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United States Department of Agriculture

Agricultural Research Service

Title: Analysis of of Clonal Germplasm from Five Saccharum Species: S. Barberi, S. Robustum, S. Officinarum, Sl. Sinense and S. Spontaneum. a Study of Inter and Intraspecies Relationships Using Microsatellite Markers

item Brown, James
item Schnell Ii, Raymond
item Power, Emilio
item Douglas, Stephanie
item Kuhn, David

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 27, 2006
Publication Date: March 12, 2007
Citation: Brown, J.S., Schnell II, R.J., Power, E.J., Douglas, S.L., David N. Kuhn. 2007. Analysis of clonal germplasm from five saccharum species: s. barberi, s. robustum, s. officinarum, sl. sinense and s. spontaneum. A study of inter- and intraspecies relationships using microsatellite markers. Genetic Resources and Crop Evolution.54:627-648.

Interpretive Summary: Applications of genetic fingerprints are well known in many fields. The modern press often publishes articles illustrating the utility of molecular markers and genetic fingerprints for a wide variety of applications. In this study, 30 randomly selected clones from each of three species of the genus Saccharum were fingerprinted using 15 'microsatellite' or 'simple sequence repeat' (SSR) markers. The genome (genetic material) of sugarcane clones is very complex, containing as many as eight to ten copies of one or two genomic sets, or basic genomes, and often partial pieces of sets. In contrast, humans and most organisms have only one copy of one set, with one pair of each chromosome, refered to as diploid genomes. Sugarcane has, then, two or more pairs of each chromosome of each genome, causing its genome to be extremely large, and rendering it to be a very complex polyploid. Many common, domesticated plants have polyploid genomes usually with only one or two repeated genomes, however sugarcane is perhaps the most complex of all domesticated plants. This matter has made obtaining genetic fingerprints of such complex polyploids and their analysis very difficult until recent years. This research demonstrates the use of current technology, that allows even such a complex polyploid to be analyzed with relatively good repeatability. Our results demonstrated that each of the three species have clones that constitute typical types for each species, but also contain clones that are very likely to have arisen from hybrids, either with one of the progenitor species, S. robustum, or with commercial sugarcane clones. The latter are composed largely of S. officinarum, which is thought to have originated from S. robustum, and this relationship appears to be confirmed in our results. The other two species are thought to have originated from crosses between S. officinarum and S. spontaneum. Thought the distinctness of these two species is demonstrated, further analyses containing specifically S. officinarum and S. spontaneum will be necessary to confirm this. SSR markers demonstrate the capability, however, to unravel the complex interrelationships of the genus, Saccharum. In addition to answering theoretical questions, these markers enable sugarcane breeders to efficiently choose new parents for crosses that will increase the amount of variability in the progeny, enabling breeders to have a larger range of selection for progeny to advance.

Technical Abstract: The first analysis of the complex Saccharum genome using 15 simmple sequence repeat (SSR) markers is presented, comparing 30 clonal accessions from each of three species of the genus (S. barberi, S. robustum, and S. sinense) with four cultivated checks. Two of the species are considered to be related to cultivated clones, and one species is thought to be ancestral to S. officinarum, the ancestor comprising the larger part of the genome of commercial cultivars. This molecular analysis confirmed these classifications to a large degree, agreed to some extent with previously named types of Saccharum barberi and Saccharum sinense, and identified some accessions that appear as hybrids between species, and others that appear to become mislabeled. Given the high ploidy of these species, the use of only 15 SSR markers enabled clear classifications generally in accord with conventional taxonomy of the genus and with reports using other types of markers, and enabled the clear identification of likely mislabeled accessions. Principal coordinates and average linkage clustering analyses of the SSR markers gave more discrimination among groups and clones, clearer understanding, and more overall information than a previously published principal components analysis of the same clones based on eight agronomic characters. Relative genetic variability of the three species estimated by observation of the resulting clusters suggested S. robustum to have more variability with in its main cluster, while S. bareri and S. sinense clustered each into two distinct, relatively compact clusters, with other accessions clustering in smaller, less distinct clusters close to a large cluster containing the checks and S. robustum. These outlying clusters of S. barberi and S. sinense seem most likely to be composed of hybrids, of mislabeled accessions, or both. The high repeatability and ease of use of SSR markers should enable such studies to be carried out more easily across laboratories, with good comparability results. The complexity of the genome and the necessity of binary coding of PCR amplification products for statistical analysis remains necessary for SSR markers, rendering more exact and formal comparisons of genetic variability theoretically impossible due to high and variable ploidy among species and clones, and the lack of knowledge of the exact inheritance of PCR amplification products of these markers.

Last Modified: 4/18/2014