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United States Department of Agriculture

Agricultural Research Service

Title: Sequence-Related Amplified Polymorphism (SRAP) markers for assessing interrelationships and genetic diversity among members of the Saccharum complex

Authors
item Suman, Andru - LSU
item Kimbeng, Collins - LSU
item Edme, Serge
item Veremis, John

Submitted to: Diversity Plant Genetic Resources Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 30, 2008
Publication Date: May 15, 2008
Citation: Suman, A., Kimbeng, C., Edme, S.J., Veremis, J.C. 2008. Sequence-Related Amplified Polymorphism (SRAP) markers for assessing interrelationships and genetic diversity among members of the Saccharum complex. Diversity Plant Genetic Resources Journal. 6:222-231.

Interpretive Summary: Sugarcane breeders are concerned with an erosion of the genetic diversity in the crop because it has a very narrow genetic base: in other words, modern sugarcane cultivars descended from a very narrow pool of founders. It is imperative to broaden its genetic base by first characterizing the wild relatives of sugarcane which are the potential sources of new genes. Characterization with molecular markers is the most appropriate since these markers are not influenced by the environment. Thirty genotypes of the Saccharum complex were fingerprinted with a new class of molecular markers, coined sequence-related amplified polymorphism (SRAP by Li and Quiros), which targets gene-rich regions of the genome. Ample polymorphisms (1135 out of 1364 bands or 83%) were detected with 31 primer combinations, giving an average of 44 fragments per primer pair. Another appealing aspect of the SRAP system in this study is its ability to amplify species-specific markers (119 or 8.7%) across the Saccharum species, with 75% of those markers scored in the S. spontaneum genome. Pending an assessment of their breeding values, these markers can be useful in introgression breeding and in broadening the genetic base of sugarcane cultivars. 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). The dendrogram grouped the genotypes according to their phylogenetic relationships: the Erianthus and Miscanthus clones were separated from all other genotypes. The S. spontaneum clones formed a very distinct group and were the most diverse. The S. robustum clones formed another cluster with some clones having close similarity with the S. officinarum, sinense, and barberi. The S. officinarum clones were interspersed within the S. robustum cluster or the group of cultivars. The cultivars were genetically the most similar with GS values ranging from 0.91 to 0.96. With its propensity to amplify markers across the Saccharum genome, the SRAP system would be also a valuable addition to genetic mapping projects that particularly employ interspecific population.

Technical 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 complex. Thirty genotypes, including clones of Miscanthus, Erianthus, S. officinarum, S. spontaneum, S. robustum, S. sinense, S. barberi, and modern cultivars were scored with 31 primer combinations. The amplifications produced 1364 fragments, of which 1135 (83%) were polymorphic, for an average of 44 bands per primer combination, and 119 (8.7%) were 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). The dendrogram obtained by the unweighted pairgroup method with arithmetic mean (UPGMA) and confirmed with the non-metric multi-dimensional scaling (NMDS) 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) to two major clusters: Cluster I separated the S. robustum, S. sinense-barberi, and cultivars as different subgroups with each one including some S. officinarum clones, while Cluster II included the S. spontaneum clones, exclusively. These results showed a high discriminatory power of SRAP markers in detecting genetic relationships within the Saccharum complex down to the cultivar level and hinted at their potential for genetic mapping aimed at marker-assisted selection in sugarcane.

Last Modified: 9/21/2014
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