Single-locus EST-SSR markers for characterization of population genetic diversity and structure across ploidy levels in switchgrass (Panicum virgatum L.)

Abstract

Polyploidy, ploidal variation between populations, and aneuploidy within some populations complicate population genetic analyses in switchgrass. We report 21 genic-simple sequence repeat marker loci with single-locus disomic segregation in tetraploids and apparently tetrasomic inheritance in octoploids, thus allowing population genetic analyses across ploidy levels. Based on 472 individuals sampled over four tetraploid and eight octoploid cultivars, six to 55 alleles were detected per locus with an average of 24.1. Genetic diversity was greater in octoploids than tetraploids, as expected from 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 may have also affected within-cultivar diversity. Amplicon number at each locus and population relationships suggest autopolyploid origin of octoploids within upland tetraploids with significant cultivar differentiation. However, model-based Bayesian clustering of individuals indicated that closely related octoploid cultivars are difficult to identify, possibly due to slowed differentiation by polysomic inheritance. The analysis of the sampling effect indicated addition of loci is more effective for cultivar identification than more individuals sampled per cultivar. Discriminating power of loci tended to correlate with their variability. The eight loci with greatest discriminatory power within tetraploids were equally successful as 20 loci at identifying the four tetraploid cultivars. The set of markers reported in this study are useful for characterization of switchgrass germplasm and identifying population structure for association studies.

Development of a genome-wide multiple duplex-SSR protocol and its applications for the identification of selfed progeny in switchgrass

“…Generally, SSR markers with dinucleotide repeats were more polymorphic than trinucleotide repeats in several plant species, such as barley [42], rice [43], wheat [44], maize [45], and soybean [46]. In this study, of all scorable PPs in the preliminary screening, the dinucleotide repeat SSRs produced a significantly greater number of alleles than those with trinucleotide repeats (Table 1), which was consistent with previous studies in switchgrass [19,24,47]. However, in the final 48 PPs selected for duplex PCR, we found that both classes of SSRs were equally polymorphic.…”

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

“…ISSR [designed by the University of British Columbia (UBC set No. 9)], EST-SSR [62], and SCoT primer [45] sequences were aligned to the Panicum reference genome using the bl2seq blast program in NCBI (www.ncbi.nlm.nih.gov/BLAST/), which was designed to eliminate redundancies. Initially, four germplasms were used to screen marker primers [PI421999 (AM-314/MS-155), PI422006 (Alamo), PI642190 (Falcon), and PI642207 (70SG 016)].…”

“…PCR products were visualized following agarose gel (1.5 %) electrophoresis at 120Vfor 1.5 h in 1 × TBE buffer, followed by staining with GelRed (Tiangen Biotech, Beijing, China). The EST-SSR PCR consisted of a denaturation for 5 min at 94 °C then 35 cycles of 30 s at 94 °C, 30 s at 53–55 °C, and 2 min at 72 °C, with a final extension of 5 min at 72 °C [62] and products were visualized as described above.…”

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].…”