ABSTRACT
Cultivated sugarcane cultivars (Saccharum spp. hybrid) are highly polyploid (> 10x) and aneuploid with large chromosome numbers (typically around 115) (D’Hont et al. 1996) making sugarcane one of the most genetically complex crop species. Cytogenetic studies of the two ancestral species, S. officinarum and S. spontaneum, using rDNA probes indicated that the basic chromosome number was different in the two species, with x = 10 and x = 8, respectively (D’Hont et al. 1998). The high level of ploidy combined with the large and irregular number of chromosomes makes genetic mapping in sugarcane very difficult. Despite this structural complexity, genetic maps have been constructed in sugarcane cultivars using simplex markers (markers that segregate 1:1 in progeny from a biparental cross or 3:1 in selfed progeny) from a variety of marker types (Hoarau et al. 2001; Rossi et al. 2003; Aitken et al. 2005; Garcia et al. 2006). The largest maps in cultivated sugarcane each contain more than 1,000 markers, mainly AFLP and SSR markers, distributed onto approximately 100 linkage groups (LGs) (Hoarau et al. 2001; Rossi et al. 2003; Aitken et al. 2005). The use of codominant markers such as those generated by restriction fragment length polymorphism (RFLP) probes, or simple sequence repeat (SSR) primers, have enabled these 100+ linkage groups (LG) to be assigned one of eight homology groups (HG) (Aitken et al. 2005; Grivet et al. 1996; Rossi et al. 2003), as x = 8 in S. spontaneum (D’Hont et al. 1998). Both maps have highly variable numbers of LGs in each HG. Some HGs currently contain less than five LGs while other HGs currently contain more than 20 (Hoarau et al. 2001; Rossi et al. 2003; Aitken et al. 2005). It is currently not known if this variation in number of LGs per HG reflects real variation in the number of homoeologous chromosomes among sugarcane HGs or reflects a sparse coverage of some chromosomes that are thus represented by more than one LG. For HG with large numbers of LGs, part of this variation must also reflect the different basic chromosome number in S. officinarum and S. spontaneum, where two S. officinarum LGs/chromosomes correspond to one S. spontaneum LG/ chromosome or sparse coverage of chromosomes, with more than one LG per chromosome. If each homology group is evenly represented approximately 12 homoeologous chromosomes are expected in each homoeology group and thus potentially 12 alleles of every gene. Many alleles could thus have contributed to every trait.
