Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms

Abstract

ABSTRACT. Switchgrass (Panicum virgatum) is a perennial warmseason grass native to North America that has been identified as a dedicated cellulosic biofuel crop. We quantified genetic diversity in tetraploid switchgrass germplasm collected at Oklahoma State University and characterized genetic relatedness among the collections from distinct regions. Fifty-six tetraploid accessions, including seven upland and 49 lowland genotypes from throughout the US, were examined. The amplified fragment length polymorphism (AFLP) procedure was utilized to generate DNA profiling patterns that were scored visually. Sixteen selective AFLP primer combinations were used to amplify 452 polymorphic bands. The accessions' genetic similarity coefficients, UPGMA (unweighted pairgroup method with arithmetic averaging) cluster analysis and principle coordinate analysis, were performed. The upland and lowland accessions clustered according to ecotypes, with one exception (TN104). Genetic similarity coefficients among the accessions ranged from 0.73 to 0.95. Analysis of molecular variance (AMOVA) was performed, showing significant differences between the upland and lowland genotypes. The trnL marker confirmed that TN104 was a lowland genotype, but the trnL marker identification of upland and lowland genotypes was not consistent with the AFLP analysis in two germplasms (Miami and AR4).

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

“…The UPGMA cluster and PCA analysis demonstrated that 134 genotypes could be clearly divided into two groups (Figs. 1 and 4), and the lowland and upland germplasm clusters were almost completely separated, which was consistent with the results of several other switchgrass studies [41, 55, 56]. For the UPGMA cluster analysis, the first group only included lowland ecotypes, while the second group contained upland ecotypes and could be further classified into two subgroups.…”

Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations

“…The least mean genetic similarity was observed between 'Kanlow' and the MME natural populations (0.635) while the highest was observed, as expected, between 'Alamo' populations collected at Vonore and Alcoa (0.936; Table 4). Similar genetic similarity coefficients ranging from 0.73 to 0.95 were observed while assessing genetic diversity in 56 accessions of tetraploid switchgrass (Todd et al 2011). In our study, the total mean genetic similarity among all switchgrass populations was 0.775, which is comparable to the mean genetic similarity of 0.813 observed in cultivated switchgrass accessions (Huang et al 2011).…”

“…The study presented here offers important information on the genetic diversity and structure of natural and agronomic switchgrass populations and concurs with previous studies in genebank accessions, based on morphological, ploidy level and different molecular markers used (Cortese et al 2010;Huang et al 2011;Todd et al 2011;). Our study highlighted that: (1) these switchgrass populations contain a high level of genetic diversity, (2) the agronomic and natural populations we studied had same ploidy levels, (3) the populations are differentiated genetically, and (4) the diversity of natural populations is comparable to the agronomic populations.…”

“…Genetic diversity values of 0.231 and 0.225 based on SRAP and EST-SSR molecular markers, respectively, have been reported in cultivated switchgrass accessions (Huang et al 2011). Genetic diversity values of 0.295 were observed in lowland switchgrass ecotypes by using amplified fragment length polymorphism (AFLP) markers (Todd et al 2011). Total genetic diversity in switchgrass was similar to that noted for other allogamous perennial grass species.…”

“…Studies on genetic diversity of switchgrass have been focused on differentiating among upland and lowland ecotypes, on polymorphisms for a nuclear gene coding for a plastid protein, and on patterns of relatedness among switchgrass accessions obtained primarily from the USDA National Plant Germplasm System (Gunter et al 1996;Hultquist et al 1996;Huang et al 2003;Casler 2005;Missaoui et al 2006;Narasimhamoorty et al 2008;Todd et al 2011;. In the few studies that have emphasized existing native switchgrass populations (see Zhang et al 2011), gaps exist in Midsouth USA states.…”