Pennisetum squamulatum is a type of grass specieswhich reproduces by apomixis. Previous studies in our lab showed that apomixis behaves as a dominant Mendelian trait in P. squamulatum and that one genomic region from a single chromosome is sufficient for inheritance of the trait. This region was designated as the apospory-specific genomic region (ASGR) (Ozias-Akins et al. 1998). Further characterization of the ASGR showed that it is hemizygous, physically large, recombinationally suppressed and highly heterochromatic (Akiyama et al. 2004; Goel et al. 2003).
The nature of maternal apomeiosis and recombinational suppression in the ASGR has hindered genetic mapping and map-based cloning since the majority of molecular markers co-segregate with the ASGR. Nevertheless, expanding the number of molecular markers could assist with physical map development. Partial sequencing of ASGR-linked BAC clones revealed abundant repetitive elements such as Opie-2-like retrotransposons in the ASGR (Akiyama et al. 2004).
Although recombination-based high-resolution mapping is unlikely to be successful, physical mapping could be accomplished if the region could be saturated with molecular markers. We sought to test the ability of the long terminal repeat (LTR) retrotransposons abundant in the ASGR to provide a unique resource for molecular marker development.
The marker system we used is called Sequence Specific Amplified Polymorphism (SSAP) which was modified from AFLP (Amplified Fragment Length Polymorphism), in which one AFLP adapter primer for selective amplification was replaced with a LTR-specific primer (Waugh et al. 1997).
Using this marker system, we generated 290 single-dose markers from 38 primer combinations (Huo et al. 2009). Out of these 184 (~63%) were closely linked with apomixis, while 153 (52.7%) completely co-segregated with the trait. Based on the genetic map, several SSAP markers were recovered and converted into SCARs. This type of SCAR will be applied to screening for BAC clones and for further physical mapping with BACs through fluorescence in situ hybridization.
This work was supported by National Science Foundation award #0115911.