Genetic Resources and Crop Evolution

, Volume 61, Issue 8, pp 1581–1596 | Cite as

Phenotypic characterization of the Miami World Collection of sugarcane (Saccharum spp.) and related grasses for selecting a representative core

  • James ToddEmail author
  • Jianping Wang
  • Barry Glaz
  • Sushma Sood
  • Tomas Ayala-Silva
  • Spurthi N. Nayak
  • Neil C. Glynn
  • Osman A. Gutierrez
  • David N. Kuhn
  • Mohammad Tahir
  • Jack C. Comstock
Research Article


The Saccharum L. genus includes important crops that are utilized for sugar and fuel production. The World Collection of Sugarcane and Related Grasses (World Collection) in Miami, FL contains diverse and potentially useful germplasm for this and related genera; however, this collection has been underutilized because little is known about the traits of its accessions. Our objectives were to phenotypically characterize the World Collection and select a representative core collection that could then be studied intensively. In total, eight morphological traits of the World Collection were evaluated three times in 1 year. A core of 300 accessions that included each species in the World Collection was selected by using the Maximization Strategy in MStrat software. The core had a higher diversity rating than random selections of 300 accessions. The Shannon–Weaver Diversity Index scores of the core and whole collection were similar indicating that the majority of the diversity was captured by the core collection. The ranges and medians between the core and World Collection were similar; only two of the trait medians were not significant at P = 0.05 using the non-parametric Wilcoxon method and the coincidence rate (CR % = 96.2) was high (>80) indicating that extreme values were retained. Thus, the phenotypic diversity of these traits in the World Collection was well represented by the core collection. Agronomic studies on the core should be useful for characterizing the World Collection and genes for useful traits should be available in the core collection.


Bioenergy Biofuel Core collection Diversity Energy cane Sugar cane yellow leaf virus 



This research was supported by the Office of Science (BER), U.S. Department of Energy. The authors wish to acknowledge the technical assistance of the following individuals in phenotypic evaluations: Miriam Baltazar, Velton Banks, Billy Cruz, Moiad Kanaan, Joseph Orsenigo, Matthew Paige, Leo Perez, Ken Peterkin, Kristen Polacik, Ricardo Ramirez, Jhonnie Tejeda, Juan Tejeda, and Liping Wang.


  1. Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet J, Koenig G, Ravel C, Mitrofanova O, Beckert M, Charmet G (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114:1265–1275PubMedCrossRefGoogle Scholar
  2. Basigalup DH, Barnes DK, Stucker RE (1995) Development of a core collection for perennial Medicago plant introductions. Crop Sci 35:1163–1168CrossRefGoogle Scholar
  3. Bisht IS, Mahajan RK, Patel DP (1998) The use of characterization data to establish the Indian mungbean core collection and assessment of genetic diversity. Genet Resour Crop Evol 45:127–133CrossRefGoogle Scholar
  4. Bull TA, Glasziou KT (1963) The evolutionary significance of sugar accumulation in Saccharum. Aust J Biol Sci 16:737–742Google Scholar
  5. Comstock JC, Schnell RJ,Miller JD (1995) Current status of the world sugarcane germplasm collection in Florida. In: Croft BJ, Piggin CM, Wallis ES, Hogarth DM (eds) Sugarcane germplasm conservation and exchange, 1996. ACIAR Proceedings No. 67, pp 17–18Google Scholar
  6. Comstock JC, Miller JD, Schnell RJ (2001) Incidence of sugarcane yellow leaf virus in clones maintained in the world collection of sugarcane and related grasses at the United States National Repository in Miami, Florida. Sugar Tech 3:128–133CrossRefGoogle Scholar
  7. Daniels J, Roach BT (1987) Taxonomy and evolution in sugarcane. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier Press, Amsterdam, pp 7–84CrossRefGoogle Scholar
  8. Davis MJ, Gillaspie AG, Vidaver AK, Harris RW (1984) Clavibacter: a new genus containing some phytopathogenic coryneform bacteria, including Clavibacter xyli subsp. xyli sp. nov., subsp. nov. and Clavibacter xyli subsp. cynodontis subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease. Int J Syst Bacteriol 34(2):107–117CrossRefGoogle Scholar
  9. Deren CW (1995) Genetic base of U.S. mainland sugarcane. Crop Sci 35:1195–1199CrossRefGoogle Scholar
  10. Dillon SL, Shapter FM, Henry RJ, Cordeiro G, Izquierdo L, Lee LS (2007) Domestication to crop improvement: genetic resources for sorghum and Saccharum (Andropogoneae). Ann Bot (London) 100:975–989CrossRefGoogle Scholar
  11. Edme SJ, Miller JD, Glaz B, Tai PYP, Comstock JC (2005) Genetic contribution to yield in the Florida sugarcane industry across 33 years. Crop Sci 45:92–97CrossRefGoogle Scholar
  12. Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman M, Buckler ES (2005) Maize association population: a high resolution platform for quantitative trait locus dissection. Plant J 44:1054–1064PubMedCrossRefGoogle Scholar
  13. Fufa H, Baenziger PS, Beecher BS, Dweikat I, Graybosch RA, Eskridge KM (2005) Comparison of phenotypic and molecular marker-based classification of hard red winter wheat cultivars. Euphytica 145:133–146CrossRefGoogle Scholar
  14. Gilbert RA, Rainbolt CR, Morris DR, Bennett AC (2007) Morphological responses of sugarcane to long-term flooding. Agron J 99:1622–1628CrossRefGoogle Scholar
  15. Glaz B, Morris DR, Daroub SH (2004) Periodic flooding and water table effects on two sugarcane genotypes. Agron J 96:832–838CrossRefGoogle Scholar
  16. Glynn NC, Dixon LJ, Castlebury LA, Szabo LJ, Comstock JC (2010) PCR assays for the sugarcane rust pathogens Puccinia kuehnii and P. melanocephala and detection of a SNP associated with geographic distribution in P. kuehnii. Plant Path 59:703–711CrossRefGoogle Scholar
  17. Goldemberg J (2008) The Brazilian biofuels industry. Biotechnol Biofuels 1:6PubMedCentralPubMedCrossRefGoogle Scholar
  18. Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: an algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. J Heredity 92:93–94CrossRefGoogle Scholar
  19. Gouesnard B, Dallard J, Bertin P, Boyat A, Charcosset A (2005) European maize landraces: genetic diversity, core collection definition and methodology of use. Maydica 50:225–234Google Scholar
  20. Heaton EA, Dohleman FG, Long SP (2008) Meeting US biofuel goals with less land: the potential of Miscanthus. Glob Chang Biol 14:2000–2014CrossRefGoogle Scholar
  21. Hennink S, Zeven AC (1990) The interpretation of Nei and Shannon-Weaver within population variation indices. Euphytica 51(3):235–240CrossRefGoogle Scholar
  22. Holbrook CC, Anderson WF, Pittman RN (1993) Selection of a core collection from the U.S. germplasm collection of peanuts. Crop Sci 33:859–861CrossRefGoogle Scholar
  23. Hu J, Zhu J, Xu HM (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101(1–2):264–268CrossRefGoogle Scholar
  24. Kaiser HF (1958) The Varimax criterion for analytic rotation in factor analysis. Psychometrika 23:187–200CrossRefGoogle Scholar
  25. Kaiser HF (1970) A second generation Little Jiffy. Psychometrika 35:401–415CrossRefGoogle Scholar
  26. Kalita J, Gupta MK (2001) Pubescence in sugarcane as a plant resistance character affecting oviposition of Plassey borer Chilo tumidicostalis Hmpsn (Lepidoptera Crambidae). Co-op Sugar 33(1):35–38Google Scholar
  27. Lee K, Daniels MJ (2008) Marginalized models for longitudinal ordinal data with application to quality of life studies. Stat Med 27(21):4359–4380PubMedCentralPubMedCrossRefGoogle Scholar
  28. Li Y, Shi Y, Cao Y, Wang T (2005) Establishment of a core collection for maize germplasm preserved in Chinese National Genebank using geographic distribution and characterization data. Genet Resour Crop Evol 51(8):845–852CrossRefGoogle Scholar
  29. McCray MJ, Newman PR, Rice RW, Ezenwa IV (2011) Sugarcane leaf tissue sample preparation for diagnostic analysis. Florida Cooperative Extension Service Pub. SS-AGR-259. ( Accessed 17 Mar 2014
  30. McKhann HI, Camilleri C, Berard A, Bataillon T, David JL, Le Reboud X, Corre V, Caloustian C, Gut IG, Brunel D (2004) Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J 38:193–202PubMedCrossRefGoogle Scholar
  31. Pandiyan M, Senthil N, Packiaraj D, Jagadeesh S (2012) Greengram germplasm for constituting of core collection. Wudpecker J Agric Res 1(6):223–232Google Scholar
  32. Park HM (2008) Univariate analysis and normality test using SAS, Stata, and SPSS. Working Paper. The University Information Technology Services (UITS Center for Statistical and Mathmatical Computing, Indiana University. Accessed 27 Aug 12 2013
  33. Perera MF, Arias ME, Costilla D, Luque AC, García MB, Romero CD, Racedo J, Ostengo S, Filippone MP, Cuenya MI, Castagnaro AP (2012) Genetic diversity assessment and genotype identification in sugarcane based on DNA markers and morphological traits. Euphytica 185:491–510CrossRefGoogle Scholar
  34. Perlack RD, Wright LL, Turhollow AF, Graham RL, Stokes BJ, Erbach DC (2005) Biomass as feedstock for a bioenergy and bioproducts industry: The technical feasibility of a billion-ton annual supply DOE/GO-102005-2135 and ORNL/TM-2005/66. Accessed 27 Jun 6 2013. NTIS, Springfield, VA
  35. Rott P, Bailey RA, Comstock JC, Craft BJ, Saumtally AS (2000) A guide to sugarcane diseases. CIRAD Publication Services, MontepellierGoogle Scholar
  36. SAS Institute Inc (2011) SAS OnlineDoc 9.3. SAS Institute Inc, CaryGoogle Scholar
  37. Schenck S, Hu JS, Lockhart BE (1997) Use of a tissue blot immunoassay to determine the distribution of sugarcane yellow leaf virus in Hawaii. Sugar Cane 4:5–8Google Scholar
  38. Singh S, Rao PN (1987) Varietal differences in growth characteristics in sugar cane. J Agric Sci 108(01):245–247CrossRefGoogle Scholar
  39. Tai PYP (1981) Freezing cold-tolerant parental clones of sugarcane. Agron J 73:423–426CrossRefGoogle Scholar
  40. Tai PYP, Miller JD (2001) A core collection for Saccharum spontaneum L. from the world collection of sugarcane. Crop Sci 41:879–885CrossRefGoogle Scholar
  41. Tew TL, Cobill RM (2008) Genetic improvement of sugarcane (Saccharum spp.) as an energy crop. In: Vermerris W (ed) Genetic improvement of bioenergy crops. Springer, New York, pp 249–272Google Scholar
  42. Union for the Protection of New Varieties of Plants (UPOV) (2005) Guidelines for the conduct of test for distinctness, uniformity, and stability. Accessed 17 Mar 2014
  43. Upadhyaya HD, Ortiz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102:1292–1298CrossRefGoogle Scholar
  44. Viswanathan R, Rao GP (2011) Disease scenario and management of major sugarcane diseases in India. Sugar Technol 13:336–353CrossRefGoogle Scholar
  45. Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM (2010) Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J 8:263–276PubMedCrossRefGoogle Scholar
  46. White WH, Tew TL, Richard EP Jr (2006) Association of sugarcane pith, rind hardness, and fiber with resistance to the sugarcane borer. J Am Soc Sugar Cane Technol 26:87–100Google Scholar
  47. Zhang H, Zhang D, Wang M, Sun J, Qi Y, Li J, Wei X, Han L, Qiu Z, Tang S, Li Z (2011) A core collection and mini core collections of Oryza sativa L. in China. Theor Appl Genet 122:49–61PubMedCrossRefGoogle Scholar
  48. Zhao D, Glaz B, Comstock JC (2010) Sugarcane response to water-deficit stress during early growth on organic and sand soils. Am J Agric Biol Sci 5(3):403CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2014

Authors and Affiliations

  • James Todd
    • 1
    Email author
  • Jianping Wang
    • 2
  • Barry Glaz
    • 1
  • Sushma Sood
    • 1
  • Tomas Ayala-Silva
    • 3
  • Spurthi N. Nayak
    • 6
  • Neil C. Glynn
    • 4
  • Osman A. Gutierrez
    • 3
  • David N. Kuhn
    • 3
  • Mohammad Tahir
    • 5
  • Jack C. Comstock
    • 1
  1. 1.USDA-ARS Sugarcane Field StationCanal PointUSA
  2. 2.Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics InstituteUniversity of FloridaGainesvilleUSA
  3. 3.USDA-ARS Subtropical Horticulture Research StationMiamiUSA
  4. 4.Syngenta Seeds, Inc.LongmontUSA
  5. 5.Sugar Crops Research InstituteMardan, Khyber PakhtunkhwaPakistan
  6. 6.Agronomy Department, Genetics InstituteUniversity of FloridaGainesvilleUSA

Personalised recommendations