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Sequence-related amplified polymorphism (SRAP) markers for assessing genetic relationships and diversity in sugarcane germplasm collections

Published online by Cambridge University Press:  15 May 2008

Andru Suman ,
Collins A. Kimbeng ,
Serge J. Edmé  and
John Veremis
Andru Suman
Affiliation:
School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
Collins A. Kimbeng*
Affiliation:
School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
Serge J. Edmé
Affiliation:
USDA-ARS, SAA, Sugarcane Field Station, 12990 US Hwy 441 North, Canal Point, FL 33438, USA
John Veremis
Affiliation:
USDA-ARS, SRRC, Sugarcane Research Unit, 5883 USDA Road, Houma, LA 70360, USA
*
*Corresponding author. E-mail: [email protected]
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Abstract

Characterization of wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The potential of the sequence-related amplified polymorphism (SRAP) technique, which preferentially amplifies gene-rich regions, was evaluated to assess the genetic relationships among members of the Saccharum species. A panel of 31 SRAP primer combinations were used to score 30 genotypes of Saccharum officinarum, Saccharum spontaneum, Saccharum robustum, Saccharum sinense, Saccharum barberi and sugarcane hybrids, with Miscanthus and Erianthus included as outgroups. The amplifications produced 1364 DNA fragments for an average of 44 per primer combination, with 83% (1135) being polymorphic and 8.7% (119) being species specific. Based on the Dice index, all 30 genotypes were differentiated from each other with genetic similarity (GS) estimates ranging from 0.60 to 0.96 (mean = 0.79). Both the dendrogram [obtained by the unweighted pairgroup method with arithmetic mean or (UPGMA)] and the non-metric multidimensional scaling method grouped the genotypes according to their phylogenetic relationships. Erianthus and Miscanthus were separated as two outgroups (at GS levels of 0.56 and 0.72, respectively) into two major clusters: cluster I separated the S. robustum, S. sinense, S. barberi and hybrids as different subgroups with each one including some S. officinarum clones, while cluster II included the S. spontaneum clones, exclusively. A S. officinarum–S. spontaneum sequence comparison of some of the monomorphic and polymorphic bands revealed 65–90% homology with rice, corn or sugarcane sequences deposited in databases. The high discriminatory power coupled with the possibility that most of the amplicons may be amplifying gene-rich regions of the genome makes SRAP a potentially robust tool for genetic mapping aimed at marker-assisted introgression in sugarcane.

Keywords

generagenetic diversitygermplasmSaccharum complexsequence-related amplified polymorphismunweighted pairgroup method with arithmetic mean
Type
Research Article
Information
Plant Genetic Resources , Volume 6 , Issue 3 , December 2008 , pp. 222 - 231
Copyright
Copyright © NIAB 2008

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References

Aitken, KS, Li, JC, Jackson, P, Piperidis, G and McIntyre, CL (2006) AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars. Australian Journal of Agricultural Research 57: 1167–1184.CrossRefGoogle Scholar
Alwala, S, Suman, A, Arro, JA, Veremis, JC and Kimbeng, CA (2006) Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Science 46: 448–455.Google Scholar
Amalraj, VA and Balasundaram, N (2006) On the taxonomy of the members of Saccharum complex. Genetic Resources and Crop Evolution 53: 35–41.CrossRefGoogle Scholar
Arceneaux, G (1967) Cultivated sugarcanes of the world and their botanical derivation. Proceedings International Society of Sugarcane Technologists 12: 844–854.Google Scholar
Arro, JA, Veremis, JC, Kimbeng, CA and Botanga, C (2006) Genetic diversity and relationships revealed by AFLP among a collection of Saccharum spontaneum and related species and genera. Journal of the American Society of Sugar Cane Technologists 26: 101–115.Google Scholar
Artschwager, E and Brandes, EW (1958) Sugarcane (Saccharum officinarum), origin, characteristics and descriptions of representative clones. US Department of Agriculture Handbook No. 122. Washington, DC: USDA..Google Scholar
Berding, N and Roach, BT (1987) Germplasm collection, maintenance, and use. In: Heinz, DJ (ed.) Sugarcane Improvement Through Breeding. Amsterdam: Elsevier, pp. 143–210.CrossRefGoogle Scholar
Besse, P, Taylor, G, Carroll, B, Berding, N, Burner, D and McIntyre, CL (1998) Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis. Genetica 104: 143–153.CrossRefGoogle Scholar
Bhat, S and Gill, SS (1985) The implication of 2n egg gametes in nobilization and breeding of sugarcane. Euphytica 34: 377–384.CrossRefGoogle Scholar
Brandes, EW (1958) Origin, classification, and characteristics. In: Artschwager, E and Brandes, EW (eds) Sugarcane (Saccharum officinarum L.). US Department of Agriculture Handbook Vol 122. Washington, D.C: U.S. Government Print Office, pp. 1–35.Google Scholar
Bremer, G (1961) Problems in breeding and cytology of sugarcane. Euphytica 10: 59–78.CrossRefGoogle Scholar
Budak, H, Shearman, RC, Parmaksiz, I, Gaussoin, RE, Riordan, TP and Dweikat, I (2004) Molecular characterization of Buffalograss germplasm using sequence related amplified polymorphism markers. Theoretical and Applied Genetics 108: 328–334.CrossRefGoogle ScholarPubMed
Burner, DM (1999) Registration of Dwarf1 sugarcane genetic stock. Crop Science 39: 309.Google Scholar
Daniels, J and Roach, BT (1987) Taxonomy and evolution. In: Heinz, DJ (ed.) Sugarcane Improvement Through Breeding. Amsterdam: Elsevier, pp. 143–210.Google Scholar
Daniels, J, Smith, P, Paton, N and Williams, CA (1975) The origin of the genus Saccharum. Sugarcane Breeding Newsletter 36: 24–39.Google Scholar
Deren, CW (1995) Genetic base of US mainland sugarcane. Crop Science 35: 1195–1199.CrossRefGoogle Scholar
d'Hont, A, Grivet, L, Feldman, P, Rao, PS, Berding, N and Glaszmann, JC (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Molecular and General Genetics 250: 405–413.CrossRefGoogle ScholarPubMed
Dudley, JW (1994) Comparison of genetic distance estimators using molecular marker data. Joint Plant Breeding Symposia Series. ASHS/CASSA5, 6 August 1994, pp. 3–7..Google Scholar
Ferriol, M, Pico, B and Nuez, F (2003a) Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theoretical and Applied Genetics 107: 271–282.CrossRefGoogle ScholarPubMed
Ferriol, M, Picó, B and Nuez, F (2003b) Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SRAP markers. Genetic Resources and Crop Evolution 50: 227–238.CrossRefGoogle Scholar
Ferriol, M, Picó, B, Córdova, PF and Nuez, F (2004) Molecular diversity of a germplasm collection of squash (Cucurbita moschata) determined by SRAP and AFLP markers. Crop Science 44: 653–664.CrossRefGoogle Scholar
Glaszmann, JC, Noyer, JL, Fautret, A, Feldmann, P and Lanaud, C (1989) Biochemical genetic markers in sugarcane. Theoretical and Applied Genetics 789: 537–543.Google Scholar
Guimaraes, CT and Sobral, WS (1998) The Saccharum complex: relation to other Andropogoneae. In: Janick, J (ed.) Plant Breeding Reviews, vol 16. New York: Wiley, pp. 269–287.CrossRefGoogle Scholar
Irvine, JE (1999) Saccharum species as horticultural classes. Theoretical and Applied Genetics 98: 186–194.CrossRefGoogle Scholar
Jannoo, N, Grivet, L, Seguin, M, Paulet, F, Domaingue, R, Rao, PS, Dookun, A, d'Hont, A and Glaszmann, JC (1999) Molecular investigation of the genetic base of sugarcane cultivars. Theoretical and Applied Genetics 99: 171–184.Google Scholar
Li, G and 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. Theoretical and Applied Genetics 103: 455–461.Google Scholar
Lu, YH, d'Hont, A, Walker, DIT and Rao, PS (1994) Relationships among ancestral species of sugarcane revealed with RFLP using single copy maize nuclear probes. Euphytica 78: 7–18.CrossRefGoogle Scholar
Mukherjee, SK (1957) Origin and distribution of Saccharum. Botanical Gazette 119: 55–61.CrossRefGoogle Scholar
Nair, NV, Nair, S, Sreenivasan, TV and Mohan, M (1999) Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers. Genetic Resources and Crop Evolution 46: 73–79.CrossRefGoogle Scholar
Nei, M and Li, WH (1979) Mathematical modelling for studying genetic variation in terms of restriction endonuclease. Proceedings National Academy of Sciences 76: 5268–5273.Google Scholar
Price, S (1963) Cytogenetics of modern sugarcane. Economic Botany 17: 97–106.Google Scholar
Price, S (1965) Cytology of Saccharum robustum and related sympatric species and natural hybrids. USDA-ARS Technical Bulletin 1337. Washington, DC: US Government Print Office..Google Scholar
Riaz, A, Li, G, Quresh, Z, Swatt, MS and Quiros, CF (2001) Genetic diversity of oilseed Brassica inbred lines based on sequence-related amplified polymorphism and its relation to hybrid performance. Plant Breeding 120: 411–415.CrossRefGoogle Scholar
Roach, B (1986) Evaluation and use of sugarcane germplasm. Proceedings International Society of Sugarcane Technologists 1: 492–503.Google Scholar
Rohlf, FJ (2000) NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System. Version 2.1. New York: Applied Biostatistics.Google Scholar
SAS Institute (2004) The SAS System for Windows Version 8.02. Cary, NC: SAS Institue.Google Scholar
Selvi, A, Nair, NV, Balasundaram, N and Mohapatra, T (2003) Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome 46: 394–403.CrossRefGoogle ScholarPubMed
Selvi, A, Nair, NV, Noyer, JL, Singh, NK, Balasundaram, N, Bansal, KC, Koundal, KR and Mohapatra, T (2006) AFLP analysis of the phonetic organization and genetic diversity in the sugarcane complex. Genetic Resources and Crop Evolution 53: 831–842.Google Scholar
Sobral, BWS, Braga, DPV, LaHood, ES and Keim, P (1994) Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb subtribe of the Andropogoneae Dumort. Tribe. Theoretical and Applied Genetics 87: 843–853.Google Scholar
Sreenivasan, TV, Ahloowalia, BS and Heinz, DJ (1987) Cytogenetics. In: Heinz, DJ (ed.) Sugarcane Improvement Through Breeding. Amsterdam: Elsevier, pp. 211–253.Google Scholar
Stevenson, GC (1965) Genetics and Breeding of Sugarcane. London: Longmans.Google Scholar
Swofford, DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4.0 b10. Sunderland, MA: Sinauer Associates.Google Scholar
Takahashi, S, Furukawa, T, Asano, T, Terajima, Y, Shimada, H, Sugimoto, A and Kadowaki, K (2005) Very close relationship of the chloroplast genomes among Saccharum species. Theoretial and Applied Genetics 110: 1523–1529.Google Scholar
Vuylsteke, M, Mank, R, Brugmans, B, Stam, P and Kuiper, M (2000) Further characterization of AFLP data as a tool in genetic diversity assessments among maize (Zea mays L.) inbred lines. Molecular Breeding 6: 265–276.CrossRefGoogle Scholar
Weir, BS (1990) Genetic Data Analysis. Sunderland, MA: Sinauer Associates.Google Scholar
Williams, CA, Harborne, JB and Smith, P (1974) The taxonomic significance of leaf flavonoids in Saccharum related genera. Phytochemistry 13: 1141–1149.CrossRefGoogle Scholar