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ARS Home » Research » Publications at this Location » Publication #104540


item Pan, Yong-Bao
item Burner, David
item Legendre, Benjamin

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2000
Publication Date: 12/20/2000
Citation: Pan, Y., Burner, D.M., Legendre, B.L. Nucleotide sequence polymorphisms among the 5s rRNA intergenic spacers in sugarcane and related taxa. Genetica. 108:285-295.

Interpretive Summary: Selection of progeny from sugarcane crosses is difficult due to the occurrence of self-fertilization and the lack of selective morphological traits. DNA sequence changes in a gene among two sugarcane cultivars and 21 related species were studied. Many of the related species are involved in the basic breeding program. Using an automated DNA sequencer, similarities among these 23 species were categorized into five groups. Sugarcane and two of its ancestor species were in the same group. The maize cultivars were in a separate group. The availability of these DNA sequences of this gene should allow us to develop species-specific DNA markers to assist in sugarcane breeding.

Technical Abstract: The 5S rRNA intergenic spacers were amplified from total nucleic acid extracts of two elite sugarcane cultivars and their related taxa by polymerase chain reaction (PCR) with two universal primers PI and PII. Only one PCR product was amplified from each taxon. These PCR products showed some degree of length polymorphisms when analyzed in 0.7% agarose/0.4% Synergel binary gels but did not always cross hybridize in Southern hybridization experiments. These PCR products were cloned into a commercial plasmid vector and sequenced. The sizes of these PCR products were 231 to 237 bp for Saccharum officinarum, 233 to 237 bp for sugarcane cultivars, 228 to 238 bp for S. spontaneum, 239 to 252 bp for S. giganteum, 385 to 410 bp for Erianthus spp., 226 to 230 bp for M. sinensis Zebra, 206 to 207 bp for M. sinensis IMP 3057, 207 to 209 bp for S. bicolor, and 247 to 249 bp for Z. mays. Nucleotide sequence polymorphisms were found at both segment and single nucleotide level. Computer-assisted multiple sequence alignment resulted in the formation of five major clusters. Cluster I contained the two sugarcane cultivars, S. officinarum, and S. spontaneum; Cluster II Erianthus spp.; Cluster III S. giganteum; Cluster IV the sorghum cultivars; and Cluster V the maize cultivars. The disclosure of these 5S rRNA intergenic spacer sequences will facilitate molecular cytogenetics and marker-assisted breeding in sugarcane.