Cross-taxon transferability of sugarcane expressed sequence tags derived microsatellite (EST-SSR) markers across the related cereal grasses

  • Ram Baran SinghEmail author
  • Balwant Singh
  • Ram Kushal Singh
Original Article


Sugarcane is a crop of economic importance providing sugar and bioenergy resource which has a substantial contribution to the national GDP of India as well as other countries. Genomes of the several grasses have co-evolved which share large-scale synteny and genome collinearity; hence it is possible to employ EST-SSR markers of one grass species for genetic study of other related species. A set of sixty potentially informative EST-derived microsatellite (SSR) markers were employed to examine their cross-taxa transferability across the limit of taxonomic boundaries of different grass genomes. The high (96.6%) rate of SSRs cross-transferability observed in genus Saccharum followed by Erianthus (93.3%), Narenga (88.3%), Sclerostachya (86.3%), and Miscanthus (83.3%). Relatively lower rates of cross amplification were observed in other cereal crops including Sorghum bicolor, Pennisetum glaucum, Zea mays, Triticum aestivum, Oryza sativa, and Avena sativa. Cross-transferable EST-SSR markers were utilized to evaluate phylogenetic relationships among genus Saccharum, closely related genera of Saccharum complex, and other allied cereal grasses. The polymorphic information content values ranged from 0.35 to 0.95, with an average of 0.71. Such a high rates of cross-taxa transferability of the EST-SSRs make them a potent tool for genetic studies and comparative genomics across wide evolutionary distances within and across genera along with technologically simplicity and cost effectiveness. EST-SSRs will facilitate to devise potent tools for genetic improvement through advance molecular breeding of such crops for high grain productivity and better quality. They will especially be useful for the orphan grass species, which contribute a major part of the global food security.


Expressed sequence tags (ESTs) Saccharum complex Saccharum species Saccharum related genera Genetic diversity Cross-taxa transferability 



Expressed sequence tags derived simple sequence repeats


Food and Agriculture Organization of the United Nations-Statistics Division

5′ UTR

Five prime untranslated regions

3′ UTR

Three prime untranslated regions


Heterogeneous nuclear RNA


MIcroSAtellite Identification Tool



Authors are thankful to Director, Sugarcane Research Institute, Shahjahanpur, India for conferring necessary accessories to perform this study.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest directly or indirectly and informed consent to publish this study.

Supplementary material

13562_2019_502_MOESM1_ESM.docx (26 kb)
Supplementary material 1 (DOCX 25 kb)


  1. Aggarwal RK, Prasad SH, Varshney RK, Prasanna R, Bhat KV, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372CrossRefGoogle Scholar
  2. Aitken KS, Jackson PA, McIntyre CL (2005) A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor Appl Genet 110:789–801CrossRefGoogle Scholar
  3. Bennetzen JL, Freeling M (1993) Grasses as a single genetic system: genome composition, co-llinearity and compatibility. Trends Genet 9:259–261CrossRefGoogle Scholar
  4. Besse P, McIntyre CL, Berding N (1997) Characterisation of Erianthus sect. Ripidium and Saccharum germplasm (Andropogoneae-Saccharinae) using RFLP markers. Euphytica 93:283–292CrossRefGoogle Scholar
  5. Brandes EW (1958) Origin, classification and characteristics. In: Artschwager E, Brandes EW (eds) Sugarcane (Saccharum officinarum L.), vol 122. US department of agriculture handbook. U.S. Government Print Office, Washington, D.C, pp 1–35Google Scholar
  6. Burnquist WL, Sorrells ME, Tanksley SD (1995) Characterization of genetic variability in Saccharum germplasm by means of Restriction Fragment Length Polymorphism (RFLP) analysis. Proc Int Soc Sugarcane Technol 21:355–365Google Scholar
  7. 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 8:97. CrossRefGoogle Scholar
  8. Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera MT, Vendramin GG, Garcia V, Frigerio JM, Echt C, Richardson T (2004) Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 109:1204–1214CrossRefGoogle Scholar
  9. Chandra A, Jain R, Soloman S, Srivastava S, Roy AK (2013) Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses. BMC Res Notes 6:47CrossRefGoogle Scholar
  10. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722CrossRefGoogle Scholar
  11. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and sorghum. Plant Sci 160:1115–1123CrossRefGoogle Scholar
  12. Daniels J, Smith P, Panton N, Williams CA (1975) The origin of the genus Saccharum. Sugarcane Breed. Newsl 36:24–39Google Scholar
  13. Dayanandan S, Bawa KS, Kesseli R (1997) Conservation of microsatellites among tropical trees (Leguminosae). Am J Bot 84:1658–1663CrossRefGoogle Scholar
  14. D’Hont A, Glaszman JC (2001) Sugarcane genome analysis with molecular markers, a first decade of research. Proc Int Soc Sugarcane Technol 24:556–559Google Scholar
  15. Dirlewanger E, Cosson P, Tavaud M, Aranzana MJ, 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 105:127–138CrossRefGoogle Scholar
  16. Disasa T, Feyissa T, Sertse D (2016) Transferability of sorghum microsatellite markers to bamboo and detection of polymorphic markers. Open Biotech J 10:223–233CrossRefGoogle Scholar
  17. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  18. Dufour P, Grivet L, D’Hont A, Deu M, Trouche G, Glaszmann JC, Hamon P (1996) Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane. Theor Appl Genet 92:1024–1030CrossRefGoogle Scholar
  19. FAOSTAT (2014) Food and Agricultural Organisation of the United Nations. Accessed 30 Apr 2018
  20. Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140:1183–1191CrossRefGoogle Scholar
  21. Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96:82658270CrossRefGoogle Scholar
  22. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971–1974CrossRefGoogle Scholar
  23. Gao LZ, Zhang CH, Jia JZ (2005) Cross-species transferability of rice microsatellites in its wild relatives and the potential for conservation genetic studies. Genet Resour Crop Evol 52:931–940CrossRefGoogle Scholar
  24. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809–6814CrossRefGoogle Scholar
  25. Grivet L, Arruda P (2002) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5:122–127CrossRefGoogle Scholar
  26. Hampl V, Pavlicek A, Flegr J (2001) Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with a freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Microbiol 51:731–735CrossRefGoogle Scholar
  27. Hancock JM (1999) Microsatellites and other simple sequences: genomic context and mutational mechanisms. In: Goldstein DB, Schlötterer C (eds) Microsatellites: evolution and applications. Oxford University Press, OxfordGoogle Scholar
  28. Ilic K, SanMiguel PJ, Bennetzen JL (2003) A complex history of rearrangement in and orthologous region of the maize, sorghum, and rice genomes. Proc Natl Acad Sci USA 100(21):12265–12270CrossRefGoogle Scholar
  29. Jarne P, Lagoda PJL (1996) Microsatellites from molecules to population and back. Trends Mol Ecol 11:424–429CrossRefGoogle Scholar
  30. Kandel R, Singh HP, Singh BP, Harris-Shultz KR, Anderson WF (2016) Assessment of genetic diversity in Napier grass (Pennisetum purpureum Schum.) using microsatellite, single-nucleotide polymorphism and insertion-deletion markers from pearl millet (Pennisetum glaucum L). Plant Mol Biol Rep 34:265–272CrossRefGoogle Scholar
  31. 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 48:501–510CrossRefGoogle Scholar
  32. Kuleung C, Baenziger PS, Dweikat I (2004) Transferability of SSR markers among wheat, rye, and triticale. Theor Appl Genet 108:1147–1150CrossRefGoogle Scholar
  33. Kumar R, Appunu C, Anna Durai A, Premachandran MN, Viola VR, Ram B, Mahadevaiah C, Meena MR, Manjunatha T (2015) Genetic confirmation and field performance comparison for yield and quality among advanced generations of Erianthus arundinaceus, E. bengalense and Saccharum spontaneum cyto-nuclear genome introgressed sugarcane intergeneric hybrids. Sugar Tech 17:379–385CrossRefGoogle Scholar
  34. Kumar S, Parekh MJ, Patel CB, Zala HN, Sharma R, Kulkarni KS, Fougat RS, Bhatt RK, Sakure AA (2016) Development and validation of EST-derived SSR markers and diversity analysis in cluster bean (Cyamopsis tetragonoloba). J Plant Biochem Biotech 25:263–269CrossRefGoogle Scholar
  35. Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Biotechnology 12:276–278CrossRefGoogle Scholar
  36. Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007CrossRefGoogle Scholar
  37. Li L, Wang J, Guo Y, Jiang F, Xu Y, Wang Y, Pan H, Han G, Li R, Li S (2008) Development of SSR markers from ESTs of gramineous species and their chromosome location on wheat. Prog Nat Sci 18:1485–1490CrossRefGoogle Scholar
  38. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J (2000) An optimized protocol for analysis of EST sequences. Nucleic Acids Res 28:3657–3665CrossRefGoogle Scholar
  39. 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 Human Genet 44:397–401Google Scholar
  40. Lorieux M, Rami JF, Glaszmann JC, Grivet L (2001) A direct comparison between the genetic maps of sorghum and rice. Theor Appl Genet 102:379–386CrossRefGoogle Scholar
  41. Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Povan J, Powell W, Waugh R (1997) Comparison of PCR-based marker system the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136CrossRefGoogle Scholar
  42. Nair NV, Nair S, Sreenivasan TV, Mohan M (1999) Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers. Genet Resour Crop Evol 46:73–79CrossRefGoogle Scholar
  43. Oliveira KM, Pinto LR, Marconi TG, Mollinari M, Ulian EC, Chabregas SM, Falco MC, Burnquist W, Garcia AA, Souza AP (2009) Characterization of new polymorphic functional markers for sugarcane. Genome 52:191–209CrossRefGoogle Scholar
  44. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. J Comp Appl Biosc 12:357–358Google Scholar
  45. Pandey G, Misra G, Kumari K, Gupta SA, Parida SK, Chattopadhyay DE, Prasad MA (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20:197–207CrossRefGoogle Scholar
  46. Parekh MJ, Kumar S, Zala HN, Fougat RS, Patel CB, Bosamia TC, Kulkarni KS, Parihar A (2016) Development and validation of novel fiber relevant dbEST–SSR markers and their utility in revealing genetic diversity in diploid cotton (Gossypium herbaceum and G. arboreum). Ind Crops Prod 83:620–629CrossRefGoogle Scholar
  47. Parida SK, Rajkumar KA, Dalal V, Singh NK, Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theor Appl Genet 112:808–817CrossRefGoogle Scholar
  48. Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338CrossRefGoogle Scholar
  49. Parida SK, Pandit A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T (2010) Functionally relevant microsatellites in sugarcane unigenes. BMC Plant Biol 10:251CrossRefGoogle Scholar
  50. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidizaion predating divergence of the cereals and its consequences for comparative genomics. Proc Natl Acad Sci 101:9903–9908CrossRefGoogle Scholar
  51. Pinto LR, Oliveira KM, Marconi T, Garcia AA, Ulian EC, De Souza AP (2006) Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breed 125:378–384CrossRefGoogle Scholar
  52. Powell W, Morgante R, Andre C, Hanafey M, Vogel J, Tingey S, Rafalsky A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238CrossRefGoogle Scholar
  53. Ramu P, Kassahun B, Senthilvel S, Kumar AC, Jayashree B, Folkertsma RT, Ananda Reddy L, Kuruvinashetti MS, Haussmann BIG, Hash CT (2009) Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map. Theor Appl Genet 119:1193–1204CrossRefGoogle Scholar
  54. Saha MC, Mian MAR, Eujayl I (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791CrossRefGoogle Scholar
  55. Selvi A, Nair NV, Balasundaram MT (2003) Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome 46:394–403CrossRefGoogle Scholar
  56. Selvi A, Nair NV, Noyer JL, Singh NK, Balasundaram N, Bansal KC, Koundal KR, Mohapatra T (2006) AFLP analysis of the phonetic organization and genetic diversity in the sugarcane complex, Saccharum and Erianthus. Genet Resour Crop Evol 53:831–842CrossRefGoogle Scholar
  57. Selvi A, Mukunthan N, Shanthi RM, Govindaraj P, Singaravelu B, Karthik Prabu T (2008) Assessment of genetic relationships and marker identification in sugarcane cultivars with different levels of top borer resistance. Sugar Tech 10:53–59CrossRefGoogle Scholar
  58. 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 51:91–103CrossRefGoogle Scholar
  59. Sim SC, Yu JK, Jo Y, Sorrells ME, Jung G (2009) Transferability of cereal EST-SSR markers to ryegrass. Genome 52:431–437CrossRefGoogle Scholar
  60. Singh NK, Raghuvanshi S, Srivastava SK, Gaur A, Pal AK et al (2004) Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct Integr Genomics 4:102–117CrossRefGoogle Scholar
  61. Singh RK, Singh RB, Singh SP, Sharma ML (2011) Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes. Euphytica 182:335–354CrossRefGoogle Scholar
  62. Singh RK, Singh RB, Singh SP, Sharma ML (2012) Genes tagging and molecular diversity of red rot susceptible/tolerant sugarcane cultivars using c-DNA and unigene derived markers. World J Microbiol Biotech 28:1669–1679CrossRefGoogle Scholar
  63. Singh RK, Jena SN, Khan S, Yadav S, Banarjee N, Raghuvanshi S, Bhardwaj V, Dattamajumder SK, Kapur R, Solomon S, Swapna M (2013a) Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene 524:309–329CrossRefGoogle Scholar
  64. Singh RK, Singh RB, Singh SP, Mishra N, Rastogi J, Sharma ML, Kumar A (2013b) Genetic diversity among the Saccharum spontaneum clones and commercial hybrids through SSR markers. Sugar Tech 15:109–115CrossRefGoogle Scholar
  65. Singh RB, Srivastva S, Verma AK, Singh B, Singh RK (2014a) Importance and progress of microsatellite markers in Sugarcane (Saccharum spp. hybrids). Ind J Sugar Techno 29:1–12Google Scholar
  66. Singh RB, Srivastava S, Rastogi J, Gupta GN, Tiwari NN, Singh B, Singh RK (2014b) Molecular markers: exploited in crop improvement practices. Res Environ Life Sci 7:223–232Google Scholar
  67. Singh RB, Singh B, Singh RK (2015) Development of microsatellite (SSRs) markers and evaluation of genetic variability within sugarcane commercial varieties (Saccharum spp. hybrids). Int J Adv Res 3:700–708Google Scholar
  68. Singh RB, Singh B, Singh RK (2017) Study of genetic diversity of sugarcane (Saccharum) species and commercial varieties through TRAP molecular markers. Ind J Plant Physiol 22:332–338CrossRefGoogle Scholar
  69. Singh RB, Singh B, Singh RK (2018) Evaluation of genetic diversity in Saccharum species clones and commercial varieties employing molecular (SSRs) and physiological markers. Ind J Plant Genet Resour 31:17–26CrossRefGoogle Scholar
  70. Singh RB, Singh B, Singh RK (2019) Development of potential dbEST-derived microsatellite markers for genetic evaluation of sugarcane and related cereal grasses. Ind Crops Prod 128:38–47CrossRefGoogle Scholar
  71. Sreenivasan TV, Ahloowalia BS, Heinz DJ (1987) Cytogenetics. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, AmsterdamGoogle Scholar
  72. Suman A, Kimbeng CA, Edme SJ, Veremis J (2008) Sequence-related amplified polymorphism (SRAP) markers for assessing genetic relationships and diversity in sugarcane germplasm collections. Plant Gene Resour 6:222–231CrossRefGoogle Scholar
  73. 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 Bio Lett 7:537–546Google Scholar
  74. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotech 23:48–55CrossRefGoogle Scholar
  75. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH (1989) Data of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86:6201–6205CrossRefGoogle Scholar
  76. Zala HN, Kulkarni KS, Bosamia TC, Shukla YM, Kumar S, Fougat RS, Patel A (2017) Development and validation of EST derived SSR markers with relevance to downy mildew (Sclerospora graminicola Sacc.) resistance in pearl millet [Pennisetum glaucum (L.) R. Br.]. J Plant Biochem Biotech 26:356–365CrossRefGoogle Scholar
  77. Zeid M, Yu JK, Goldowitz I, Denton ME, Costich DE, Jayasuriya CT, Saha M, Elshire R, Benscher D, Breseghello F, Munkvold J (2010) Cross-amplification of EST-derived markers among 16 grass species. Field Crops Res 118:28–35CrossRefGoogle Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.I.K. Gujral Punjab Technical UniversityJalandharIndia
  2. 2.Swami Satyanand College of Management and TechnologyAmritsarIndia
  3. 3.Sugarcane Research InstituteUttar Pradesh Council of Sugarcane ResearchShahjahanpurIndia

Personalised recommendations