Genetic Variations in a Complex Polyploid: Unveiling the Sugarcane Allelic Dynamics

Keywords: Sugarcane, Allelic dosage, Gene duplication, Ethanol

Sugarcane (Saccharum spp.) is a highly polyploid, heterozygous, aneuploid and genetically complex plant species. Modern sugarcane cultivars are derived from hybridization between S. officinarum (2n = 80) and S. spontaneum (2n = 40 – 128). In order to identify the number of haplotypes of a hypothetical gene, the sugarcane (SP80-3280 variety) BAC (Bacterial Artificial Chromosome) library was screened (221,184 clones). Twenty-two positive BAC clones were sequenced, individually assembled, and manually annotated for genes and repeat regions. The macro differences among BACs show two different regions where the target gene was inserted, revealing a duplicated region. The different repeat regions among BACs were used to identify different haplotypes: a region with seven haplotypes, and a duplicated region with nine haplotypes. The first region showed a high level of gene retention and colinearity with orthologous genes. The region with duplication showed a low colinearity, but a high conservative gene structure. The analyses among the home(o)logous BAC clones and orthologous genes suggest that the gene used for screening was duplicated in another region in the sugarcane genome, resulting in a non-collinearity region. When using BAC-FISH, it was possible to observe a region with eight markers, while the duplicated region presented ten markers in different chromosomes. SNPs along the BACs were located, and genotyped in a bi-parental population (SP80-3280 x RB835486), using mass spectrometry and analyzed in SuperMASSA software. The results showed an allelic dynamic difference in sugarcane that can be useful for understanding the complex polyploid genome.

Financial Support: FAPESP, CAPES and CNPq