Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers

Alikhani, Leila; Rahmani, Mohammad-Shafie; Shabanian, Naghi; Badakhshan, Hedieh; Khadivi, Ali

doi:10.1016/j.gene.2014.09.034

Cited by 66 publications

(28 citation statements)

References 30 publications

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“…Compared with ISSR and inter-retrotransposon amplified polymorphism (IRAP), SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among Persian oak ( Quercus brantii Lindl.) individuals [50]. Results from the evaluation on the genetic variation of mango ( Mangifera indica L.) cultivars indicated that the SCoT analysis represents actual relationships better than the ISSR analysis [51].…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2016

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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.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2016

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“…(Velasco-Ramírez et al, 2014), Quercus brantii Lindl. (Alikhani et al, 2014) and Trifolium ssp. (Aryanegad et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

ISSR molecular markers for the study of the genetic diversity of Mimosa caesalpiniaefolia Benth.

Araújo

Pacheco

Vieira

et al. 2016

Idesia

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Knowledge of the genetic diversity of the threatened tree species in the Brazilian semiarid region may contribute to the creation of effective strategies for their preservation and future use. The aim of this study was to select ISSR (Inter-Simple Sequence Repeat) primers capable of detecting genetic polymorphism among Mimosa caesalpiniaefolia Benth. individuals for a study of the genetic diversity of this species. A total of 27 ISSR primers were tested for their ability to amplify genomic DNA of three individuals (bulk); all of them amplified regions between the simple sequence repeats of the genome, however seven ISSR primers showed a good standard of amplification compared to the others. The seven primers selected were used to amplify the genomic DNA of nine individuals and generated a total of 78 loci, of which 52.7% were polymorphic. The content of polymorphic information of the primers ranged from 0.261 to 0.489, showing that selected primers are moderately informative; bootstrap analysis determined that 51 loci were enough to estimate the genetic diversity of the samples of individuals. We concluded that the markers generated by the primers UBC 807, UBC 824, UBC 827, UBC 840, UBC 851, UBC 873 and UBC 881 allow detection of the genetic polymorphism among individuals of M. caesalpiniaefolia, being useful to determine the genetic diversity of this species.Key words: semiarid, forest species, primers, polymorphism. RESUMEN Conocer la diversidad genética de las especies de árboles forestales en la región semiárida de Brasil puede contribuir al desarrollo de estrategias eficaces para su conservación y uso futuro. El objetivo de este estudio fue seleccionar iniciadores de ISSR (Secuencias

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“…They are widespread used on account of their simple operation and high detection efficiency [8]. The different DNA-based molecular markers unfold plant variability directly at genetic levels with reliable data required for the estimation of genetic diversity [2], such as inter-simple sequence repeats (ISSR), inter-retrotransposon amplified polymorphism (IRAP), or start codon targeted (SCoT) polymorphism [13]. In this investigation, SCoT and IRAP were used to assess genetic constancy of Bletilla striata.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Bletilla striata assessed by SCoT and IRAP markers

Guo

Zhai

et al. 2018

Hereditas

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BackgroundBletilla striata is a well-known traditional Chinese herb with varieties of functions. In China, the natural resources of Bletilla striata have been severely damaged because of the excessive exploitation and destruction of natural habitats. The aim of present study was to provide a reference for fully exploiting and utilizing the germplasm resources of Bletilla striata.ResultsThe genetic diversity of 50 varieties of Bletilla striata from different area in China was analyzed by SCoT and IRAP molecular marker technique. A total of 209 bands were amplified by 20 groups of SCoT primers, of which 201 (96.17%) were polymorphic, and 47 polymorphic bands (94%) were observed in 50 bands amplified by 8 groups of IRAP primers. The 50 populations of Bletilla striata were divided into two major groups by SCoT and IRAP at the genetic similarity coefficient value of 0.60 and 0.68 individually. The partition of clusters in the unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis plot based on the SCoT and IRAP markers was similar.ConclusionsResults indicated the abundant genetic diversity of Bletilla striata among different areas. Our results will provide useful information for resource protection.

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Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers

Cited by 66 publications

References 30 publications

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

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

ISSR molecular markers for the study of the genetic diversity of Mimosa caesalpiniaefolia Benth.

Genetic diversity of Bletilla striata assessed by SCoT and IRAP markers

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