogle Scholar
  145. Rode J, In-Chol K, Saal B, Flachowsky H, Kriese U, Weber WE (2005) Sex-linked SSR markers in hemp. Plant Breed 124:167–170CrossRefGoogle Scholar
  146. Romero G, Adeva C, Battad Z (2009) Genetic fingerprinting: advancing the frontiers of crop biology research. Philipp Sci Lett 2:8–13Google Scholar
  147. Rossi M, Araujo PG, Sluys MV (2001) Survey of transposable elements in sugarcane expressed sequence tags (ESTs). Genet Mol Biol 24:147–154CrossRefGoogle Scholar
  148. Roy CB, Nazeer MA, Saha T (2004) Identification of simple sequence repeats in rubber (Hevea brasiliensis). Curr Sci 87:807–811Google Scholar
  149. Ruan CJ, Li H, Mopper S (2009) Characterization and identification of ISSR markers associated with resistance to dried-shrink disease in sea buckthorn. Mol Breed 24:255–268CrossRefGoogle Scholar
  150. Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722CrossRefGoogle Scholar
  151. 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
  152. Saha MC, Mian MAR, Zwonitzer JC, Chekhovskiy K, Hopkins AA (2005) An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.). Theor Appl Genet 110:323–336PubMedCrossRefGoogle Scholar
  153. Saha MC, Cooper JD, Mian MAR, Chekhovskiy K (2006) Tall Fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet 113:1449–1458PubMedCrossRefGoogle Scholar
  154. Sawadogo M, Ouedraogo JT, Balma D, Ouedraogo M, Gowda BS, Botanga C, Timko MP (2009) The use of cross species SSR primers to study genetic diversity of okra from Burkina Faso. Afr J Biotechol 8:2476–2482Google Scholar
  155. Schnell RJ, Olano CT, Quintanilla WE, Meerow AW (2005) Isolation and characterization of 15 microsatellite loci from mango (Mangifera indica L.) and cross-species amplification in closely related taxa. Mol Ecol Notes 5:625–627CrossRefGoogle Scholar
  156. Schranz ME, Song BH, Windsor AJ, Mitchell-Olds T (2007) Comparative genomics in the Brassicaceae: a family-wide perspective. Curr Opin Plant Biol 10:168–175PubMedCrossRefGoogle Scholar
  157. Sehgal D, Raina SN (2008) DNA markers and germplasm resource diagnostics: new perspectives in crop improvement and conservation strategies. In: Arya ID, Arya S (eds) Utilization of biotechnology in plant sciences. Microsoft Printech (I) Pvt. Ltd, Dehradun, pp 39–54Google Scholar
  158. Sharma RK, Gupta P, Sharma V, Sood A, Mohapatra T, Ahuja PS (2008) Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bamboo. Genome 51:91–103PubMedCrossRefGoogle Scholar
  159. Sharma V, Bhardwaj P, Kumar R, Sharma RK, Sood A, Ahuja PS (2009) Identification and cross-species amplification of EST derived SSR markers in different bamboo species. Conserv Genet 10:721–724CrossRefGoogle Scholar
  160. Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Davis G, Coe EH (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481PubMedCrossRefGoogle Scholar
  161. Shoemaker RC, Grant D, Olson T, Warren WC, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Nelson W, Davito J, Walker J, Wallis J, Kremitski C, Scheer D, Clifton SW, Graves T, Nguyen H, Wu X, Luo M, Dvorak J, Nelson R, Cannon S, Tomkins J, Schmutz J, Stacey G, Jackson S (2008) Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome 51:294–302PubMedCrossRefGoogle Scholar
  162. Shultz JL, Kazi S, Bashir R, Afzal JA, Lightfoot DA (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114:1081–1090PubMedCrossRefGoogle Scholar
  163. Siju S, Dhanya K, Syamkumar S, Sasikumar B, Sheeja TE, Bhat AI, Parthasarathy VA (2010) Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of Turmeric (Curcuma longa L.). Mol Biotechnol 44:140–147PubMedCrossRefGoogle Scholar
  164. Sim SC, Yu JK, Jo YK, Sorrells ME, Jung G (2009) Transferability of cereal EST–SSR markers to ryegrass. Genome 52:431–437PubMedCrossRefGoogle Scholar
  165. Simko I, Costanzo S, Haynes KG, Christ BJ, Jones RW (2004) Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach. Theor Appl Genet 108:217–224PubMedCrossRefGoogle Scholar
  166. Singh H, Deshmukh RK, Singh A, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK (2010) Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol Breed 25:359–364CrossRefGoogle Scholar
  167. Soranzo N, Provan J, Powell W (1999) An example of microsatellite length variation in the mitochondrial genome of conifers. Genome 42:158–161PubMedCrossRefGoogle Scholar
  168. Spigler RB, Lewers KS, Main DS, Ashman TL (2008) Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity 101:507–517PubMedCrossRefGoogle Scholar
  169. Spooner DM, Nunez J, Trujillo G, Mdel RH, Guzman F, Ghislain M (2007) Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Nat Acad Sci USA 104:19398–19403PubMedCrossRefGoogle Scholar
  170. Srinivas G, Satish K, Madhusudhana R, Seetharama N (2009) Exploration and mapping of microsatellite markers from subtracted drought stress ESTs in Sorghum bicolor (L.) Moench. Theor Appl Genet 118:703–717PubMedCrossRefGoogle Scholar
  171. Stagel A, Portis E, Toppino L, Rotino GL, Lanteri S (2008) Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics 9:357PubMedCrossRefGoogle Scholar
  172. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 114:823–839PubMedCrossRefGoogle Scholar
  173. Studer B, Asp T, Frei U, Hentrup S, Meally H, Guillard A, Barth S, Muylle H, Roldán-Ruiz I, Barre P, Koning-Boucoiran C, Stunnenberg GU, Dolstra O, Skøt L, Skøt KP, Turner LB, Humphreys MO, Kölliker R, Roulund N, Nielsen KK, Lübberstedt T (2008) Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.). Mol Breed 21:533–548Google Scholar
  174. Su CC, Zhai HQ, Wang CM, Sun LH, Wan JM (2006) SSR mapping of brown planthopper resistance gene Bph9 in Kaharamana, an Indica rice (Oryza sativa L.). Yi Chuan Xue Bao 33:262–268PubMedGoogle Scholar
  175. Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Kondo M, Fujimura M, Nunome T, Fukuoka H, Hirai M, Matsumoto S (2006) Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 173:309–319PubMedCrossRefGoogle Scholar
  176. Tamilkumar P, Jerlin R, Senthil N, Ganesan KN, Jeevan RJ, Raveendran M (2009) Fingerprinting of rice hybrids and their parental lines using microsatellite markers and their tilization in genetic purity assessment of hybrid rice. Res J Seed Sci 2:40–47CrossRefGoogle Scholar
  177. Tang J, Gao L, Cao Y, Jia J (2006) Homologous analysis of SSR-ESTs and transferability of wheat SSR-EST markers across barley, rice and maize. Euphytica 151:87–93CrossRefGoogle Scholar
  178. Tang J, Baldwin SJ, Jacobs JME, van der Linden CG, Voorrips RE, Leunissen JAM, Van EH, Vosman B (2008) Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics 9:374PubMedCrossRefGoogle Scholar
  179. Tang DQ, Lu JJ, Fang W, Zhang S, Zhou MB (2010) Development, characterization and utilization of GenBank microsatellite markers in Phyllostachys pubescens and related species. Mol Breed 25:299–311CrossRefGoogle Scholar
  180. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acid Res 17:6463–6471PubMedCrossRefGoogle Scholar
  181. Tautz D (1993) Notes on the definition and nomenclature of tandemly repetitive DNA sequences. In: Pena SDJ, Chakraborty R, Epplen JT, Jeffreys AJ (eds) DNA fingerprinting: state of the science. Birkhaiiser Verlag, Basel, pp 21–28Google Scholar
  182. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138PubMedCrossRefGoogle Scholar
  183. 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
  184. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  185. Trifonov EN (2003) Tuning function of tandemly repeating sequences: a molecular device for fast adaptation. In: Wasser SP (ed) Evolutionary theory and processes: nodern horizons, papers in honor of Eviatar Nevo. Kluwer, Amsterdam, pp 1–24Google Scholar
  186. Tyrka M, Perovic D, Wardynska A, Ordon F (2008) A new diagnostic SSR marker for selection of the Rym4/Rym5 locus in barley breeding. J Appl Genet 49:127–134PubMedCrossRefGoogle Scholar
  187. Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546PubMedGoogle Scholar
  188. Varshney RK, Graner A, Sorrells ME (2005a) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55PubMedCrossRefGoogle Scholar
  189. Varshney RK, Sigmund R, Borner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A (2005b) Interspecific transferability and comparative mapping of barley EST–SSR markers in wheat rye and rice. Plant Sci 168:195–202CrossRefGoogle Scholar
  190. Varshney RK, Thudi M, Aggarwal R, Börner A (2007) Genic molecular markers in plants: development and applications. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement: genomics approaches and platforms, vol 1. Springer, Dordrecht, pp 13–29CrossRefGoogle Scholar
  191. Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KHM, Town CD, Hoisington DA (2009) Comprehensive resource of drought- and salinity responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10:523PubMedCrossRefGoogle Scholar
  192. Vezzulli S, Troggio M, Coppola G, Jermakow A, Cartwright D, Zharkikh A, Stefanini M, Grando MS, Viola R, Adam-Blondon AF, Thomas M, This P, Velasco R (2008) A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers. Theor Appl Genet 117:499–511PubMedCrossRefGoogle Scholar
  193. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabean M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  194. Wang Z, Weber JL, Zhang G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6Google Scholar
  195. Wang ML, Huang L, Bongard-Pierce DK, Belmonte S, Zachgo EA, Morris JW, Dolan M, Goodman HM (1997) Construction of an approximately 2 Mb contig in the region around 80 cM of Arabidopsis thaliana chromosome 2. Plant J 12:711–730PubMedCrossRefGoogle Scholar
  196. Wang ML, Gillaspie AG, Newman ML, Dean RE, Pittman RN, Morris JB, Pederson GA (2004) Transfer of simple sequence repeat (SSR) markers across the legume family for germplasm characterization and evaluation. Plant Genet Resour 2:107–119CrossRefGoogle Scholar
  197. Wang ML, Barkley NA, Yu JK, Dean RE, Newman ML, Sorrells ME, Pederson GA (2005) Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet Resour 3:45–57CrossRefGoogle Scholar
  198. Wang ML, Chen ZB, Barkley NA, Newman ML, Kim W, Raymer P, Pederson GA (2006a) Characterization of seashore paspalum (Paspalum vaginatum Swartz) germplasm by transferred SSRs from wheat, maize and sorghum. Genet Resour Crop Evol 53:779–791CrossRefGoogle Scholar
  199. Wang ML, Mosjidis JA, Morris JB, Dean RE, Jenkins TM, Pederson GA (2006b) Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST–SSR markers. Genome 49:707–715PubMedCrossRefGoogle Scholar
  200. Wang ML, Morris JB, Barkley NA, Dean RE, Jenkins TM, Pederson GA (2007) Evaluation of genetic diversity of the USDA Lablab purpureus germplasm collection using simple sequence repeat markers. J Hort Sci Biotechnol 82:571–578Google Scholar
  201. Wang A, Zhang Q, Wan D, Yang Y, Liu J (2008a) Nine microsatellite DNA primers for Hippophae rhamnoides ssp. sinensis (Elaeagnaceae). Conserv Genet 9:969–971CrossRefGoogle Scholar
  202. Wang Y, Kang M, Huang H (2008b) Microsatellite loci transferability in chestnut. J Am Soc Hort Sci 133:692–700Google Scholar
  203. Wang JPM, Lee R, Goos RJ, Helms T (2008c) Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor Appl Genet 116:777–787PubMedCrossRefGoogle Scholar
  204. Wang ML, Barkley NA, Jenkins TM (2009a) Microsatellite markers in plants and insects. Part I. Applications of biotechnology. Genes Genomes Genomics 3:54–67Google Scholar
  205. Wang ML, Mosjidis JA, Morris JB, Chen ZB, Barkley NA, Pederson GA (2009b) Evaluation of Lespedeza germplasm genetic diversity and its phylogenetic relationship with the genus Kummerowia. Conserv Genet 10:79–85CrossRefGoogle Scholar
  206. Warrington CV, Zhu S, Parrott WA, All JN, Boerma HR (2008) Seed yield of near-isogenic soybean lines with introgressed quantitative trait loci conditioning resistance to corn earworm (Lepidoptera: Noctuidae) and soybean looper (Lepidoptera: Noctuidae) from PI 229358. J Eco Entomol 101:1471–1477CrossRefGoogle Scholar
  207. Weber JL (1990) Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms. Genomics 7:524–530PubMedCrossRefGoogle Scholar
  208. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396PubMedGoogle Scholar
  209. Weising K, Gardner RC (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42:9–19PubMedCrossRefGoogle Scholar
  210. Weising K, Nybom H, Wolff K, Meyer W (1995) DNA fingerprinting in plant and fungi. CRC Press, Boca RatonGoogle Scholar
  211. Woodhead M, Russell J, Squirrell J, Hollingsworth PM, Cardle L, Ramsay L, Gibby M, Powell W (2003) Development of EST–SSRs from the alpine lady-fern, Athyrium distentifolium. Mol Ecol Notes 3:287–290CrossRefGoogle Scholar
  212. Wu K, Jones R, Dannaeberger L, Scolnik PA (1994) Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res 22:3257–3258PubMedCrossRefGoogle Scholar
  213. Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME (2004a) Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805–818PubMedCrossRefGoogle Scholar
  214. Yu JK, La Rota M, Kantety RV, Sorrells ME (2004b) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742–751PubMedCrossRefGoogle Scholar
  215. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16PubMedCrossRefGoogle Scholar
  216. Zavodna M, Arens P, Van Dijk PJ, Vosman B (2005) Development and characterization of microsatellite markers for two dioecious Ficus species. Mol Ecol Notes 5:355–357CrossRefGoogle Scholar
  217. Zhang LY, Ravel C, Bernard M, Balfourier F, Leroy P, Feuillet C, Sourdille P (2006) Transferable bread wheat EST–SSRs can be useful for phylogenetic studies among the Triticeae species. Theor Appl Genet 113:407–418PubMedCrossRefGoogle Scholar
  218. Zhao XF, Sun WB, Yang JB, Meng J (2009) Isolation and characterization of 12 microsatellite loci for Michelia coriacea (Magnoliaceae), a critically endangered endemic to Southeast Yunnan China. Conserv Genet 10:1583–1585CrossRefGoogle Scholar
  219. Zietkiewitcz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Rajwant K. Kalia
    • 1
    • 4
  • Manoj K. Rai
    • 1
  • Sanjay Kalia
    • 2
  • Rohtas Singh
    • 1
  • A. K. Dhawan
    • 3
  1. 1.Plant Molecular Biology DivisionCentre for Plant BiotechnologyHisarIndia
  2. 2.NRC on Plant BiotechnologyNew DelhiIndia
  3. 3.Centre for Plant BiotechnologyHisarIndia
  4. 4.Botany and Plant SciencesUniversity of CaliforniaRiversideUSA

Personalised recommendations