Genetic Diversity in Switchgrass Collections Assessed by EST-SSR Markers

Abstract

Switchgrass (Panicum virgatum L.), is a warm season C 4 perennial grass, native to North American tall grass prairies. The high biomass production potential of switchgrass with low inputs makes it an excellent choice as a sustainable bioenergy crop. The objective of this study was to determine the genetic variability within and among 31 switchgrass populations obtained from Germplasm Resources Information Network (GRIN). Six plants from each population (186 genotypes) were characterized with 24 conserved grass expressed sequence tag-simple sequence repeats (EST-SSR) and 39 switchgrass EST-SSR markers. The partitioning of variance components based on the analysis of molecular variance (AMOVA) revealed that the variability within population was significantly higher (80%) than among populations (20%). Pair-wise genetic distance estimates based on SSR data revealed dissimilarity coefficients for genotypes ranging from 0.45 to 0.81. The uplands and lowlands were generally grouped in distinct sub-clusters. The genotypes were grouped into the different adaptive zones based on the geographical locations of the collections. Ploidy estimation showed that 20 of the accessions were tetraploid, four of them were octoploids and the remaining seven had mixed ploidy levels. Flow cytometry analysis of genotypes within cultivars collected from commercial seed sources did not always support the ploidy mixtures that were found in GRIN collections. Three genotypes of two accessions that clustered differently from other genotypes of the same accessions also had different ploidy levels.

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 recently, we showed the first case of clear genetic differentiation among switchgrass ploidy levels using molecular markers (Zalapa et al 2011). However, genetic studies showing geographic differentiation are lacking or inconsistent (Missaoui et al 2006;Narasimhamoorthy et al 2008;Cortese et al 2010).…”

Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes

“…In a compensating allopolyploid, a chromosome from one of the subgenomes is replaced by its homoeologs so that the overall chromosome number remains unchanged. The DNA content of VS16 has been determined to be within the range expected for tetraploid switchgrass accessions [9] but, since no GISH or FISH have been performed on VS16, it is unknown whether this clone carries intersubgenome translocations. However, rearrangements and compensating aneuploidy in VS16 would likely lead to multivalent formation during meiosis resulting in tetrasomic inheritance of some markers.…”

“…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].…”

Production of Autopolyploid Lowland Switchgrass Lines Through In Vitro Chromosome Doubling

“…In nature, switchgrass plants with the same ploidy level can usually be easily intercrossed regardless of ecotype; however, hybrids between different ploidy levels are very rare [7,8]. Due to the ploidy barrier, genetic flow between upland and lowland ecotypes is limited, which has ultimately maintained a high level of genetic diversity in switchgrass germplasm [9][10][11][12][13][14]. Hybrid breeding, which has significantly impacted modern agriculture, is a method of creating new cultivars by crossing between genetic lines that have different backgrounds [15].…”