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

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.

Assessment of genetic diversity in Lepidium sativum L. using inter simple sequence repeat (ISSR) marker

“…Almost, similar magnitude of He and I was reported by Said and Kassahun (2015) in Ethiopian population of L. sativum. The LD analysis revealed that the average recombination coefficient (r 2 ) was found to be 0.2010 which was higher than that reported by Zhang et al (2016) in Switchgrass using ISSR markers. Further, the percentage of linkage decay was found to be 16.74% (P \ 0.01).…”

Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers

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