Location: Genomics and Gene Discovery
Title: Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (Panicum virgatum L.) Authors
Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 11, 2010
Publication Date: N/A
Interpretive Summary: In this study, 12 switchgrass cultivars were analyzed with EST-SSR markers to gain insight into the factors influencing the genetic diversity and structure and to assess the feasibility of cultivar identification based on markers alone. The objectives of the study were to quantify 1) the population genetic diversity within and among the cultivars, 2) the clustering of individuals according to the source cultivars, and 3) the effect of the number of loci and individuals per cultivar sampled on cultivar identification.
Technical Abstract: Switchgrass is a promising bioenergy crop native to North America. Population genetic diversity was characterized in 12 cultivars that included upland and lowland ecotypes encompassing variation in ploidy levels, geographical origins, and breeding history using 21 EST-SSR marker loci that showed single-locus disomic segregation in tetraploids and apparently tetrasomic inheritance in octoploids. Genetic diversity was found to be greater in octoploids than tetraploids and cultivar relationships suggest an autopolyploid origin of octoploids within upland tetraploids. Model-based Bayesian clustering of individuals indicated that closely related octoploid cultivars are difficult to descriminate, possibly due to slowed differentiation by polysomic inheritance. One tetraploid cultivar displayed comparable diversity to the least diverse octoploid cultivars, suggesting breeding history or population history in the native stands of origin also affected within-cultivar diversity. Pleistocene climate oscillations may be a factor shaping the population genetic structure in the native stands and consequently the cultivars, based on the geographical distribution of genetic diversity detected. Overall and pairwise FST indicated significant cultivar differentiation. The analysis of the sampling effect indicated addition of loci and/or individuals to achieve identification in some octoploid cultivars with high accuracy appears impractical.