Genetic diversity assessment and genotype identification in sugarcane based on DNA markers and morphological traits

Euphytica

Volumn 185, Issue 3, 2012, Pages 491-510

  Perera, M F ^a   Arias, M E ^b   Costilla, D ^a   Luque, A C ^b   Garcia M B ^a   Romero, C Díaz ^a   Racedo, J ^a   Ostengo, S ^a   Filippone, M P ^a   Cuenya, M I ^a   Castagnaro, A P ^a  

^a Estacion Experimental Agroindustrial Obispo Colombres   (Argentina)

^b UNIVERSIDAD NACIONAL DE TUCUMÁN   (Argentina)

Author keywords

AFLP; Breeding program; Morphological descriptors; Similarity coefficient; SSR; Sugarcane germplasm bank

Indexed keywords

EID: 84861228155     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-012-0661-9     Document Type: Article

References (73)

1. Ahmed MA, Cuenya MI, García MB, Díaz Romero C (2007) Dinámica y características del recambio de variedades de caña de azúcar en tucumán desde las primeras décadas del siglo xx hasta la actualidad. Avance Agroindustrial 28: 17-22.
2. Aljanabi SM, Forget L, Dookun A (1999) An improved and rapid protocol for the isolation of polysaccharide and polyphenol-free sugarcane DNA. Plant Mol Biol Rep 17: 1-8.
3. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36(1): 181-186.
4. Angiolillo AM, Mencuccini M, Baldoni L (1999) Olive genetic diversity assessed using amplified fragment length polymorphisms. TAG 98: 411-421.
5. Arro JA (2004) Genetic diversity among sugarcane clones using target region amplification polymorphism (TRAP) markers and pedigree relationships. Master of Science Thesis, Agronomy & Environmental Management.
6. Balzarini M, Di Rienzo J (2003) Info-gen: software para análisis estadístico de datos genéticos. Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Argentina.
7. Balzarini M, Arroyo A, Bruno C, Di Renzo J (2006) Análisis de datos de marcadores con Info-gen. XXXV Congreso Argentino de Genética, San Luis.
8. Barret BA, Kidwell KK (1998) Comparison of AFLP and pedigree-based genetic diversity assessment methods using wheat cultivars from the Pacific Northwest. Crop Sci 38: 1271-1278.
9. Besse PG, Taylor B, Carroll N, Berding D, Burner CL (1998) Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis. Genetica 104: 143-153.
10. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3): 314-331.
11. Breaux RD, Legendre BL (1983) The USDA commercial breeding program in Louisiana. Proc Inter Am Sugar Cane Sem Var Breed III: 99-105.
12. Bremer G (1961a) Problems in breeding and cytology of sugarcane. Euphytica 10: 59-78.
13. Bremer G (1961b) Cytological crossing research of sugar cane. Euphytica 10: 229-243.
14. Budak H, Shearman RC, Parmaksiz I, Gaussoin RE, Riordan TP, Dweikat I (2004) Molecular characterization of buffalograss germplasm using sequence-related amplified polymorphism markers. TAG 108(2): 328-334. doi: 10. 1007/s00122-003-1428-4.
15. Caetano-Anollés G, Gresshoff PM (1994) Staining nucleic acids with silver: an alternative to radioisotopic and fluorescent labeling. Promega Notes Mag 45: 13.
16. Chang YS, Lo CC (1993) Genetic relationship among major sugar cane cultivars in Taiwan. Rep Taiwan Sugar Res Inst 140: 1-10.
17. Coburn JR, Temnykh SV, Paul EM, McCouch SR (2002) Design and application of microsatellite marker panels for semiautomated genotyping of rice (Oryza sativa L.). Crop Sci 42: 2092-2099.
18. Cordeiro GM (2001) Molecular marker systems for sugarcane germplams analysis, Chap. 9. In: Henry RJ (ed) Plant genotyping, the DNA fingerprinting of plants. Cabi publishing, Wallingford.
19. Cordeiro GM, Taylor GO, Henry RJ (2000) Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species. Plant Sci 155(2): 161-168.
20. 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(6): 1115-1123.
21. Cordeiro GM, Pan YB, Henry RJ (2003) Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Sci 165: 181-189.
22. Cox TS, Kiang YT, Gorman MB, Rogers DM (1985) Relationships between coefficient of parentage and genetic similarity indices in the soybean. Crop Sci 25: 529-532.
23. Cuenya MI, Ostengo S, Chavanne ER, Espinosa MA, Costilla DD, Ahmed MA (2009) Relevamiento de la distribución de variedades comerciales y de la aplicación de otras tecnologías en el área de cultivo de la provincia de Tucumán: Campaña 2007-2008. Gacetilla Agroindustrial EEAOC 72.
24. Cuenya MI, Chavanne ER, Ostengo S, Garcia MB, Ahmed M, Costilla DD, Diaz Romero C, Espinosa MA, Delgado N, Diaz JV (2011) TUC 95-10: una nueva variedad de caña de azúcar altamente productiva. Gacetilla Agroindustrial EEAOC 75.
25. Da Silva JA, Bressiani JA (2005) Sucrose synthase molecular marker associated with sugar content in elite sugarcane progeny. Genet Mol Biol 28(2): 294-298. doi: 10. 1590/S1415-47572005000200020.
26. Degani C, Rowland LJ, Saunders JA, Hokanson SC, Ogden E, Golan-Goldrish A, Galetta GL (2001) A comparison of genetic relationship measures in strawberry (Fragaria ananassa duch.) based on AFLP, RAPDs and pedigree data. Euphytica 117: 1-12.
27. Demey JR, Zambrano AY, Fuenmayor F, Segovia V (2003) Relación entre caracterizaciones molecular y morfológica en una colección de yuca. Interciencia 28(12): 684-689.
28. Deren CW (1995) Genetic base of U. S. mainland sugar cane. Crop Sci 35: 1195-1199.
29. D'Hont A, Rao PS, Feldman P, Grivet LN, Islam-Faridi N, Taylo P, Glaszmann JC (1995) Identification and characterization of sugarcane intergereric hybrids, Saccharum officinarum × Eriantus arudinaceus, with molecular markers and DNA in situ hybridisation. TAG 91: 320-326.
30. D'Hont A, Seshagiri Rao P, Alleyne S, Glaszmann JC, Feldmann P (1997) Application of molecular markers in sugarcane breeding. Proceedings West Indies sugar technologists, pp 77-79.
31. Di Rienzo JA, Casanoves F, Balzarini MG, Gonzalez L, Tablada M, Robledo CW (2010) InfoStat versión 2009. Grupo InfoStat, FCA, Universidad Nacional de Córdoba, Argentina.
32. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26: 297-302.
33. Durán LA, Blair MW, Giraldo MC, Macchiavelli R, Prophete E, Nin JC, Beaver JS (2005) Morphological and molecular characterization of common bean landraces and cultivars from the Caribbean. Crop Sci 45: 1320-1328.
34. Gallacher DJ (1997) Optimised descriptors recommended for Australian sugarcane germplasm (Saccharum spp. Hybrid). Aust J Agric Res 48(6): 775-779.
35. García MG, Ontivero M, Díaz Ricci JC, Castagnaro AP (2002) Morphological traits and high resolution rapd markers for the identification of the main strawberry varieties cultivated in Argentina. Plant Breed 121: 76-80.
36. Gillet EM (1991) Genetic analysis of nuclear DNA restriction fragment patterns. Genome 34(5): 693-703.
37. Graner A, Ludwig WF, Melchinger AE (1994) Relationships among European barley germplasm. II. Comparisons of RFLP and pedigree data. Crop Sci 34: 1199-1205.
38. Heinz DJ (1987) Sugarcane improvement through breeding. Elsevier, Amsterdam 603 pp.
39. Hill MH, Witsenboer M, Zabeau P, Vos R, Kesseli R, Michelmore R (1996) PCR-based fingerprinting using AFLPs as a tool for studying genetic relationships in Lactuca spp. TAG 93: 1202-1210.
40. Junjian N, Colowit PM, Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42: 601-607.
41. Kempthorne O (1957) An introduction to genetic statistics. Wiley, New York.
42. Lima ML, Garcia AA, Oliveira KM, Matsuoka S, Arizono H, De Souza CL Jr, De Souza AP (2002) Analysis of genetic similarity detected by aflp and coefficient of parentage among genotypes of sugar cane (Saccharum spp.). TAG 104(1): 30-38.
43. Link W, Dixkens C, Singh M (1995) Genetic diversity in European and Mediterranean faba bean germplasm revealed by RAPD markers. TAG 90: 27-32.
44. Lu YH, D′Hont A, Paulet F, Grivet L, Arnaud M, Glaszmann JC (1994) Molecular diversity and genome structure in modern sugarcane varieties. Euphytica 78: 217-226.
45. Machado JR, Walker DI, Bressiani JA, Goncalves A, da Silva J (1995) Emasculation of sugarcane tassels using hot water. Proc ISSCT 22: 346-348.
46. Manifesto MM, Schlatter AR, Hopp HE, Suarez EY, Dubcovsky J (2001) Quantitative evaluation of genetic diversity in wheat germplasm using molecular markers. Crop Sci 41: 682-690.
47. Manigbas NL, Villegas LC (2004) Microsatellite markers in hybridity tests to identify true hybrids of sugarcane. Phil Crop Sci 29: 23-32.
48. Martínez L, Cavagnaro P, Masuelli R, Rodriguez J (2005) Evaluation of diversity among Argentine grapevine (Vitis vinifera L.) varieties using morphological data and AFLP markers. Elect J Biotechnol 6: 37-45.
49. Maughan PJ, Saghai MA, Maroof GR, Buss GR, Huestis GM (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis. TAG 93: 392-401.
50. McIntyre CL, Jackson PA (2001) Low level of selfing found in a sample of crosses in Australian sugarcane breeding programs. Euphytica 117: 245-249.
51. Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants-salient statistical tools and considerations. Crop Sci 43: 1235-1248.
52. Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14: 384-394.
53. Nagai C (1984) Emasculation of sugarcane tassels by hot water. Am Rept HSPA 3-4.
54. Paul S, Wachira FN, Powell W, Waugh R (1997) Diversity and genetic differentiation among populations of India and Kenyan tea [Camellia sinensis (L) O. Kuntze] revealed by AFLP-markers. TAG 94: 255-263.
55. Plaschke J, Ganal MW, Roder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. TAG 91: 1001-1007.
56. Powell W, Machray G, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1: 215-222.
57. Queme JL, Molina L, Melgar M (2005) Analysis of genetic similarity among 48 sugarcane varieties using microsatellite DNA sequences. Proc ISSCT 25: 592-595.
58. Rohlf FJ (1993) Ntsys-pc. Version 2. 0. Applied biostatistics inc., Exeter Software, New York.
59. Salem KFM, El-Zanaty AM, Esmail RM (2008) Assessing wheat (Triticum aestivum L.) genetic diversity using morphological characters and microsatallite markers. World J Agric Sci 4(5): 538-544.
60. SAS Institute (2003) SAS/STAT release 9. 1. SAS Inst., Cary, NC.
61. Schut JW, Qi X, Stam P (1997) Association between relationship measures based on AFLP markers, pedigree data and morphological traits in barley. Theor Appl Genet 95: 1161-1168.
62. Selvi A, Nair NV, Balasundaram N, Mohapatra T (2003) Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome 46: 394-403.
63. Semagn K (2002) Genetic relationships among ten endod types as revealed by a combination of morphological, RAPD and AFLP markers. Hereditas 137: 149-156.
64. Smith S, Luk S, Sobral B, Muhawish S, Peleman J, Zabeau M (1994) Associations among inbred lines of maize using rflp and DNA amplification technologies (AFLP and AP-PCR), and correlations with pedigree, f1 yield and heterosis. Maize Genet Newslett 68: 45.
65. Sneath PHA, Sokal RR (1973) Numerical taxonomy. W. Freeman, San francisco 573 pp.
66. Souza E, Sorrells ME (1989) Pedigree analysis of North American oat cultivars released from 1951 to 1985. Crop Sci 29: 595-601.
67. Tinker NA, Fortin MG, Mather DE (1993) Random amplified polymorphic DNA and pedigree relationships in spring barley. Theor Appl Genet 85: 976-984.
68. Union for the Protection of New Varieties of Plants (UPOV) (2005) Directrices para la ejecución del examen de la distinción, la homogeneidad y la estabilidad tg/186/1. www.Upov.Int/es/publications/tg-rom/tg186/tg_186_1.Pdf.
69. Vettore AL, da Silva FR, Kemper EL, Arruda P (2001) The Libraries that made SUCEST. Genet Mol Biol 24: 1-7.
70. Vollmann J, Grausgruber H, Stift G, Dryzhyruk V, Lelley T (2005) Genetic diversity in camelina germplasm as revealed by seed quality characteristics and RAPD polymorphism. Plant Breed 124: 446-453.
71. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21): 4407-4414.
72. Wagih ME, Musa Y, Ala A (2004) Fundamental botanical and agronomical characterization of sugarcane cultivars for clonal identification and monitoring genetic variations. Sugar Tech 6(3): 127-140.
73. Zhang MQ, Zheng XF, Yu AL, Xu JS, Zheng H (2004) Molecular marker application in sugarcane. Sugarcane Biotechnol 6(4): 251-254.