Characterization of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR

Abstract

Amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat markers were employed to characterize a genetic resource collection of Miscanthus, a grass under trial in Europe as a biomass crop. The 26 polymorphic markers produced by two ISSR fingerprinting primers were able to discriminate taxa and identify putative clones. AFLP fingerprints were fully reproducible and produced a larger number of markers for the three primer pairs tested, of which 998 were polymorphic (representing 79.3% of all bands). AFLP markers distinguished species, infra-specific taxa (varieties and cultivars) and putatively clonal material. They were also used to assess the inter-relationships of the taxa, to investigate the origin of important hybrid plants and to estimate the overall level of genetic variation in the collection. They were useful for assessing the species status of certain taxa such as M. transmorrisonensis, an endemic from Taiwan that was clearly distinct from M. sinensis; whereas other taxa of disputed species status, such as M. condensatus and M. yakushimanum were not genetically distinct from M. sinensis. The AFLP markers detected a high degree of infra-specific variation and allowed subdivisions of the genetic resource collection to be made, particularly within M. sinensis.

Fig. 1. Unrooted neighbour joining tree for ISSR data. The NJ tree shows the results of two primers, (GACA)₄ and (CA)₈RG. Values above the branches are genetic distances. Values below the branches are bootstrap percentages.

Fig. 2. Principal coordinates analysis (PCO) for ISSR data using Dice distances. The accessions can be separated using the first two axes of the PCO and these cumulatively account for 87·2 % (73·7 % and 13·5 %, respectively) of the data variance.

Fig. 3. AFLP traces of two Miscanthus accessions: M. × giganteus, originally called M. sacchariflorus 23 (red) and M. × giganteus 22 (blue). Note the two are identical in all fragments in the analysis.

Fig. 4. Neighbour joining (NJ) tree of AFLP data. Branch length is proportional to genetic distance. Values above branches are bootstrap percentages. Species are unambiguously separated using the AFLP markers. Furthermore, cultivars are also accurately grouped on the basis of genetic distance and have been highlighted with different colours.