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

Yu Zhang,Xiaomei Jiang,Lexin Zhang,Bin Xu,Linkai Huang,Xiaoli Wang,Xinquan Zhang,Haidong Yan

doi:10.1186/s41065-016-0007-z

Abstract

BackgroundTo evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs.ResultsIn this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei’s gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 (P < 0.01).ConclusionsThe population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

Highlights

To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 inter simple sequence repeat marker (ISSR), 20 Start codon targeted marker (SCoT), and 15 Expressed sequence tag-simple sequence repeats marker (EST-SSR)
We present 134 switchgrass accessions supplied by Plant Genetic Resources Conservation Unit, Griffin, Georgia USA to identify the levels of genetic variation, population structure, and extent of LD using 51 markers including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs
Our results suggested that ISSR, SCoT, and EST-SSR analyses could contribute to the detection of genetic variation

Summary

Introduction

Population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. Genetic diverstiy is a significant factor that contributes to crop improvement. Evaluation of genetic variation in contemporary germplasm through breeding programs may be indirectly favorable for genetic progress in future cultivars [1]. Estimation of plant diversity is crucial for the efficacious use of genetic resources in breeding programs. As particular segments of DNA that represent different functional classes, play an essential role in all aspects of plant breeding, and have been widely used to estimate genetic variation. Compared with conventional phenotyping methods, molecular markers have numerous advantages as they are detectable and stable in plant tissues regardless of environmental influences [2].

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