Abstract
The Sugarcane Breeding Programme of the Instituto Agronômico de Campinas has been using routinely different types of molecular markers for the characterization of their breeding clones and varieties. In the present work we compared the genetic relationships among 82 sugarcane clones/varieties based on three types of molecular markers; AFLP, TRAP and Microsatellites (SSRs). Five AFLP selective primer combinations, 10 SSRs and four TRAP fixed primers, designed from candidate genes involved in the drought tolerance response metabolism, were used in combination with three arbitrary primers. The pair-wise genetic similarity based on the Jaccard’s coefficient, the dedrogram and matrix comparison were done using NTSYS Software. A total of 410 polymorphic markers were obtained: 145 AFLPs, 103 SSRs, and 160 TRAPs. Although the average genetic similarity estimates based on AFLP (0,675) and TRAP (0,655) was closer to each other than to SSRs (0,522), the correlation between TRAP and SSRs was higher (r= 0.24). The coefficient of variation was lower for AFLP and TRAP (∼6.55%) than for SSRs (13%). These results indicate that the choice of molecular markers should be considered carefully, based on the purpose of the application in the breeding programme, as it is not possible to select a marker system that fits all the requirements for germplasm characterization.
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Aitken KS, Li JC, Jackson P, Piperidis G, McIntyre CL (2006). AFLP analysis genetic diversity within Saccharum officinarum and comparison with sugarcane varieties. Aus J Agr Res 57: 1167–1184.
Al-Janabi SM, Forget L, Dookun A (1999). An improved and rapid protocol for the isolation of polysaccharide- and polyphenol-free sugarcane DNA. Plant Mol. Bio. Rep. 17: 1–8.
Alwala S, Suman A, Arro JA, Veremis JC, Kimberg CA (2006). Target region amplification polymorphism for assessing genetic diversity in sugarcane germplasm collections. Crop Sci. 46: 448–445.
Becelaere GV, Lubbers EL, Paterson AH, Chee PW (2005). Pedigree vs DNA marker-based genetic similarity estimates in cotton. Crop Sci. 45: 2281–2287.
Cordeiro GM, Eliott F, McIntyre L, Casu RE, Henry RJ (2006). Characterization of single nucleotide polymorphisms in sugarcane ESTs. Theor. Appl. Genet. 113:331–343
Cox TS, Kiang YT, Gorman MB, Rodgers DM (1985). Relationship between the coefficient of parentage and genetic similarity in soybean. Crop Sci. 25:529–532.
Creste S, Tulmann-Neto A, Figueira A (2001). Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gel by silver staining. Plant Mol. Biol. Rep. 19: 299–306.
Farooq S, Azam F (2002). Molecular markers in plant breeding III: practical applications and difficulties encountered. Pakistan J Biol Sci 10:1148–1154.
Jarne P, Lagoda PJL (1996). “Microsatellites, form molecules to populations and back.” Trends Ecol. Evol 11: 424–429
Li G, Quiros CF (2001). Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103:455–561.
Lima MLA, Garcia AAF, Oliveira KM, Matsouka S, Arizono A, Souza Jr. CL, Souza AP (2002). Analysis of genetic similarity detected by AFLP and coefficent of parentage among genotypes of sugar cane (Saccharum spp.). Theor. Appl. Genet. 104:30–38.
Messmer MM, Melchinger AE, Herrmannv, RG, Boppenmaier J (1993). Relationships among early European maize inbreds: Comparison of pedigree and RFLP data. Crop Sci. 33:944–950.
Oliveira KM, Pinto LR, Marconi TG, Margarido GRA, Pastina MM, Teixeira LHM, Figueira AV, Ulian EC, Garcia AAF, Souza AP (2007). Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Mol Breeding 20:189–208.
Oliveira KM, Pinto LR, Marconi TG, Mollinari M, Ulian EC, Chabregas SM, Falco MC, Burnquist W, Garcia AAF, Souza AP (2009). Characterization of new polymorphic functional markers for sugarcane. Genome 52: 191–209.
Pan YB (2006). Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech 8: 246–256.
Pinto LR, Oliveira KM, Marconi T, Garcia AAF, Ulian EC, Souza AP (2006). Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breeding 125: 378–384.
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: 53–59.
Singh RK, Srivastava S, Singh SP, Sharma ML, Mohopatra T, Singh NK, Singh SB (2008). Identification of new microsatellite DNA markers for sugar and related traits in sugarcane. Sugar Tech 10: 327–333.
Tienderen PH, Haan AA, Van Der Linden CG, Vosman B (2002). Biodiversity assessment using markers for ecologically important traits. Trends Ecol Evol 17:577–582.
Vos P, Hogers R, Bleeker M, Reijams M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407–4414.
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Creste, S., Sansoli, D.M., Tardiani, A.C.S. et al. Comparison of AFLP, TRAP and SSRs in the estimation of genetic relationships in sugarcane. Sugar Tech 12, 150–154 (2010). https://doi.org/10.1007/s12355-010-0029-1
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DOI: https://doi.org/10.1007/s12355-010-0029-1