Diversity among Populations of Switchgrass Based on RAPD Markers

Abstract

Information on the amount of genetic diversity in switchgrass (Panicum virgatum L.) is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. This study characterized and assessed genetic diversity by means of RAPD markers among 14 populations representing upland and lowland switchgrass ecotypes. Forty-five of 128 primers produced polymorphic markers among sets of genomic DNA pooled from individual genotypes of each population. Five primers were selected to amplify a total of 91 polymorphic loci among genotypes. The RAPD markers were scored for presence or absence of bands to generate distance matrices for cluster analysis. Overall similarity was 65% among populations compared to 81% within populations. Blackwell and Caddo were the most similar populations (78%) based on RAPD markers, whereas Alamo and Forestburg were the most divergent (53%). Cluster analysis clearly segregated populations into two main groups (putatively based on ecotype) and united individual genotypes within a population into discrete groups within the larger clusters. Although the relationship between ploidy level and ecotype remained unclear, RAPD profiles can be used to identify switchgrass populations and may be useful in predicting relationships between experimental germplasm sources and released populations. S WITCHGRASS is a highly outcrossing, perennial warmseason grass which is propagated through seed dispersal and rhizome establishment (Weaver and Fitzpatrick, 1932). It is a widespread component of native North American tall grass prairie with a range of adaptation from Nova Scotia, Ontario, and Maine to North Dakota and Wyoming, south to Florida, Nevada, and Arizona into Mexico and Central America (Hitchcock, 1971). Across this range, switchgrass populations exist either as upland or lowland ecotypes that differ in habitat preference, morphology, and, to some extent, ploidy level (Archer and Bunch, 1953; Porter, 1966). The base chromosome number of switchgrass is n = 9, and lowland ecotypes are believed to be predominantly tetraploid (2n-4x = 36), whereas upland types are presumed hexaploid (2n = 6x = 54) or octoploid (2n = 8x = (Church, 1940; Burton, 1942; Nielson, 1944). Current studies using flow cytometry differ in assessment of switchgrass ploidy levels (Lu et al., 1995; Wullschleger et al. 1996), and octoploid chromosome sets have been reported in populations previously thought to be hexaploid (Taliaferro and Hopkins, 1994). Porter (1966) studied upland and lowland populations of switchgrass under various environmental conditions to determine whether any consistent pattern of morphological variability was associated with ecotype, and if such variation was associated with genetic, environmental, or genetic by environmental influences. Although some modifications of phenotypic expression were observed in greenhouse experiments, the ecotypes exhibited

Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences

“…These studies consistently illustrate significant differentiation between upland and lowland ecotypes, based on both nuclear DNA markers and cpDNA sequences (Cortese et al 2010;Gunter et al 1996;Missaoui et al 2006;Narasimhamoorthy et al 2008;Zalapa et al 2011). More recently, we showed the first case of clear genetic differentiation among switchgrass ploidy levels using molecular markers (Zalapa et al 2011).…”

“…More recent applications of DNA markers and sequencing methodologies have suggested that both cpDNA sequence data and nuclear DNA markers are highly correlated with the upland and lowland phenotypic classes. Differentiation between upland and lowland accessions is generally very obvious, representing the first level of clustering or grouping in DNA marker diversity studies (Cortese et al 2010;Gunter et al 1996;Narasimhamoorthy et al 2008). These studies have generally been based on numerous DNA markers scattered throughout the genome, none of which have been singled out as specifically diagnostic or exclusively associated with the lowland-upland phenotypic polymorphism.…”

Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes

“…The combination of PstI and MspI was selected to construct two libraries of 6,144 and 1,536 genomic clones (7,680 clones in total) as described by Jaccoud et al [20]. In order to produce genomic representations, approximately 50 ng of genomic DNA was digested with PstI/MspI combinations and the resulting fragments ligated to a PstI overhang compatible oligonucleotide adapter.…”

“…Upland types are shorter, have finer leaves, and a slower growth rate than the lowland types and are adapted to the northern USA [1,4]. Lowland ecotypes are primarily tetraploid (2n=4x=36) while upland ecotypes can be tetraploid but are predominantly octoploid (2n=8x=72) [7][8][9]. Although lowland switchgrass had originally been considered an autotetraploid with a high degree of preferential pairing [10], genetic mapping has strongly suggested that it is a disomic tetraploid [11].…”

Genetic differentiation among populations of Sesleria albicans Kit. ex Schultes (Poaceae) from ecologically different habitats in central Europe

“…Ecological differences among the habitats colonized by a plant species can, therefore, result in the development of ecotypes (Gunter et al, 1996).…”