Abstract
A 527 marker linkage map ofSaccharum spontaneum L. ‘SES 208’ (2n = 64) was established by analyzing 208 single-dose (SD) arbitrarily primed PCR polymorphisms, 234 SD RFLPs, 41 double-dose (DD) and one triple-dose (TD) polymorphisms. A map hypothesis constructed using these markers (minimum LOD = 4.00,θ = 0.25 M) had 64 linkage groups with 13 SD, nine DD, and one TD markers unlinked. Eight chromosome homology groups were identified by using DD fragments as well as SD RFLPs that identified more than one linkage group. Linkages in repulsion phase were absent from the map, as found in two previous genetic studies of this species. Together, these data demonstrate that SES 208 displayed polysomic segregation, a genetic behavior typical of autopolyploid species. As with previous studies, it was concluded that SES 208 behaved like an auto-octoploid, which was also in agreement with the number of homology groups observed. Aχ 2 was used to test whether the 527 markers were randomly distributed throughout the genome: both arbitrarily primed PCR markers and RFLPs had a distribution that was statistically indistinguishable from random. The integrated arbitrarily primed PCR-RFLP map had a predicted genomic coverage of 93% (considering only 442 SD polymorphisms) and an average interval between markers of 6 cM. SD markers were used to estimate the genome size of SES 208 at ca. 33 00 cM.
Similar content being viewed by others
References
Al-Janabi SM, Honeycutt RJ, McClelland M, Sobral BWS: A genetic linkage map ofSaccharum spontaneum (L.) ‘SES 208’. Genetics 134: 1249–1260 (1993).
Al-Janabi SM, Honeycutt RJ, Sobral BWS: Chromosome assortment inSaccharum. Theor Appl Genet 89: 959–963 (1994).
Bishop DT, Cannings C, Skolnick M, Williamson JA: The number of polymorphic clones required to map the human genome. In: Weir BS (ed) Statistical Analysis of DNA Sequence Data, pp. 181–200 (1983).
Bonierbale MW, Plaisted RL, Tanksley SD: RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120: 1095–1103 (1988).
Botstein D, White RL, Skolnick M, Davis RW: Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314–331 (1980).
Bridges W, Sobral BWS: A genealogical approach to identification of quantitative trait loci in plants. In: Sobral, BWS (ed) The Impact of Plant Molecular Genetics. Birkhäuser, Boston, in press (1996).
Burner DM, Legendre BL: Chromosome transmission and meiotic stability of sugarcane (Saccharum spp.) hybrid derivatives. Crop Scil 33: 600–606 (1993).
Burnquist WB: Development and application of restriction fragment length polymorphism technology in sugarcane (Saccharum spp.) breeding. Ph.D. dissertation, Cornell University, Ithaca, NY (1991).
Burr BJ, Evola SV, Burr FA, Beckmann JS: The application of restriction fragment length polymorphism to plant breeding In: Setlow JK, Hollaender A (eds) Genetic Engineering, vol. 5, pp. 45–59. Plenum Press, New York (1983).
Da Silva J: A methodology for genome mapping of autopolyploids and its application to sugarcane (Saccharum spp.). Ph. D. dissertation, Cornell University, Ithaca, NY (1993).
Da Silva J, Sorrells ME, Burnquist WL, Tanksley SD: RFLP linkage map and genome analysis ofSaccharum spontaneum. Genome 36: 782–791 (1993).
Fitch MM, Moore PH: Haploid production from anther culture ofSaccharum spontaneum L. Z Pflanzenphysiol S: 197–206 (1983).
Giovannoni J, Wing RA, Ganal MW, Tanksley SD: Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucl Acids Res 19: 6553–6551 (1991).
Honeycutt RJ, Sobral BWS, Keim P, Irvine JE: A rapid DNA extraction method for sugarcane and its relatives. Plant Mol Biol Rep 10: 66–72 (1992).
Hulbert SH, Ilot TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW: Genetic analysis of the fungusBremia lactucae using restriction fragment length polymorphisms. Genetics 120: 947–958 (1987).
Janaki-Ammal EK: Cytogenetic analysis ofSaccharum spontaneum L. 1. Chromosome studies in Indian forms. Indian J Agric Sci 6: 1–8 (1936).
Lander ES, Botstein D: Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199 (1989).
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L: Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174–181 (1987).
Michelmore RW, Paran I, Kesseli RV: Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions using segregating populations. Proc Natl Acad Sci USA 88: 9828–9832 (1991).
Moore PH, Nagai C, Fitch MMM: Production and evaluation of sugarcane haploids. Proc Intl Soc Sugar Cane Technol 20: 599–607 (1989).
O'Brien SJ: Genetic Maps: Locus Maps of Complex Genomes. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1990).
Paterson AH, Lander ES, Hewitt JD, Peterson S, Licoln SE, Tanksley SD: Resolution of quantitative traits into Mendelian factors using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721–726 (1988).
Ritter E, Gebhardt C, Salamini F: Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 125: 645–654 (1990).
Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N: Enzymatic amplification of betaglobin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350–1354 (1985).
Sobral BWS, Honeycutt RJ: High output genetic mapping in polyploids using PCR-generated markers. Theor Appl Genet 86: 105–112 (1993).
Sobral BWS, Honeycutt RJ: Genetics, plants, and the polymerase chain reaction. In: Mullis KB, Ferre F, Gibbs RA (eds) The Polymerase Chain Reaction, pp. 304–320. Birkhauser, Boston, MA (1994).
Soltis DE, Soltis PS: Molecular data and the dynamic nature of polyploidy. Crit Rev Plant Sci 12: 243–273 (1993).
Tanksley SD: Mapping polygenes. Annu Rev Genet 27, in press (1993).
Templeton AR, Boerwinkle E, Sing CR: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and analysis of alcohol dehydrogenase activity inDrosophila. Genetics 117: 343–351 (1987).
Templeton AR, Sing CF, Kessling A, Humphries S: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations. Genetics 120: 1145–1154 (1988).
Templeton AR, Crandall A, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. III. Cladogram estimation. Genetics 132: 619–633 (1992).
Weir BS: Genetic Data Analysis. Sinauer Associates, Sunderland, 377 pp (1990).
Welsh J, McClelland M: Fingerprinting genomes using PCR with arbitrary primers. Nucl Acids Res 18: 7213–7218 (1990).
Wicking C, Williamson B: From linked markers to genes. Trends Genet 7: 288–293 (1991).
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV: DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18: 6531–6535 (1990).
Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD: The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83: 294–300 (1992).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
da Silva, J., Honeycutt, R.J., Burnquist, W. et al. Saccharum spontaneum L. ‘SES 208’ genetic linkage map combining RFLP- and PCR-based markers. Mol Breeding 1, 165–179 (1995). https://doi.org/10.1007/BF01249701
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF01249701