ARS | Publication request: Hierarchical classification of switchgrass using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 22, 2010
Publication Date: November 23, 2010
Repository URL: http://handle.nal.usda.gov/10113/56397
Citation: Zalapa, J., Price, D., Kaeppler, S., Tobias, C.M., Okada, M., Casler, M.D. 2010. Hierarchical classification of switchgrass using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars. Theoretical and Applied Genetics. 122:805-817.

Interpretive Summary: Classification of switchgrass varieties is very important because they differ in adaptation to different climatic stresses, resulting in widely different adaptation zones. We used DNA markers to organize switchgrass varieties into five groups that represent different regions of the USA. There were two groups of "lowland" switchgrass, one from the Southern Great Plains and one from Florida. There were three groups of "upland" switchgrass, one from the Southern Great Plains, one from the Northern Great Plains, and one from the Eastern USA, east of the Mississippi River. Each group represent a significant and unique pool of genetic resources for use in agronomic, breeding, restoration, and conservation projects. These results will be of value to agronomists, breeders, and conservationists.

Technical Abstract: Switchgrass (Panicum virgatum L.) is an important crop for bioenergy feedstock development. Switchgrass has two main ecotypes: the lowland ecotype being exclusively tetraploid (2n = 4x = 36) and the upland ecotype being mainly tetraploid and octoploid (2n = 8x = 72). Because there is a significant difference in ploidy, morphology, growth pattern, and zone of adaptation between and within the upland and lowland ecotypes, it is important to discriminate switchgrass plants belonging to different genetic pools. Moreover, the presence of hybrid vigor in upland x lowland crosses suggests that switchgrass genetic pools may act as natural heterotic groups creating a further need to accurately and efficiently discriminate switchgrass. We used 55 simple sequence repeats (SSR) loci and five chloroplast sequences to identify patterns of variation between and within 18 switchgrass cultivars representing seven lowland and eleven upland cultivars from different geographic regions and of varying ploidy levels. Additionally, we investigated the possibility of cultivar fingerprinting and classification of switchgrass genotypes of uncertain origin. We report consistent discrimination of switchgrass cultivars into ecotype membership and demonstrate unambiguous molecular differentiation among switchgrass ploidy levels using genetic markers. Also, SSR and chloroplast markers identified genetic pools related to the geographic origin of the 18 cultivars with respect to ecotype, ploidy, and geographical, and cultivar sources. SSR loci were highly informative for cultivar fingerprinting and to classify plants of unknown origin. This classification system is the first step toward developing switchgrass complementary gene pools that can be expected to provide a significant heterotic increase in biomass yield.