Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers
Zhang, Yu (Centre de Recerca en Agrigenòmica)
Yan, Haidong (Sichuan Agricultural University. Grassland Science Department)
Jiang, Xiaomei (Sichuan Agricultural University. Grassland Science Department)
Wang, Xiaoli (Guizhou Institute of Prataculture)
Huang, Linkai (Sichuan Agricultural University. Grassland Science Department)
Xu, Bin (Nanjing Agricultural University. College of Grassland Science)
Zhang, Xinquan (Sichuan Agricultural University. Grassland Science Department)
Zhang, Lexin (Sichuan Agricultural University. Grassland Science Department)

Date:	2016
Abstract:	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 ISSRs, 20 SCoTs, and 15 EST-SSRs. In 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). The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.
Note:	This work was supported by the National High-Technology Research and Development Program (863 Program) of China (No. 2012AA101801-02), the National Natural Science Foundation of China (NSFC) (No. 31201845), the spring plan of Ministry of Education, and the Sichuan Agricultural University Students Innovation Plan (No. 121062603)
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Genetic variation ; Linkage disequilibrium ; Panicum virgatum L ; Population structure
Published in:	Hereditas, Vol. 153. art. 4 (April 2016) , ISSN 1601-5223

DOI: 10.1186/s41065-016-0007-z
PMID: 28096766

12 p, 1.0 MB

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